Thread: [Apbs-users] FeTK support in APBS
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From: patrizio a. <p.a...@in...> - 2010-07-21 07:39:14
|
Is it possibile to compile apbs with fetk support? I have understod that FeTk must be installed ( http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil/source-installation) but I can't find a repository where I can download it. Any sugestion how to fix this problem ? thanks in advance Patrizio |
From: Baker, N. <Nat...@pn...> - 2010-07-21 14:25:30
|
Hello - Yes, FEtk is available for download at http://fetk.org/codes/download/. I will be updating the documentation in the next few weeks with revised instructions on how to compile, etc. Thanks, Nathan __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory From: patrizio ansalone [mailto:p.a...@in...] Sent: Wednesday, July 21, 2010 12:39 AM To: apb...@li... Subject: [Apbs-users] FeTK support in APBS Is it possibile to compile apbs with fetk support? I have understod that FeTk must be installed (http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil/source-installation) but I can't find a repository where I can download it. Any sugestion how to fix this problem ? thanks in advance Patrizio |
From: George K. <ge...@me...> - 2010-07-21 18:31:22
Attachments:
config.log
make_log
|
Dear APBS users, I am trying to compile APBS version 1.2 with Fetk support (Fetk version 1.1). I have downloaded and installed the entire Fetk package, and now I moved on to installing APBS itself. While configuring apparently worked since all the necessary Fetk library and header files where found, the compilation crushed when I run "make". I have attached log files from configuration step as well as "make" step. Obviously there is a problem while compiling fetk.c file. I would appreciate if somebody can take a look at the attached files and suggest what is missing. Thank you, George Baker, Nathan wrote: > > Hello – > > Yes, FEtk is available for download at > http://fetk.org/codes/download/. I will be updating the documentation > in the next few weeks with revised instructions on how to compile, etc. > > Thanks, > > Nathan > > __________________________________________________ > *Nathan Baker* > Chief Scientist for Signature Science > Pacific Northwest National Laboratory > > *From:* patrizio ansalone [mailto:p.a...@in...] > *Sent:* Wednesday, July 21, 2010 12:39 AM > *To:* apb...@li... > *Subject:* [Apbs-users] FeTK support in APBS > > > Is it possibile to compile apbs with fetk support? I have understod > that FeTk must be installed > (http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil/source-installation) > but I can't find a repository where I can download it. Any sugestion > how to fix this problem ? > thanks in advance > Patrizio > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > ------------------------------------------------------------------------ > > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA ge...@me... Phone: 1-212-746-6539 Fax: 1-212-746-6226 |
From: Baker, N. <Nat...@pn...> - 2010-07-23 16:21:44
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Hi George -- This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. Thanks, __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory > -----Original Message----- > From: George Khelashvili [mailto:ge...@me...] > Sent: Wednesday, July 21, 2010 11:31 AM > To: apb...@li... > Subject: Re: [Apbs-users] FeTK support in APBS > > Dear APBS users, > > I am trying to compile APBS version 1.2 with Fetk support (Fetk version > 1.1). I have downloaded and installed the entire Fetk package, and now > I moved on to installing APBS itself. While configuring apparently > worked since all the necessary Fetk library and header files where > found, the compilation crushed when I run "make". I have attached log > files from configuration step as well as "make" step. Obviously there > is a problem while compiling fetk.c file. I would appreciate if > somebody can take a look at the attached files and suggest what is > missing. > > Thank you, > George > > Baker, Nathan wrote: > > > > Hello - > > > > Yes, FEtk is available for download at > > http://fetk.org/codes/download/. I will be updating the documentation > > in the next few weeks with revised instructions on how to compile, > etc. > > > > Thanks, > > > > Nathan > > > > __________________________________________________ > > *Nathan Baker* > > Chief Scientist for Signature Science > > Pacific Northwest National Laboratory > > > > *From:* patrizio ansalone [mailto:p.a...@in...] > > *Sent:* Wednesday, July 21, 2010 12:39 AM > > *To:* apb...@li... > > *Subject:* [Apbs-users] FeTK support in APBS > > > > > > Is it possibile to compile apbs with fetk support? I have understod > > that FeTk must be installed > > (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- > avil > > /source-installation) but I can't find a repository where I can > > download it. Any sugestion how to fix this problem ? > > thanks in advance > > Patrizio > > > > --------------------------------------------------------------------- > - > > -- > > > > --------------------------------------------------------------------- > - > > -------- This SF.net email is sponsored by Sprint What will you do > > first with EVO, the first 4G phone? > > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > > --------------------------------------------------------------------- > - > > -- > > > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > -- > George Khelashvili, Ph.D. > Department of Physiology and Biophysics > Weill Medical College of Cornell University 1300 York Avenue, Room > LC501 New York, NY, 10065, USA ge...@me... > Phone: 1-212-746-6539 > Fax: 1-212-746-6226 > |
From: George K. <ge...@me...> - 2010-07-23 16:25:22
Attachments:
config.log
make.log
|
Hi Nathan, The listing of /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ directory is "bin doc fetk-env include lib". By the way, I realized that I sent you wrong log files, which did not exactly correspond to the versions of APBS and FETK I used (I played with several combinations and I accidentally mixed them up). Sorry for that. Here are the corrected log files which were obtained by installing Fetk version 1.1 first, and then installing APBS 1.2.1. The log files were generated during the APBS installation. This log file produced somewhat different error message. I do realize that APBS-FETK link is in the beginning stages so I will be glad to contribute as I can to resolve this issue so that the community can use this what I think will be a wonderful tool. Sincerely, George Baker, Nathan wrote: > Hi George -- > > This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? > > All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. > > Thanks, > > __________________________________________________ > Nathan Baker > Chief Scientist for Signature Science > Pacific Northwest National Laboratory > > > >> -----Original Message----- >> From: George Khelashvili [mailto:ge...@me...] >> Sent: Wednesday, July 21, 2010 11:31 AM >> To: apb...@li... >> Subject: Re: [Apbs-users] FeTK support in APBS >> >> Dear APBS users, >> >> I am trying to compile APBS version 1.2 with Fetk support (Fetk version >> 1.1). I have downloaded and installed the entire Fetk package, and now >> I moved on to installing APBS itself. While configuring apparently >> worked since all the necessary Fetk library and header files where >> found, the compilation crushed when I run "make". I have attached log >> files from configuration step as well as "make" step. Obviously there >> is a problem while compiling fetk.c file. I would appreciate if >> somebody can take a look at the attached files and suggest what is >> missing. >> >> Thank you, >> George >> >> Baker, Nathan wrote: >> >>> Hello - >>> >>> Yes, FEtk is available for download at >>> http://fetk.org/codes/download/. I will be updating the documentation >>> in the next few weeks with revised instructions on how to compile, >>> >> etc. >> >>> Thanks, >>> >>> Nathan >>> >>> __________________________________________________ >>> *Nathan Baker* >>> Chief Scientist for Signature Science >>> Pacific Northwest National Laboratory >>> >>> *From:* patrizio ansalone [mailto:p.a...@in...] >>> *Sent:* Wednesday, July 21, 2010 12:39 AM >>> *To:* apb...@li... >>> *Subject:* [Apbs-users] FeTK support in APBS >>> >>> >>> Is it possibile to compile apbs with fetk support? I have understod >>> that FeTk must be installed >>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>> >> avil >> >>> /source-installation) but I can't find a repository where I can >>> download it. Any sugestion how to fix this problem ? >>> thanks in advance >>> Patrizio >>> >>> --------------------------------------------------------------------- >>> >> - >> >>> -- >>> >>> --------------------------------------------------------------------- >>> >> - >> >>> -------- This SF.net email is sponsored by Sprint What will you do >>> first with EVO, the first 4G phone? >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>> --------------------------------------------------------------------- >>> >> - >> >>> -- >>> >>> _______________________________________________ >>> apbs-users mailing list >>> apb...@li... >>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>> >>> >> -- >> George Khelashvili, Ph.D. >> Department of Physiology and Biophysics >> Weill Medical College of Cornell University 1300 York Avenue, Room >> LC501 New York, NY, 10065, USA ge...@me... >> Phone: 1-212-746-6539 >> Fax: 1-212-746-6226 >> >> > > -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA ge...@me... Phone: 1-212-746-6539 Fax: 1-212-746-6226 |
From: Michael H. <mh...@ma...> - 2010-07-23 17:09:20
|
Nathan and all, A quick look at the make.log indicates that MALOC calls within MC are not being resolved, so MALOC (via libmaloc.a) was either not built or not being found. best, -mike George Khelashvili <ge...@me...> (07-23-2010 12:25:07-0400): >Hi Nathan, > >The listing of >/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ >directory is "bin doc fetk-env include lib". By the way, I >realized that I sent you wrong log files, which did not exactly >correspond to the versions of APBS and FETK I used (I played with >several combinations and I accidentally mixed them up). Sorry for >that. Here are the corrected log files which were obtained by >installing Fetk version 1.1 first, and then installing APBS 1.2.1. >The log files were generated during the APBS installation. This log >file produced somewhat different error message. >I do realize that APBS-FETK link is in the beginning stages so I will >be glad to contribute as I can to resolve this issue so that the >community can use this what I think will be a wonderful tool. > >Sincerely, >George > >Baker, Nathan wrote: >>Hi George -- >> >>This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? >> >>All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. >> >>Thanks, >> >>__________________________________________________ Nathan Baker >>Chief Scientist for Signature Science >>Pacific Northwest National Laboratory >> >> >>>-----Original Message----- >>>From: George Khelashvili [mailto:ge...@me...] >>>Sent: Wednesday, July 21, 2010 11:31 AM >>>To: apb...@li... >>>Subject: Re: [Apbs-users] FeTK support in APBS >>> >>>Dear APBS users, >>> >>>I am trying to compile APBS version 1.2 with Fetk support (Fetk version >>>1.1). I have downloaded and installed the entire Fetk package, and now >>>I moved on to installing APBS itself. While configuring apparently >>>worked since all the necessary Fetk library and header files where >>>found, the compilation crushed when I run "make". I have attached log >>>files from configuration step as well as "make" step. Obviously there >>>is a problem while compiling fetk.c file. I would appreciate if >>>somebody can take a look at the attached files and suggest what is >>>missing. >>> >>>Thank you, >>>George >>> >>>Baker, Nathan wrote: >>>>Hello - >>>> >>>>Yes, FEtk is available for download at >>>>http://fetk.org/codes/download/. I will be updating the documentation >>>>in the next few weeks with revised instructions on how to compile, >>>etc. >>>>Thanks, >>>> >>>>Nathan >>>> >>>>__________________________________________________ >>>>*Nathan Baker* >>>>Chief Scientist for Signature Science >>>>Pacific Northwest National Laboratory >>>> >>>>*From:* patrizio ansalone [mailto:p.a...@in...] >>>>*Sent:* Wednesday, July 21, 2010 12:39 AM >>>>*To:* apb...@li... >>>>*Subject:* [Apbs-users] FeTK support in APBS >>>> >>>> >>>>Is it possibile to compile apbs with fetk support? I have understod >>>>that FeTk must be installed >>>>(http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>>avil >>>>/source-installation) but I can't find a repository where I can >>>>download it. Any sugestion how to fix this problem ? >>>>thanks in advance >>>>Patrizio >>>> >>>>--------------------------------------------------------------------- >>>- >>>>-- >>>> >>>>--------------------------------------------------------------------- >>>- >>>>-------- This SF.net email is sponsored by Sprint What will you do >>>>first with EVO, the first 4G phone? >>>>Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>>>--------------------------------------------------------------------- >>>- >>>>-- >>>> >>>>_______________________________________________ >>>>apbs-users mailing list >>>>apb...@li... >>>>https://lists.sourceforge.net/lists/listinfo/apbs-users >>>> >>>-- >>>George Khelashvili, Ph.D. >>>Department of Physiology and Biophysics >>>Weill Medical College of Cornell University 1300 York Avenue, Room >>>LC501 New York, NY, 10065, USA ge...@me... >>>Phone: 1-212-746-6539 >>>Fax: 1-212-746-6226 >>> >> > > >-- >George Khelashvili, Ph.D. >Department of Physiology and Biophysics >Weill Medical College of Cornell University >1300 York Avenue, Room LC501 >New York, NY, 10065, USA >ge...@me... >Phone: 1-212-746-6539 >Fax: 1-212-746-6226 > >This file contains any messages produced by compilers while >running configure, to aid debugging if configure makes a mistake. > >It was created by APBS configure 1.2.1, which was >generated by GNU Autoconf 2.61. Invocation command line was > > $ ./configure --with-fetk-include=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include --with-fetk-library=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib --prefix=/home/khelgeo/apbs_fetk/ > >## --------- ## >## Platform. ## >## --------- ## > >hostname = osiris >uname -m = ia64 >uname -r = 2.4.21-sgi301rp04091014_10105 >uname -s = Linux >uname -v = #1 SMP Fri Sep 10 15:02:03 PDT 2004 > >/usr/bin/uname -p = unknown >/bin/uname -X = unknown > >/bin/arch = ia64 >/usr/bin/arch -k = unknown >/usr/convex/getsysinfo = unknown >/usr/bin/hostinfo = unknown >/bin/machine = unknown >/usr/bin/oslevel = unknown >/bin/universe = unknown > >PATH: /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin >PATH: /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin >PATH: /softlib/exe/osiris/bin >PATH: /softlib/exe/ia64/bin >PATH: /softlib/exe/linux/bin >PATH: /softlib/exe/all/bin >PATH: /usr/kerberos/bin >PATH: /usr/local/bin >PATH: /bin >PATH: /usr/bin >PATH: /usr/X11R6/bin > > >## ----------- ## >## Core tests. ## >## ----------- ## > >configure:2051: checking build system type >configure:2069: result: ia64-unknown-linux-gnu >configure:2091: checking host system type >configure:2106: result: ia64-unknown-linux-gnu >configure:2128: checking target system type >configure:2143: result: ia64-unknown-linux-gnu >configure:2187: checking for a BSD-compatible install >configure:2243: result: /usr/bin/install -c >configure:2254: checking whether build environment is sane >configure:2297: result: yes >configure:2325: checking for a thread-safe mkdir -p >configure:2364: result: /bin/mkdir -p >configure:2377: checking for gawk >configure:2393: found /bin/gawk >configure:2404: result: gawk >configure:2415: checking whether make sets $(MAKE) >configure:2436: result: yes >configure:2641: checking for --enable-fast option >configure:2661: result: no >configure:2669: checking for --enable-python >configure:2688: result: no >configure:2756: checking for icc >configure:2772: found /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin/icc >configure:2783: result: icc >configure:2819: checking for C compiler version >configure:2826: icc --version >&5 >icc (ICC) 9.1 20060928 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:2829: $? = 0 >configure:2836: icc -v >&5 >Version 9.1 >configure:2839: $? = 0 >configure:2846: icc -V >&5 >Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:2849: $? = 0 >configure:2872: checking for C compiler default output file name >configure:2899: icc conftest.c >&5 >configure:2902: $? = 0 >configure:2940: result: a.out >configure:2957: checking whether the C compiler works >configure:2967: ./a.out >configure:2970: $? = 0 >configure:2987: result: yes >configure:2994: checking whether we are cross compiling >configure:2996: result: no >configure:2999: checking for suffix of executables >configure:3006: icc -o conftest conftest.c >&5 >configure:3009: $? = 0 >configure:3033: result: >configure:3039: checking for suffix of object files >configure:3065: icc -c conftest.c >&5 >configure:3068: $? = 0 >configure:3091: result: o >configure:3095: checking whether we are using the GNU C compiler >configure:3124: icc -c conftest.c >&5 >configure:3130: $? = 0 >configure:3147: result: yes >configure:3152: checking whether icc accepts -g >configure:3182: icc -c -g conftest.c >&5 >configure:3188: $? = 0 >configure:3287: result: yes >configure:3304: checking for icc option to accept ISO C89 >configure:3378: icc -c -g -O2 conftest.c >&5 >configure:3384: $? = 0 >configure:3407: result: none needed >configure:3436: checking for style of include used by make >configure:3464: result: GNU >configure:3489: checking dependency style of icc >configure:3580: result: none >configure:3643: checking for gcc >configure:3670: result: icc >configure:3908: checking for C compiler version >configure:3915: icc --version >&5 >icc (ICC) 9.1 20060928 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:3918: $? = 0 >configure:3925: icc -v >&5 >Version 9.1 >configure:3928: $? = 0 >configure:3935: icc -V >&5 >Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:3938: $? = 0 >configure:3941: checking whether we are using the GNU C compiler >configure:3993: result: yes >configure:3998: checking whether icc accepts -g >configure:4133: result: yes >configure:4150: checking for icc option to accept ISO C89 >configure:4253: result: none needed >configure:4273: checking dependency style of icc >configure:4364: result: none >configure:4440: checking for g++ >configure:4456: found /usr/bin/g++ >configure:4467: result: g++ >configure:4498: checking for C++ compiler version >configure:4505: g++ --version >&5 >g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >Copyright (C) 2002 Free Software Foundation, Inc. >This is free software; see the source for copying conditions. There is NO >warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > >configure:4508: $? = 0 >configure:4515: g++ -v >&5 >Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >Thread model: posix >gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >configure:4518: $? = 0 >configure:4525: g++ -V >&5 >g++: argument to `-V' missing > >configure:4528: $? = 1 >configure:4531: checking whether we are using the GNU C++ compiler >configure:4560: g++ -c conftest.cpp >&5 >configure:4566: $? = 0 >configure:4583: result: yes >configure:4588: checking whether g++ accepts -g >configure:4618: g++ -c -g conftest.cpp >&5 >configure:4624: $? = 0 >configure:4723: result: yes >configure:4748: checking dependency style of g++ >configure:4839: result: none >configure:4907: checking for ifort >configure:4923: found /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin/ifort >configure:4934: result: ifort >configure:4964: checking for Fortran 77 compiler version >configure:4971: ifort --version >&5 >ifort (IFORT) 9.1 20060928 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:4974: $? = 0 >configure:4981: ifort -v >&5 >Version 9.1 >configure:4984: $? = 0 >configure:4991: ifort -V >&5 >Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:4994: $? = 0 >configure:5002: checking whether we are using the GNU Fortran 77 compiler >configure:5021: ifort -c conftest.F >&5 >fortcom: Error: conftest.F, line 3: Syntax error, found END-OF-STATEMENT when expecting one of: => = . ( : % > choke me >---------------^ >fortcom: Error: conftest.F, line 3: This statement is positioned incorrectly and/or has syntax errors. > choke me >---------------^ >compilation aborted for conftest.F (code 1) >configure:5027: $? = 1 >configure: failed program was: >| program main >| #ifndef __GNUC__ >| choke me >| #endif >| >| end >configure:5044: result: no >configure:5050: checking whether ifort accepts -g >configure:5067: ifort -c -g conftest.f >&5 >configure:5073: $? = 0 >configure:5089: result: yes >configure:5180: icc -c -g -O2 noformain.c 1>&5 >configure:5183: $? = 0 >configure:5194: checking if Fortran 77 compiler accepts -nofor_main >configure:5203: ifort -nofor_main -g noformain.o -o noformain 1>&5 >configure:5206: $? = 0 >configure:5209: result: yes >configure:5211: checking if Fortran 77 compilers requires -nofor_main >configure:5221: ifort -g noformain.o -o noformain > 1>&5 >noformain.o(.text+0x0): In function `main': >/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/noformain.c:1: multiple definition of `main' >/softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0x0): first defined here >ld: Warning: size of symbol `main' changed from 384 in /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o to 32 in noformain.o >/softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0xf2): In function `main': >: undefined reference to `MAIN__' >configure:5224: $? = 1 >configure:5230: result: yes >configure:5253: checking how f77 mangles function names >configure:5264: ifort -c -g -nofor_main mangle-func.f 1>&5 >configure:5267: $? = 0 >configure:5310: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >conftest.c(14): warning #266: function declared implicitly > foobar(); > ^ > >/tmp/iccqc5Wny.o(.text+0x12): In function `main': >/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:14: undefined reference to `foobar' >configure:5316: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| /* end confdefs.h. */ >| >| int >| main () >| { >| foobar(); >| ; >| return 0; >| } >configure:5348: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >conftest.c(14): warning #266: function declared implicitly > foobar_(); > ^ > >configure:5354: $? = 0 >configure:5466: result: lowercase-underscore >configure:5542: checking how to run the C preprocessor >configure:5582: icc -E conftest.c >configure:5588: $? = 0 >configure:5619: icc -E conftest.c >conftest.c(12): error #5: could not open source file "ac_nonexistent.h" > #include <ac_nonexistent.h> > ^ > >configure:5625: $? = 2 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| /* end confdefs.h. */ >| #include <ac_nonexistent.h> >configure:5658: result: icc -E >configure:5687: icc -E conftest.c >configure:5693: $? = 0 >configure:5724: icc -E conftest.c >conftest.c(12): error #5: could not open source file "ac_nonexistent.h" > #include <ac_nonexistent.h> > ^ > >configure:5730: $? = 2 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| /* end confdefs.h. */ >| #include <ac_nonexistent.h> >configure:5823: checking for a sed that does not truncate output >configure:5902: result: /bin/sed >configure:5920: checking for grep that handles long lines and -e >configure:5994: result: /bin/grep >configure:5999: checking for egrep >configure:6077: result: /bin/grep -E >configure:6082: checking for fgrep >configure:6160: result: /bin/grep -F >configure:6195: checking for ld used by icc >configure:6262: result: /usr/bin/ld >configure:6271: checking if the linker (/usr/bin/ld) is GNU ld >configure:6286: result: yes >configure:6298: checking for BSD- or MS-compatible name lister (nm) >configure:6347: result: /usr/bin/nm -B >configure:6469: checking the name lister (/usr/bin/nm -B) interface >configure:6476: icc -c -g -O2 conftest.c >&5 >configure:6479: /usr/bin/nm -B "conftest.o" >configure:6482: output >0000000000000000 N .debug_info_seg >0000000000000000 S some_variable >configure:6489: result: BSD nm >configure:6492: checking whether ln -s works >configure:6496: result: yes >configure:6504: checking the maximum length of command line arguments >configure:6624: result: 98304 >configure:6641: checking whether the shell understands some XSI constructs >configure:6651: result: yes >configure:6655: checking whether the shell understands "+=" >configure:6661: result: no >configure:6696: checking for /usr/bin/ld option to reload object files >configure:6703: result: -r >configure:6730: checking how to recognize dependent libraries >configure:6920: result: pass_all >configure:6980: checking for ar >configure:6996: found /usr/bin/ar >configure:7007: result: ar >configure:7089: checking for strip >configure:7105: found /usr/bin/strip >configure:7116: result: strip >configure:7192: checking for ranlib >configure:7208: found /usr/bin/ranlib >configure:7219: result: ranlib >configure:7313: checking command to parse /usr/bin/nm -B output from icc object >configure:7431: icc -c -g -O2 conftest.c >&5 >configure:7434: $? = 0 >configure:7438: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm >configure:7441: $? = 0 >configure:7495: icc -o conftest -g -O2 conftest.c conftstm.o >&5 >configure:7498: $? = 0 >configure:7536: result: ok >configure:8410: checking for ANSI C header files >configure:8440: icc -c -g -O2 conftest.c >&5 >configure:8446: $? = 0 >configure:8542: icc -o conftest -g -O2 conftest.c >&5 >configure:8545: $? = 0 >configure:8551: ./conftest >configure:8554: $? = 0 >configure:8571: result: yes >configure:8595: checking for sys/types.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for sys/stat.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for stdlib.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for string.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for memory.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for strings.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for inttypes.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for stdint.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8595: checking for unistd.h >configure:8616: icc -c -g -O2 conftest.c >&5 >configure:8622: $? = 0 >configure:8638: result: yes >configure:8654: checking for dlfcn.h >configure:8675: icc -c -g -O2 conftest.c >&5 >configure:8681: $? = 0 >configure:8697: result: yes >configure:8826: checking for C++ compiler version >configure:8833: g++ --version >&5 >g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >Copyright (C) 2002 Free Software Foundation, Inc. >This is free software; see the source for copying conditions. There is NO >warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > >configure:8836: $? = 0 >configure:8843: g++ -v >&5 >Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >Thread model: posix >gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >configure:8846: $? = 0 >configure:8853: g++ -V >&5 >g++: argument to `-V' missing > >configure:8856: $? = 1 >configure:8859: checking whether we are using the GNU C++ compiler >configure:8911: result: yes >configure:8916: checking whether g++ accepts -g >configure:9051: result: yes >configure:9076: checking dependency style of g++ >configure:9167: result: none >configure:9190: checking how to run the C++ preprocessor >configure:9226: g++ -E conftest.cpp >configure:9232: $? = 0 >configure:9263: g++ -E conftest.cpp >conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >configure:9269: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| /* end confdefs.h. */ >| #include <ac_nonexistent.h> >configure:9302: result: g++ -E >configure:9331: g++ -E conftest.cpp >configure:9337: $? = 0 >configure:9368: g++ -E conftest.cpp >conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >configure:9374: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| /* end confdefs.h. */ >| #include <ac_nonexistent.h> >configure:9525: checking for Fortran 77 compiler version >configure:9532: ifort --version >&5 >ifort (IFORT) 9.1 20060928 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:9535: $? = 0 >configure:9542: ifort -v >&5 >Version 9.1 >configure:9545: $? = 0 >configure:9552: ifort -V >&5 >Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >Copyright (C) 1985-2006 Intel Corporation. All rights reserved. > >configure:9555: $? = 0 >configure:9563: checking whether we are using the GNU Fortran 77 compiler >configure:9605: result: no >configure:9611: checking whether ifort accepts -g >configure:9650: result: yes >configure:9824: checking for objdir >configure:9839: result: .libs >configure:10131: checking if icc supports -fno-rtti -fno-exceptions >configure:10152: icc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 >configure:10156: $? = 0 >configure:10166: result: yes >configure:10186: checking for icc option to produce PIC >configure:10443: result: -fPIC -DPIC >configure:10455: checking if icc PIC flag -fPIC -DPIC works >configure:10476: icc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5 >configure:10480: $? = 0 >configure:10490: result: yes >configure:10514: checking if icc static flag -static works >configure:10542: result: yes >configure:10557: checking if icc supports -c -o file.o >configure:10581: icc -c -g -O2 -o out/conftest2.o conftest.c >&5 >configure:10585: $? = 0 >configure:10604: result: yes >configure:10612: checking if icc supports -c -o file.o >configure:10659: result: yes >configure:10692: checking whether the icc linker (/usr/bin/ld) supports shared libraries >configure:11746: result: yes >configure:11985: checking dynamic linker characteristics >configure:12428: icc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5 >configure:12434: $? = 0 >configure:12664: result: GNU/Linux ld.so >configure:12766: checking how to hardcode library paths into programs >configure:12791: result: immediate >configure:13604: checking whether stripping libraries is possible >configure:13609: result: yes >configure:13644: checking if libtool supports shared libraries >configure:13646: result: yes >configure:13649: checking whether to build shared libraries >configure:13670: result: no >configure:13673: checking whether to build static libraries >configure:13677: result: yes >configure:13827: checking for ld used by g++ >configure:13894: result: /usr/bin/ld >configure:13903: checking if the linker (/usr/bin/ld) is GNU ld >configure:13918: result: yes >configure:13973: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >configure:14935: result: yes >configure:14963: g++ -c -g -O2 conftest.cpp >&5 >configure:14966: $? = 0 >configure:15148: checking for g++ option to produce PIC >configure:15457: result: -fPIC -DPIC >configure:15466: checking if g++ PIC flag -fPIC -DPIC works >configure:15487: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5 >configure:15491: $? = 0 >configure:15501: result: yes >configure:15522: checking if g++ static flag -static works >configure:15550: result: yes >configure:15562: checking if g++ supports -c -o file.o >configure:15586: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 >configure:15590: $? = 0 >configure:15609: result: yes >configure:15614: checking if g++ supports -c -o file.o >configure:15661: result: yes >configure:15691: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >configure:15717: result: yes >configure:15854: checking dynamic linker characteristics >configure:16245: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5 >configure:16251: $? = 0 >configure:16481: result: GNU/Linux ld.so >configure:16532: checking how to hardcode library paths into programs >configure:16557: result: immediate >configure:16698: checking if libtool supports shared libraries >configure:16700: result: yes >configure:16703: checking whether to build shared libraries >configure:16723: result: no >configure:16726: checking whether to build static libraries >configure:16730: result: yes >configure:16744: checking for ifort option to produce PIC >configure:17001: result: -KPIC >configure:17010: checking if ifort PIC flag -KPIC works >configure:17031: ifort -c -g -nofor_main -KPIC conftest.f >&5 >configure:17035: $? = 0 >configure:17045: result: yes >configure:17066: checking if ifort static flag -static works >configure:17094: result: yes >configure:17106: checking if ifort supports -c -o file.o >configure:17130: ifort -c -g -nofor_main -o out/conftest2.o conftest.f >&5 >configure:17134: $? = 0 >configure:17153: result: yes >configure:17158: checking if ifort supports -c -o file.o >configure:17205: result: yes >configure:17235: checking whether the ifort linker (/usr/bin/ld) supports shared libraries >configure:18269: result: yes >configure:18406: checking dynamic linker characteristics >configure:18787: ifort -o conftest -g -nofor_main -Wl,-rpath -Wl,/foo conftest.f >&5 >configure:18793: $? = 0 >configure:19023: result: GNU/Linux ld.so >configure:19074: checking how to hardcode library paths into programs >configure:19099: result: immediate >configure:19155: checking for pow in -lm >configure:19190: icc -o conftest -g -O2 conftest.c -lm >&5 >conftest.c(35): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "pow" > >configure:19196: $? = 0 >configure:19214: result: yes >configure:19229: checking for strerrno in -liberty >configure:19264: icc -o conftest -g -O2 conftest.c -liberty >&5 >/usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/../../..//libiberty.a(strerror.o)(.text+0x240): In function `errno_max': >: `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead >configure:19270: $? = 0 >configure:19288: result: yes >configure:19304: checking for gethostbyname >configure:19360: icc -o conftest -g -O2 conftest.c >&5 >configure:19366: $? = 0 >configure:19383: result: yes >configure:19468: checking for connect >configure:19524: icc -o conftest -g -O2 conftest.c >&5 >configure:19530: $? = 0 >configure:19547: result: yes >configure:19632: checking for thr_create >configure:19688: icc -o conftest -g -O2 conftest.c >&5 >/tmp/iccv8SYca.o(.text+0x12): In function `main': >/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:58: undefined reference to `thr_create' >configure:19694: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| /* end confdefs.h. */ >| /* Define thr_create to an innocuous variant, in case <limits.h> declares thr_create. >| For example, HP-UX 11i <limits.h> declares gettimeofday. */ >| #define thr_create innocuous_thr_create >| >| /* System header to define __stub macros and hopefully few prototypes, >| which can conflict with char thr_create (); below. >| Prefer <limits.h> to <assert.h> if __STDC__ is defined, since >| <limits.h> exists even on freestanding compilers. */ >| >| #ifdef __STDC__ >| # include <limits.h> >| #else >| # include <assert.h> >| #endif >| >| #undef thr_create >| >| /* Override any GCC internal prototype to avoid an error. >| Use char because int might match the return type of a GCC >| builtin and then its argument prototype would still apply. */ >| #ifdef __cplusplus >| extern "C" >| #endif >| char thr_create (); >| /* The GNU C library defines this for functions which it implements >| to always fail with ENOSYS. Some functions are actually named >| something starting with __ and the normal name is an alias. */ >| #if defined __stub_thr_create || defined __stub___thr_create >| choke me >| #endif >| >| int >| main () >| { >| return thr_create (); >| ; >| return 0; >| } >configure:19711: result: no >configure:19720: checking for thr_create in -lthread >configure:19755: icc -o conftest -g -O2 conftest.c -lthread >&5 >ld: cannot find -lthread >configure:19761: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| /* end confdefs.h. */ >| >| /* Override any GCC internal prototype to avoid an error. >| Use char because int might match the return type of a GCC >| builtin and then its argument prototype would still apply. */ >| #ifdef __cplusplus >| extern "C" >| #endif >| char thr_create (); >| int >| main () >| { >| return thr_create (); >| ; >| return 0; >| } >configure:19779: result: no >configure:19796: checking for time >configure:19852: icc -o conftest -g -O2 conftest.c >&5 >conftest.c(58): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "time" > >configure:19858: $? = 0 >configure:19875: result: yes >configure:19892: checking for rand >configure:19948: icc -o conftest -g -O2 conftest.c >&5 >configure:19954: $? = 0 >configure:19971: result: yes >configure:19988: checking for srand >configure:20044: icc -o conftest -g -O2 conftest.c >&5 >conftest.c(60): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "srand" > >configure:20050: $? = 0 >configure:20067: result: yes >configure:20085: checking the machine epsilon for VFLOOR >configure:20111: icc -g -O2 -c fperror.c 1>&5 >configure:20114: $? = 0 >configure:20123: result: yes >configure:20167: ----------------------------------------------------------- >configure:20169: ---------- begin configuring for MALOC linkage ------------ >configure:20171: ----------------------------------------------------------- >configure:20178: WARNING: Error... FETK_INCLUDE is no longer supported. >configure:20180: WARNING: Use --with-fetk-include=PATH instead. >configure:20182: WARNING: Ignoring these variables... >configure:20187: WARNING: Error... FETK_LIBRARY is no longer supported. >configure:20189: WARNING: Use --with-fetk-library=PATH instead. >configure:20191: WARNING: Ignoring these variables... >configure:20195: checking for --with-fetk-include option >configure:20205: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >configure:20213: checking for --with-fetk-library option >configure:20223: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >configure:20235: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include/maloc/maloc.h >configure:20251: result: yes >configure:20267: Using MALOC headers in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >configure:20273: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib/libmaloc.a >configure:20289: result: yes >configure:20306: Using MALOC libraries in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >configure:20316: checking for --with-mpich option >configure:20331: result: no >configure:20337: checking for --with-mpich2 option >configure:20351: result: no >configure:20358: checking for --with-lam option >configure:20372: result: no >configure:20379: checking for --with-openmpi option >configure:20392: result: no >configure:20771: --------------------------------------------------------------- >configure:20773: ---------- begin configuring for Python wrappers -------------- >configure:20775: --------------------------------------------------------------- >configure:20779: checking for --enable-python >configure:21049: result: no >configure:21058: Python wrappers disabled >configure:21094: checking for python >configure:21112: found /usr/bin/python >configure:21124: result: /usr/bin/python >configure:21214: Skipping MALOC installation; will use MALOC provided with FEtk >configure:21225: checking for maloc_needs_rl in -lmaloc >configure:21260: icc -o conftest -g -O2 /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmaloc /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -lvf2c -liberty -lm >&5 >/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include: file not recognized: Is a directory >configure:21266: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| #define HAVE_TIME_FUNC >| #define HAVE_RAND_FUNC >| #define HAVE_SRAND_FUNC >| #define FLOAT_ERRORS 1 >| #define MACHINE_EPS 1.19209E-07 >| /* end confdefs.h. */ >| >| /* Override any GCC internal prototype to avoid an error. >| Use char because int might match the return type of a GCC >| builtin and then its argument prototype would still apply. */ >| #ifdef __cplusplus >| extern "C" >| #endif >| char maloc_needs_rl (); >| int >| main () >| { >| return maloc_needs_rl (); >| ; >| return 0; >| } >configure:21284: result: no >configure:21529: ------------------------------------------------------------ >configure:21531: ---------- begin configuring for FEtk linkage -------------- >configure:21533: ------------------------------------------------------------ >configure:21542: checking for --disable-fetk >configure:21554: result: no >configure:21556: checking for user-specified FEtk include path >configure:21559: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >configure:21567: checking for user-specified FEtk library path >configure:21570: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >configure:21593: checking mc/mc.h usability >configure:21610: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >configure:21616: $? = 0 >configure:21630: result: yes >configure:21634: checking mc/mc.h presence >configure:21649: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >configure:21655: $? = 0 >configure:21669: result: yes >configure:21702: checking for mc/mc.h >configure:21709: result: yes >configure:21720: checking for mc_link in -lmc >configure:21755: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >configure:21761: $? = 0 >configure:21779: result: yes >configure:21800: checking mcx/mcx.h usability >configure:21817: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >conftest.c(62): catastrophic error: could not open source file "mcx/mcx.h" > #include <mcx/mcx.h> > ^ > >compilation aborted for conftest.c (code 4) >configure:21823: $? = 4 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| #define HAVE_TIME_FUNC >| #define HAVE_RAND_FUNC >| #define HAVE_SRAND_FUNC >| #define FLOAT_ERRORS 1 >| #define MACHINE_EPS 1.19209E-07 >| /* end confdefs.h. */ >| #include <stdio.h> >| #ifdef HAVE_SYS_TYPES_H >| # include <sys/types.h> >| #endif >| #ifdef HAVE_SYS_STAT_H >| # include <sys/stat.h> >| #endif >| #ifdef STDC_HEADERS >| # include <stdlib.h> >| # include <stddef.h> >| #else >| # ifdef HAVE_STDLIB_H >| # include <stdlib.h> >| # endif >| #endif >| #ifdef HAVE_STRING_H >| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H >| # include <memory.h> >| # endif >| # include <string.h> >| #endif >| #ifdef HAVE_STRINGS_H >| # include <strings.h> >| #endif >| #ifdef HAVE_INTTYPES_H >| # include <inttypes.h> >| #endif >| #ifdef HAVE_STDINT_H >| # include <stdint.h> >| #endif >| #ifdef HAVE_UNISTD_H >| # include <unistd.h> >| #endif >| #include <mcx/mcx.h> >configure:21837: result: no >configure:21841: checking mcx/mcx.h presence >configure:21856: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >conftest.c(29): error #5: could not open source file "mcx/mcx.h" > #include <mcx/mcx.h> > ^ > >configure:21862: $? = 2 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| #define HAVE_TIME_FUNC >| #define HAVE_RAND_FUNC >| #define HAVE_SRAND_FUNC >| #define FLOAT_ERRORS 1 >| #define MACHINE_EPS 1.19209E-07 >| /* end confdefs.h. */ >| #include <mcx/mcx.h> >configure:21876: result: no >configure:21909: checking for mcx/mcx.h >configure:21916: result: no >configure:21927: checking for mcx_link in -lmcx >configure:21962: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmcx -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >ld: cannot find -lmcx >configure:21968: $? = 1 >configure: failed program was: >| /* confdefs.h. */ >| #define PACKAGE_NAME "APBS" >| #define PACKAGE_TARNAME "apbs" >| #define PACKAGE_VERSION "1.2.1" >| #define PACKAGE_STRING "APBS 1.2.1" >| #define PACKAGE_BUGREPORT "ba...@bi..." >| #define PACKAGE "apbs" >| #define VERSION "1.2.1" >| #define VF77_ONEUNDERSCORE >| #define VF77_LOWERCASE >| #define STDC_HEADERS 1 >| #define HAVE_SYS_TYPES_H 1 >| #define HAVE_SYS_STAT_H 1 >| #define HAVE_STDLIB_H 1 >| #define HAVE_STRING_H 1 >| #define HAVE_MEMORY_H 1 >| #define HAVE_STRINGS_H 1 >| #define HAVE_INTTYPES_H 1 >| #define HAVE_STDINT_H 1 >| #define HAVE_UNISTD_H 1 >| #define HAVE_DLFCN_H 1 >| #define LT_OBJDIR ".libs/" >| #define HAVE_TIME_FUNC >| #define HAVE_RAND_FUNC >| #define HAVE_SRAND_FUNC >| #define FLOAT_ERRORS 1 >| #define MACHINE_EPS 1.19209E-07 >| /* end confdefs.h. */ >| >| /* Override any GCC internal prototype to avoid an error. >| Use char because int might match the return type of a GCC >| builtin and then its argument prototype would still apply. */ >| #ifdef __cplusplus >| extern "C" >| #endif >| char mcx_link (); >| int >| main () >| { >| return mcx_link (); >| ; >| return 0; >| } >configure:21986: result: no >configure:22000: FEtk component MC found: enabled. >configure:22025: WARNING: FEtk component MCX not found: hierarchical basis methods disabled. >configure:22039: --------------------------------------------------------------- >configure:22041: ------------ begin processing APBS configure options ---------- >configure:22043: --------------------------------------------------------------- >configure:22046: checking for EMBED macro can be used >configure:22070: icc -c -g -O2 conftest.c >&5 >configure:22076: $? = 0 >configure:22094: result: yes >configure:22098: checking --enable-pansi >configure:22116: result: no >configure:22123: checking for strcasecmp >configure:22179: icc -o conftest -g -O2 conftest.c >&5 >conftest.c(65): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "strcasecmp" > >configure:22185: $? = 0 >configure:22202: result: yes >configure:22225: checking for --disable-tools >configure:22237: result: no >configure:22239: tools will be compiled >configure:22258: checking for --with-blas >configure:22353: result: no >configure:22383: checking for --with-arpack >configure:22399: result: no >configure:22405: checking for --disable-inline >configure:22416: result: no >configure:22418: inline functions will be used >configure:22432: checking for --enable-tinker >configure:22456: result: no >configure:22460: checking for --enable-abps-quiet >configure:22479: result: no >configure:22483: checking for --disable-openmp >configure:22497: result: no >configure:22876: creating ./config.status > >## ---------------------- ## >## Running config.status. ## >## ---------------------- ## > >This file was extended by APBS config.status 1.2.1, which was >generated by GNU Autoconf 2.61. Invocation command line was > > CONFIG_FILES = > CONFIG_HEADERS = > CONFIG_LINKS = > CONFIG_COMMANDS = > $ ./config.status > >on osiris > >config.status:1044: creating Makefile >config.status:1044: creating contrib/Makefile >config.status:1044: creating contrib/blas/Makefile >config.status:1044: creating contrib/pmgZ/Makefile >config.status:1044: creating contrib/aqua/Makefile >config.status:1044: creating contrib/opal/Makefile >config.status:1044: creating contrib/opal/ZSI/Makefile >config.status:1044: creating tools/Makefile >config.status:1044: creating tools/mesh/Makefile >config.status:1044: creating tools/manip/Makefile >config.status:1044: creating tools/python/Makefile >config.status:1044: creating tools/arpack/Makefile >config.status:1044: creating tools/python/vgrid/Makefile >config.status:1044: creating src/Makefile >config.status:1044: creating src/generic/Makefile >config.status:1044: creating src/mg/Makefile >config.status:1044: creating src/fem/Makefile >config.status:1044: creating src/aaa_inc/Makefile >config.status:1044: creating src/aaa_inc/apbs/Makefile >config.status:1044: creating src/aaa_lib/Makefile >config.status:1044: creating examples/Makefile >config.status:1044: creating examples/actin-dimer/Makefile >config.status:1044: creating examples/alkanes/Makefile >config.status:1044: creating examples/born/Makefile >config.status:1044: creating examples/FKBP/Makefile >config.status:1044: creating examples/hca-bind/Makefile >config.status:1044: creating examples/ion-pmf/Makefile >config.status:1044: creating examples/ion-protein/Makefile >config.status:1044: creating examples/ionize/Makefile >config.status:1044: creating examples/pka-lig/Makefile >config.status:1044: creating examples/point-pmf/Makefile >config.status:1044: creating examples/protein-rna/Makefile >config.status:1044: creating examples/smpbe/Makefile >config.status:1044: creating examples/solv/Makefile >config.status:1044: creating examples/opal/Makefile >config.status:1044: creating bin/Makefile >config.status:1044: creating src/aaa_inc/apbscfg.h >config.status:1327: executing depfiles commands >config.status:1327: executing libtool commands >configure:25486: > >APBS to be compiled with following settings: icc -g -O2 -openmp >APBS to be compiled with following settings: ifort -g -nofor_main -nofor_main -openmp -assume cc_omp >APBS to be linked with following libraries : -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas >APBS to be compiled with following includes: -I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include > >Please type "make; make install" > > >## ---------------- ## >## Cache variables. ## >## ---------------- ## > >ac_cv_build=ia64-unknown-linux-gnu >ac_cv_c_compiler_gnu=yes >ac_cv_cxx_compiler_gnu=yes >ac_cv_env_CCC_set= >ac_cv_env_CCC_value= >ac_cv_env_CC_set= >ac_cv_env_CC_value= >ac_cv_env_CFLAGS_set= >ac_cv_env_CFLAGS_value= >ac_cv_env_CPPFLAGS_set= >ac_cv_env_CPPFLAGS_value= >ac_cv_env_CPP_set= >ac_cv_env_CPP_value= >ac_cv_env_CXXCPP_set= >ac_cv_env_CXXCPP_value= >ac_cv_env_CXXFLAGS_set= >ac_cv_env_CXXFLAGS_value= >ac_cv_env_CXX_set= >ac_cv_env_CXX_value= >ac_cv_env_F77_set= >ac_cv_env_F77_value= >ac_cv_env_FFLAGS_set= >ac_cv_env_FFLAGS_value= >ac_cv_env_LDFLAGS_set= >ac_cv_env_LDFLAGS_value= >ac_cv_env_LIBS_set= >ac_cv_env_LIBS_value= >ac_cv_env_build_alias_set= >ac_cv_env_build_alias_value= >ac_cv_env_host_alias_set= >ac_cv_env_host_alias_value= >ac_cv_env_target_alias_set= >ac_cv_env_target_alias_value= >ac_cv_f77_compiler_gnu=no >ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__include_maloc_maloc_h=yes >ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__lib_libmaloc_a=yes >ac_cv_func_connect=yes >ac_cv_func_gethostbyname=yes >ac_cv_func_rand=yes >ac_cv_func_srand=yes >ac_cv_func_strcasecmp=yes >ac_cv_func_thr_create=no >ac_cv_func_time=yes >ac_cv_header_dlfcn_h=yes >ac_cv_header_inttypes_h=yes >ac_cv_header_mc_mc_h=yes >ac_cv_header_mcx_mcx_h=no >ac_cv_header_memory_h=yes >ac_cv_header_stdc=yes >ac_cv_header_stdint_h=yes >ac_cv_header_stdlib_h=yes >ac_cv_header_string_h=yes >ac_cv_header_strings_h=yes >ac_cv_header_sys_stat_h=yes >ac_cv_header_sys_types_h=yes >ac_cv_header_unistd_h=yes >ac_cv_host=ia64-unknown-linux-gnu >ac_cv_lib_iberty_strerrno=yes >ac_cv_lib_m_pow=yes >ac_cv_lib_maloc_maloc_needs_rl=no >ac_cv_lib_mc_mc_link=yes >ac_cv_lib_mcx_mcx_link=no >ac_cv_lib_thread_thr_create=no >ac_cv_objext=o >ac_cv_path_EGREP='/bin/grep -E' >ac_cv_path_FGREP='/bin/grep -F' >ac_cv_path_GREP=/bin/grep >ac_cv_path_SED=/bin/sed >ac_cv_path_install='/usr/bin/install -c' >ac_cv_path_mkdir=/bin/mkdir >ac_cv_path_py_path=/usr/bin/python >ac_cv_prog_AWK=gawk >ac_cv_prog_CPP='icc -E' >ac_cv_prog_CXXCPP='g++ -E' >ac_cv_prog_ac_ct_AR=ar >ac_cv_prog_ac_ct_CC=icc >ac_cv_prog_ac_ct_CXX=g++ >ac_cv_prog_ac_ct_F77=ifort >ac_cv_prog_ac_ct_RANLIB=ranlib >ac_cv_prog_ac_ct_STRIP=strip >ac_cv_prog_cc_c89= >ac_cv_prog_cc_g=yes >ac_cv_prog_cxx_g=yes >ac_cv_prog_f77_g=yes >ac_cv_prog_make_make_set=yes >ac_cv_target=ia64-unknown-linux-gnu >am_cv_CC_dependencies_compiler_type=none >am_cv_CXX_dependencies_compiler_type=none >am_cv_prog_cc_stdc= >lt_cv_deplibs_check_method=pass_all >lt_cv_file_magic_cmd='$MAGIC_CMD' >lt_cv_file_magic_test_file= >lt_cv_ld_reload_flag=-r >lt_cv_nm_interface='BSD nm' >lt_cv_objdir=.libs >lt_cv_path_LD=/usr/bin/ld >lt_cv_path_LDCXX=/usr/bin/ld >lt_cv_path_NM='/usr/bin/nm -B' >lt_cv_prog_compiler_c_o=yes >lt_cv_prog_compiler_c_o_CXX=yes >lt_cv_prog_compiler_c_o_F77=yes >lt_cv_prog_compiler_pic_works=yes >lt_cv_prog_compiler_pic_works_CXX=yes >lt_cv_prog_compiler_pic_works_F77=yes >lt_cv_prog_compiler_rtti_exceptions=yes >lt_cv_prog_compiler_static_works=yes >lt_cv_prog_compiler_static_works_CXX=yes >lt_cv_prog_compiler_static_works_F77=yes >lt_cv_prog_gnu_ld=yes >lt_cv_prog_gnu_ldcxx=yes >lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\''' >lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' >lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' >lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' >lt_cv_sys_max_cmd_len=98304 > >## ----------------- ## >## Output variables. ## >## ----------------- ## > >ACLOCAL=':' >AMDEPBACKSLASH='\' >AMDEP_FALSE='#' >AMDEP_TRUE='' >AMTAR='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run tar' >APBS_VERSION='1:2:1' >AR='ar' >AUTOCONF=':' >AUTOHEADER=':' >AUTOMAKE=':' >AWK='gawk' >CC='icc' >CCDEPMODE='depmode=none' >CFLAGS='-g -O2 -openmp' >CPP='icc -E' >CPPFLAGS='' >CXX='g++' >CXXCPP='g++ -E' >CXXDEPMODE='depmode=none' >CXXFLAGS='-g -O2' >CYGPATH_W='echo' >DEFS='-DHAVE_CONFIG_H' >DEPDIR='.deps' >DSYMUTIL='' >DUMPBIN='' >ECHO_C='' >ECHO_N='-n' >ECHO_T='' >EGREP='/bin/grep -E' >EXEEXT='' >F77='ifort' >FFLAGS=' -g -nofor_main -nofor_main -openmp -assume cc_omp' >FGREP='/bin/grep -F' >GREP='/bin/grep' >INSTALL_DATA='${INSTALL} -m 644' >INSTALL_PROGRAM='${INSTALL}' >INSTALL_SCRIPT='${INSTALL}' >INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' >LD='/usr/bin/ld' >LDFLAGS=' -static-intel' >LIBOBJS='' >LIBS='' >LIBTOOL='$(SHELL) $(top_builddir)/libtool' >LIPO='' >LN_S='ln -s' >LTLIBOBJS='' >MAKEINFO='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run makeinfo' >NM='/usr/bin/nm -B' >NMEDIT='' >OBJEXT='o' >OTOOL64='' >OTOOL='' >PACKAGE='apbs' >PACKAGE_BUGREPORT='ba...@bi...' >PACKAGE_NAME='APBS' >PACKAGE_STRING='APBS 1.2.1' >PACKAGE_TARNAME='apbs' >PACKAGE_VERSION='1.2.1' >PATH_SEPARATOR=':' >PY_CC='' >PY_CFLAGS='' >PY_LDFLAGS='' >PY_LINKFLAGS='' >PY_PRESENT_FALSE='' >PY_PRESENT_TRUE='#' >PY_SHARED='' >RANLIB='ranlib' >SED='/bin/sed' >SET_MAKE='' >SHELL='/bin/sh' >SITEPKGS='/home/khelgeo/apbs_fetk//lib/python2.2/site-packages' >STRIP='strip' >UHBD_COMPILE_FALSE='#' >UHBD_COMPILE_TRUE='' >VERSION='1.2.1' >ac_ct_CC='icc' >ac_ct_CXX='g++' >ac_ct_DUMPBIN='' >ac_ct_F77='ifort' >am__fastdepCC_FALSE='' >am__fastdepCC_TRUE='#' >am__fastdepCXX_FALSE='' >am__fastdepCXX_TRUE='#' >am__include='include' >am__isrc='' >am__leading_dot='.' >am__quote='' >am__tar='${AMTAR} chof - "$$tardir"' >am__untar='${AMTAR} xf -' >apbs_build_libraries='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/bin/libapbsmainroutines.la /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/src/aaa_lib/libapbs.la -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas' >apbs_do_blas='blas' >apbs_do_maloc='' >apbs_do_python='' >apbs_do_tools='tools' >arpack_do_tools='' >arpack_lib='' >bindir='${exec_prefix}/bin' >build='ia64-unknown-linux-gnu' >build_alias='' >build_cpu='ia64' >build_os='linux-gnu' >build_vendor='unknown' >contrib_path='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >datadir='${datarootdir}' >datarootdir='${prefix}/share' >docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' >dvidir='${docdir}' >exec_prefix='${prefix}' >fetk_cpu_vendor_os='' >host='ia64-unknown-linux-gnu' >host_alias='' >host_cpu='ia64' >host_os='linux-gnu' >host_vendor='unknown' >htmldir='${docdir}' >inc_list='-I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include ' >includedir='${prefix}/include' >infodir='${datarootdir}/info' >install_sh='$(SHELL) /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/install-sh' >lib_list=' -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas' >libdir='${exec_prefix}/lib' >liberty_lib='-liberty' >libexecdir='${exec_prefix}/libexec' >localedir='${datarootdir}/locale' >localstatedir='${prefix}/var' >lt_ECHO='echo' >maloc_inc='-I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include' >maloc_lib='-L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc' >mandir='${datarootdir}/man' >math_lib='-lm' >mc_inc='' >mc_lib='-L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc' >mcx_inc='' >mcx_lib='' >mkdir_p='/bin/mkdir -p' >mpi_inc='' >mpi_lib='' >nsl_lib='' >oldincludedir='/usr/include' >pdfdir='${docdir}' >pedantic_ansi='' >prefix='/home/khelgeo/apbs_fetk/' >program_transform_name='s,x,x,' >psdir='${docdir}' >py_path='/usr/bin/python' >rl_lib='' >sbindir='${exec_prefix}/sbin' >sharedstatedir='${prefix}/com' >socket_lib='' >sysconfdir='${prefix}/etc' >target='ia64-unknown-linux-gnu' >target_alias='' >target_cpu='ia64' >target_os='linux-gnu' >target_vendor='unknown' >thread_lib='' >top_apbsdir='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source' >wall='' >wall_pedantic='' >wall_pedantic_ansi='' > >## ----------- ## >## confdefs.h. ## >## ----------- ## > >#define PACKAGE_NAME "APBS" >#define PACKAGE_TARNAME "apbs" >#define PACKAGE_VERSION "1.2.1" >#define PACKAGE_STRING "APBS 1.2.1" >#define PACKAGE_BUGREPORT "ba...@bi..." >#define PACKAGE "apbs" >#define VERSION "1.2.1" >#define VF77_ONEUNDERSCORE >#define VF77_LOWERCASE >#define STDC_HEADERS 1 >#define HAVE_SYS_TYPES_H 1 >#define HAVE_SYS_STAT_H 1 >#define HAVE_STDLIB_H 1 >#define HAVE_STRING_H 1 >#define HAVE_MEMORY_H 1 >#define HAVE_STRINGS_H 1 >#define HAVE_INTTYPES_H 1 >#define HAVE_STDINT_H 1 >#define HAVE_UNISTD_H 1 >#define HAVE_DLFCN_H 1 >#define LT_OBJDIR ".libs/" >#define HAVE_TIME_FUNC >#define HAVE_RAND_FUNC >#define HAVE_SRAND_FUNC >#define FLOAT_ERRORS 1 >#define MACHINE_EPS 1.19209E-07 >#define HAVE_MC_H >#define HAVE_EMBED > >configure: exit 0 >Making all in contrib >make[1]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >Making all in blas >make[2]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas' >Making all in . >make[3]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas' >make[3]: Nothing to be done for `all-am'. >make[3]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas' >make[2]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas' >Making all in pmgZ >make[2]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/pmgZ' >Making all in . >make[3]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/pmgZ' >cp -p ../../src/mg/apbs/*.h ../../src/aaa_inc/apbs/. >make[3]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/pmgZ' >make[2]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/pmgZ' >Making all in aqua >make[2]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/aqua' >Making all in . >make[3]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/aqua' >make[3]: Nothing to be done for `all-am'. >make[3]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/aqua' >make[2]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/aqua' >Making all in opal >make[2]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal' >Making all in ZSI >make[3]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal/ZSI' >Making all in . >make[4]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal/ZSI' >make[4]: Nothing to be done for `all-am'. >make[4]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal/ZSI' >make[3]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal/ZSI' >Making all in . >make[3]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal' >make[3]: Nothing to be done for `all-am'. >make[3]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal' >make[2]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/opal' >Making all in . >make[2]: Entering directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >make[2]: Nothing to be done for `all-am'. >make[2]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >make[1]: Leaving directory `/homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >Making all in src >make[1]: En... [truncated message content] |
From: Baker, N. <Nat...@pn...> - 2010-07-24 14:35:53
|
Thanks, George! __________________________________________________ Nathan Baker Chief Scientist for Signature Science Pacific Northwest National Laboratory > -----Original Message----- > From: George Khelashvili [mailto:ge...@me...] > Sent: Friday, July 23, 2010 9:25 AM > To: Baker, Nathan > Cc: apb...@li...; Yong Huang; Dave Gohara > (sd...@gm...) > Subject: Re: [Apbs-users] FeTK support in APBS > > Hi Nathan, > > The listing of > /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ > directory is "bin doc fetk-env include lib". By the way, I realized > that I sent you wrong log files, which did not exactly correspond to > the versions of APBS and FETK I used (I played with several > combinations and I accidentally mixed them up). Sorry for that. Here > are the corrected log files which were obtained by installing Fetk > version 1.1 first, and then installing APBS 1.2.1. The log files were > generated during the APBS installation. This log file produced somewhat > different error message. > I do realize that APBS-FETK link is in the beginning stages so I will > be glad to contribute as I can to resolve this issue so that the > community can use this what I think will be a wonderful tool. > > Sincerely, > George > > Baker, Nathan wrote: > > Hi George -- > > > > This is very strange. Can you send me a listing of your > /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? > > > > All: please note that FEtk has just been released and the APBS/FEtk > interface is very much in a "beta" state. > > > > Thanks, > > > > __________________________________________________ > > Nathan Baker > > Chief Scientist for Signature Science > > Pacific Northwest National Laboratory > > > > > > > >> -----Original Message----- > >> From: George Khelashvili [mailto:ge...@me...] > >> Sent: Wednesday, July 21, 2010 11:31 AM > >> To: apb...@li... > >> Subject: Re: [Apbs-users] FeTK support in APBS > >> > >> Dear APBS users, > >> > >> I am trying to compile APBS version 1.2 with Fetk support (Fetk > version > >> 1.1). I have downloaded and installed the entire Fetk package, and > now > >> I moved on to installing APBS itself. While configuring apparently > >> worked since all the necessary Fetk library and header files where > >> found, the compilation crushed when I run "make". I have attached > log > >> files from configuration step as well as "make" step. Obviously > there > >> is a problem while compiling fetk.c file. I would appreciate if > >> somebody can take a look at the attached files and suggest what is > >> missing. > >> > >> Thank you, > >> George > >> > >> Baker, Nathan wrote: > >> > >>> Hello - > >>> > >>> Yes, FEtk is available for download at > >>> http://fetk.org/codes/download/. I will be updating the > documentation > >>> in the next few weeks with revised instructions on how to compile, > >>> > >> etc. > >> > >>> Thanks, > >>> > >>> Nathan > >>> > >>> __________________________________________________ > >>> *Nathan Baker* > >>> Chief Scientist for Signature Science > >>> Pacific Northwest National Laboratory > >>> > >>> *From:* patrizio ansalone [mailto:p.a...@in...] > >>> *Sent:* Wednesday, July 21, 2010 12:39 AM > >>> *To:* apb...@li... > >>> *Subject:* [Apbs-users] FeTK support in APBS > >>> > >>> > >>> Is it possibile to compile apbs with fetk support? I have understod > >>> that FeTk must be installed > >>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- > >>> > >> avil > >> > >>> /source-installation) but I can't find a repository where I can > >>> download it. Any sugestion how to fix this problem ? > >>> thanks in advance > >>> Patrizio > >>> > >>> ------------------------------------------------------------------- > -- > >>> > >> - > >> > >>> -- > >>> > >>> ------------------------------------------------------------------- > -- > >>> > >> - > >> > >>> -------- This SF.net email is sponsored by Sprint What will you do > >>> first with EVO, the first 4G phone? > >>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > >>> ------------------------------------------------------------------- > -- > >>> > >> - > >> > >>> -- > >>> > >>> _______________________________________________ > >>> apbs-users mailing list > >>> apb...@li... > >>> https://lists.sourceforge.net/lists/listinfo/apbs-users > >>> > >>> > >> -- > >> George Khelashvili, Ph.D. > >> Department of Physiology and Biophysics > >> Weill Medical College of Cornell University 1300 York Avenue, Room > >> LC501 New York, NY, 10065, USA ge...@me... > >> Phone: 1-212-746-6539 > >> Fax: 1-212-746-6226 > >> > >> > > > > > > > -- > George Khelashvili, Ph.D. > Department of Physiology and Biophysics > Weill Medical College of Cornell University > 1300 York Avenue, Room LC501 > New York, NY, 10065, USA > ge...@me... > Phone: 1-212-746-6539 > Fax: 1-212-746-6226 |
From: George K. <ge...@me...> - 2010-07-23 18:13:41
|
Dear Michael, Thank you for your comment. I used fetk_build script to build the entire fetk by running "./fetk-build all". Are there any other options that I missed? It looks like that both maloc and mc are in place. Sincerely, George Michael Holst wrote: > Nathan and all, > > A quick look at the make.log indicates that MALOC calls within MC > are not being resolved, so MALOC (via libmaloc.a) was either not > built or not being found. > > best, -mike > > George Khelashvili <ge...@me...> (07-23-2010 12:25:07-0400): > >> Hi Nathan, >> >> The listing of >> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ >> directory is "bin doc fetk-env include lib". By the way, I >> realized that I sent you wrong log files, which did not exactly >> correspond to the versions of APBS and FETK I used (I played with >> several combinations and I accidentally mixed them up). Sorry for >> that. Here are the corrected log files which were obtained by >> installing Fetk version 1.1 first, and then installing APBS 1.2.1. >> The log files were generated during the APBS installation. This log >> file produced somewhat different error message. >> I do realize that APBS-FETK link is in the beginning stages so I will >> be glad to contribute as I can to resolve this issue so that the >> community can use this what I think will be a wonderful tool. >> >> Sincerely, >> George >> >> Baker, Nathan wrote: >> >>> Hi George -- >>> >>> This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? >>> >>> All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. >>> >>> Thanks, >>> >>> __________________________________________________ Nathan Baker >>> Chief Scientist for Signature Science >>> Pacific Northwest National Laboratory >>> >>> >>> >>>> -----Original Message----- >>>> From: George Khelashvili [mailto:ge...@me...] >>>> Sent: Wednesday, July 21, 2010 11:31 AM >>>> To: apb...@li... >>>> Subject: Re: [Apbs-users] FeTK support in APBS >>>> >>>> Dear APBS users, >>>> >>>> I am trying to compile APBS version 1.2 with Fetk support (Fetk version >>>> 1.1). I have downloaded and installed the entire Fetk package, and now >>>> I moved on to installing APBS itself. While configuring apparently >>>> worked since all the necessary Fetk library and header files where >>>> found, the compilation crushed when I run "make". I have attached log >>>> files from configuration step as well as "make" step. Obviously there >>>> is a problem while compiling fetk.c file. I would appreciate if >>>> somebody can take a look at the attached files and suggest what is >>>> missing. >>>> >>>> Thank you, >>>> George >>>> >>>> Baker, Nathan wrote: >>>> >>>>> Hello - >>>>> >>>>> Yes, FEtk is available for download at >>>>> http://fetk.org/codes/download/. I will be updating the documentation >>>>> in the next few weeks with revised instructions on how to compile, >>>>> >>>> etc. >>>> >>>>> Thanks, >>>>> >>>>> Nathan >>>>> >>>>> __________________________________________________ >>>>> *Nathan Baker* >>>>> Chief Scientist for Signature Science >>>>> Pacific Northwest National Laboratory >>>>> >>>>> *From:* patrizio ansalone [mailto:p.a...@in...] >>>>> *Sent:* Wednesday, July 21, 2010 12:39 AM >>>>> *To:* apb...@li... >>>>> *Subject:* [Apbs-users] FeTK support in APBS >>>>> >>>>> >>>>> Is it possibile to compile apbs with fetk support? I have understod >>>>> that FeTk must be installed >>>>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>>>> >>>> avil >>>> >>>>> /source-installation) but I can't find a repository where I can >>>>> download it. Any sugestion how to fix this problem ? >>>>> thanks in advance >>>>> Patrizio >>>>> >>>>> --------------------------------------------------------------------- >>>>> >>>> - >>>> >>>>> -- >>>>> >>>>> --------------------------------------------------------------------- >>>>> >>>> - >>>> >>>>> -------- This SF.net email is sponsored by Sprint What will you do >>>>> first with EVO, the first 4G phone? >>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>>>> --------------------------------------------------------------------- >>>>> >>>> - >>>> >>>>> -- >>>>> >>>>> _______________________________________________ >>>>> apbs-users mailing list >>>>> apb...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>> >>>>> >>>> -- >>>> George Khelashvili, Ph.D. >>>> Department of Physiology and Biophysics >>>> Weill Medical College of Cornell University 1300 York Avenue, Room >>>> LC501 New York, NY, 10065, USA ge...@me... >>>> Phone: 1-212-746-6539 >>>> Fax: 1-212-746-6226 >>>> >>>> >> -- >> George Khelashvili, Ph.D. >> Department of Physiology and Biophysics >> Weill Medical College of Cornell University >> 1300 York Avenue, Room LC501 >> New York, NY, 10065, USA >> ge...@me... >> Phone: 1-212-746-6539 >> Fax: 1-212-746-6226 >> >> > > >> This file contains any messages produced by compilers while >> running configure, to aid debugging if configure makes a mistake. >> >> It was created by APBS configure 1.2.1, which was >> generated by GNU Autoconf 2.61. Invocation command line was >> >> $ ./configure --with-fetk-include=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include --with-fetk-library=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib --prefix=/home/khelgeo/apbs_fetk/ >> >> ## --------- ## >> ## Platform. ## >> ## --------- ## >> >> hostname = osiris >> uname -m = ia64 >> uname -r = 2.4.21-sgi301rp04091014_10105 >> uname -s = Linux >> uname -v = #1 SMP Fri Sep 10 15:02:03 PDT 2004 >> >> /usr/bin/uname -p = unknown >> /bin/uname -X = unknown >> >> /bin/arch = ia64 >> /usr/bin/arch -k = unknown >> /usr/convex/getsysinfo = unknown >> /usr/bin/hostinfo = unknown >> /bin/machine = unknown >> /usr/bin/oslevel = unknown >> /bin/universe = unknown >> >> PATH: /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin >> PATH: /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin >> PATH: /softlib/exe/osiris/bin >> PATH: /softlib/exe/ia64/bin >> PATH: /softlib/exe/linux/bin >> PATH: /softlib/exe/all/bin >> PATH: /usr/kerberos/bin >> PATH: /usr/local/bin >> PATH: /bin >> PATH: /usr/bin >> PATH: /usr/X11R6/bin >> >> >> ## ----------- ## >> ## Core tests. ## >> ## ----------- ## >> >> configure:2051: checking build system type >> configure:2069: result: ia64-unknown-linux-gnu >> configure:2091: checking host system type >> configure:2106: result: ia64-unknown-linux-gnu >> configure:2128: checking target system type >> configure:2143: result: ia64-unknown-linux-gnu >> configure:2187: checking for a BSD-compatible install >> configure:2243: result: /usr/bin/install -c >> configure:2254: checking whether build environment is sane >> configure:2297: result: yes >> configure:2325: checking for a thread-safe mkdir -p >> configure:2364: result: /bin/mkdir -p >> configure:2377: checking for gawk >> configure:2393: found /bin/gawk >> configure:2404: result: gawk >> configure:2415: checking whether make sets $(MAKE) >> configure:2436: result: yes >> configure:2641: checking for --enable-fast option >> configure:2661: result: no >> configure:2669: checking for --enable-python >> configure:2688: result: no >> configure:2756: checking for icc >> configure:2772: found /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin/icc >> configure:2783: result: icc >> configure:2819: checking for C compiler version >> configure:2826: icc --version >&5 >> icc (ICC) 9.1 20060928 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:2829: $? = 0 >> configure:2836: icc -v >&5 >> Version 9.1 >> configure:2839: $? = 0 >> configure:2846: icc -V >&5 >> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:2849: $? = 0 >> configure:2872: checking for C compiler default output file name >> configure:2899: icc conftest.c >&5 >> configure:2902: $? = 0 >> configure:2940: result: a.out >> configure:2957: checking whether the C compiler works >> configure:2967: ./a.out >> configure:2970: $? = 0 >> configure:2987: result: yes >> configure:2994: checking whether we are cross compiling >> configure:2996: result: no >> configure:2999: checking for suffix of executables >> configure:3006: icc -o conftest conftest.c >&5 >> configure:3009: $? = 0 >> configure:3033: result: >> configure:3039: checking for suffix of object files >> configure:3065: icc -c conftest.c >&5 >> configure:3068: $? = 0 >> configure:3091: result: o >> configure:3095: checking whether we are using the GNU C compiler >> configure:3124: icc -c conftest.c >&5 >> configure:3130: $? = 0 >> configure:3147: result: yes >> configure:3152: checking whether icc accepts -g >> configure:3182: icc -c -g conftest.c >&5 >> configure:3188: $? = 0 >> configure:3287: result: yes >> configure:3304: checking for icc option to accept ISO C89 >> configure:3378: icc -c -g -O2 conftest.c >&5 >> configure:3384: $? = 0 >> configure:3407: result: none needed >> configure:3436: checking for style of include used by make >> configure:3464: result: GNU >> configure:3489: checking dependency style of icc >> configure:3580: result: none >> configure:3643: checking for gcc >> configure:3670: result: icc >> configure:3908: checking for C compiler version >> configure:3915: icc --version >&5 >> icc (ICC) 9.1 20060928 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:3918: $? = 0 >> configure:3925: icc -v >&5 >> Version 9.1 >> configure:3928: $? = 0 >> configure:3935: icc -V >&5 >> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:3938: $? = 0 >> configure:3941: checking whether we are using the GNU C compiler >> configure:3993: result: yes >> configure:3998: checking whether icc accepts -g >> configure:4133: result: yes >> configure:4150: checking for icc option to accept ISO C89 >> configure:4253: result: none needed >> configure:4273: checking dependency style of icc >> configure:4364: result: none >> configure:4440: checking for g++ >> configure:4456: found /usr/bin/g++ >> configure:4467: result: g++ >> configure:4498: checking for C++ compiler version >> configure:4505: g++ --version >&5 >> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >> Copyright (C) 2002 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >> >> configure:4508: $? = 0 >> configure:4515: g++ -v >&5 >> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >> Thread model: posix >> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >> configure:4518: $? = 0 >> configure:4525: g++ -V >&5 >> g++: argument to `-V' missing >> >> configure:4528: $? = 1 >> configure:4531: checking whether we are using the GNU C++ compiler >> configure:4560: g++ -c conftest.cpp >&5 >> configure:4566: $? = 0 >> configure:4583: result: yes >> configure:4588: checking whether g++ accepts -g >> configure:4618: g++ -c -g conftest.cpp >&5 >> configure:4624: $? = 0 >> configure:4723: result: yes >> configure:4748: checking dependency style of g++ >> configure:4839: result: none >> configure:4907: checking for ifort >> configure:4923: found /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin/ifort >> configure:4934: result: ifort >> configure:4964: checking for Fortran 77 compiler version >> configure:4971: ifort --version >&5 >> ifort (IFORT) 9.1 20060928 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:4974: $? = 0 >> configure:4981: ifort -v >&5 >> Version 9.1 >> configure:4984: $? = 0 >> configure:4991: ifort -V >&5 >> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:4994: $? = 0 >> configure:5002: checking whether we are using the GNU Fortran 77 compiler >> configure:5021: ifort -c conftest.F >&5 >> fortcom: Error: conftest.F, line 3: Syntax error, found END-OF-STATEMENT when expecting one of: => = . ( : % >> choke me >> ---------------^ >> fortcom: Error: conftest.F, line 3: This statement is positioned incorrectly and/or has syntax errors. >> choke me >> ---------------^ >> compilation aborted for conftest.F (code 1) >> configure:5027: $? = 1 >> configure: failed program was: >> | program main >> | #ifndef __GNUC__ >> | choke me >> | #endif >> | >> | end >> configure:5044: result: no >> configure:5050: checking whether ifort accepts -g >> configure:5067: ifort -c -g conftest.f >&5 >> configure:5073: $? = 0 >> configure:5089: result: yes >> configure:5180: icc -c -g -O2 noformain.c 1>&5 >> configure:5183: $? = 0 >> configure:5194: checking if Fortran 77 compiler accepts -nofor_main >> configure:5203: ifort -nofor_main -g noformain.o -o noformain 1>&5 >> configure:5206: $? = 0 >> configure:5209: result: yes >> configure:5211: checking if Fortran 77 compilers requires -nofor_main >> configure:5221: ifort -g noformain.o -o noformain >> 1>&5 >> noformain.o(.text+0x0): In function `main': >> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/noformain.c:1: multiple definition of `main' >> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0x0): first defined here >> ld: Warning: size of symbol `main' changed from 384 in /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o to 32 in noformain.o >> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0xf2): In function `main': >> : undefined reference to `MAIN__' >> configure:5224: $? = 1 >> configure:5230: result: yes >> configure:5253: checking how f77 mangles function names >> configure:5264: ifort -c -g -nofor_main mangle-func.f 1>&5 >> configure:5267: $? = 0 >> configure:5310: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >> conftest.c(14): warning #266: function declared implicitly >> foobar(); >> ^ >> >> /tmp/iccqc5Wny.o(.text+0x12): In function `main': >> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:14: undefined reference to `foobar' >> configure:5316: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | /* end confdefs.h. */ >> | >> | int >> | main () >> | { >> | foobar(); >> | ; >> | return 0; >> | } >> configure:5348: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >> conftest.c(14): warning #266: function declared implicitly >> foobar_(); >> ^ >> >> configure:5354: $? = 0 >> configure:5466: result: lowercase-underscore >> configure:5542: checking how to run the C preprocessor >> configure:5582: icc -E conftest.c >> configure:5588: $? = 0 >> configure:5619: icc -E conftest.c >> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >> #include <ac_nonexistent.h> >> ^ >> >> configure:5625: $? = 2 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | /* end confdefs.h. */ >> | #include <ac_nonexistent.h> >> configure:5658: result: icc -E >> configure:5687: icc -E conftest.c >> configure:5693: $? = 0 >> configure:5724: icc -E conftest.c >> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >> #include <ac_nonexistent.h> >> ^ >> >> configure:5730: $? = 2 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | /* end confdefs.h. */ >> | #include <ac_nonexistent.h> >> configure:5823: checking for a sed that does not truncate output >> configure:5902: result: /bin/sed >> configure:5920: checking for grep that handles long lines and -e >> configure:5994: result: /bin/grep >> configure:5999: checking for egrep >> configure:6077: result: /bin/grep -E >> configure:6082: checking for fgrep >> configure:6160: result: /bin/grep -F >> configure:6195: checking for ld used by icc >> configure:6262: result: /usr/bin/ld >> configure:6271: checking if the linker (/usr/bin/ld) is GNU ld >> configure:6286: result: yes >> configure:6298: checking for BSD- or MS-compatible name lister (nm) >> configure:6347: result: /usr/bin/nm -B >> configure:6469: checking the name lister (/usr/bin/nm -B) interface >> configure:6476: icc -c -g -O2 conftest.c >&5 >> configure:6479: /usr/bin/nm -B "conftest.o" >> configure:6482: output >> 0000000000000000 N .debug_info_seg >> 0000000000000000 S some_variable >> configure:6489: result: BSD nm >> configure:6492: checking whether ln -s works >> configure:6496: result: yes >> configure:6504: checking the maximum length of command line arguments >> configure:6624: result: 98304 >> configure:6641: checking whether the shell understands some XSI constructs >> configure:6651: result: yes >> configure:6655: checking whether the shell understands "+=" >> configure:6661: result: no >> configure:6696: checking for /usr/bin/ld option to reload object files >> configure:6703: result: -r >> configure:6730: checking how to recognize dependent libraries >> configure:6920: result: pass_all >> configure:6980: checking for ar >> configure:6996: found /usr/bin/ar >> configure:7007: result: ar >> configure:7089: checking for strip >> configure:7105: found /usr/bin/strip >> configure:7116: result: strip >> configure:7192: checking for ranlib >> configure:7208: found /usr/bin/ranlib >> configure:7219: result: ranlib >> configure:7313: checking command to parse /usr/bin/nm -B output from icc object >> configure:7431: icc -c -g -O2 conftest.c >&5 >> configure:7434: $? = 0 >> configure:7438: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm >> configure:7441: $? = 0 >> configure:7495: icc -o conftest -g -O2 conftest.c conftstm.o >&5 >> configure:7498: $? = 0 >> configure:7536: result: ok >> configure:8410: checking for ANSI C header files >> configure:8440: icc -c -g -O2 conftest.c >&5 >> configure:8446: $? = 0 >> configure:8542: icc -o conftest -g -O2 conftest.c >&5 >> configure:8545: $? = 0 >> configure:8551: ./conftest >> configure:8554: $? = 0 >> configure:8571: result: yes >> configure:8595: checking for sys/types.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for sys/stat.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for stdlib.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for string.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for memory.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for strings.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for inttypes.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for stdint.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8595: checking for unistd.h >> configure:8616: icc -c -g -O2 conftest.c >&5 >> configure:8622: $? = 0 >> configure:8638: result: yes >> configure:8654: checking for dlfcn.h >> configure:8675: icc -c -g -O2 conftest.c >&5 >> configure:8681: $? = 0 >> configure:8697: result: yes >> configure:8826: checking for C++ compiler version >> configure:8833: g++ --version >&5 >> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >> Copyright (C) 2002 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >> >> configure:8836: $? = 0 >> configure:8843: g++ -v >&5 >> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >> Thread model: posix >> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >> configure:8846: $? = 0 >> configure:8853: g++ -V >&5 >> g++: argument to `-V' missing >> >> configure:8856: $? = 1 >> configure:8859: checking whether we are using the GNU C++ compiler >> configure:8911: result: yes >> configure:8916: checking whether g++ accepts -g >> configure:9051: result: yes >> configure:9076: checking dependency style of g++ >> configure:9167: result: none >> configure:9190: checking how to run the C++ preprocessor >> configure:9226: g++ -E conftest.cpp >> configure:9232: $? = 0 >> configure:9263: g++ -E conftest.cpp >> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >> configure:9269: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | /* end confdefs.h. */ >> | #include <ac_nonexistent.h> >> configure:9302: result: g++ -E >> configure:9331: g++ -E conftest.cpp >> configure:9337: $? = 0 >> configure:9368: g++ -E conftest.cpp >> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >> configure:9374: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | /* end confdefs.h. */ >> | #include <ac_nonexistent.h> >> configure:9525: checking for Fortran 77 compiler version >> configure:9532: ifort --version >&5 >> ifort (IFORT) 9.1 20060928 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:9535: $? = 0 >> configure:9542: ifort -v >&5 >> Version 9.1 >> configure:9545: $? = 0 >> configure:9552: ifort -V >&5 >> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >> >> configure:9555: $? = 0 >> configure:9563: checking whether we are using the GNU Fortran 77 compiler >> configure:9605: result: no >> configure:9611: checking whether ifort accepts -g >> configure:9650: result: yes >> configure:9824: checking for objdir >> configure:9839: result: .libs >> configure:10131: checking if icc supports -fno-rtti -fno-exceptions >> configure:10152: icc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 >> configure:10156: $? = 0 >> configure:10166: result: yes >> configure:10186: checking for icc option to produce PIC >> configure:10443: result: -fPIC -DPIC >> configure:10455: checking if icc PIC flag -fPIC -DPIC works >> configure:10476: icc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5 >> configure:10480: $? = 0 >> configure:10490: result: yes >> configure:10514: checking if icc static flag -static works >> configure:10542: result: yes >> configure:10557: checking if icc supports -c -o file.o >> configure:10581: icc -c -g -O2 -o out/conftest2.o conftest.c >&5 >> configure:10585: $? = 0 >> configure:10604: result: yes >> configure:10612: checking if icc supports -c -o file.o >> configure:10659: result: yes >> configure:10692: checking whether the icc linker (/usr/bin/ld) supports shared libraries >> configure:11746: result: yes >> configure:11985: checking dynamic linker characteristics >> configure:12428: icc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5 >> configure:12434: $? = 0 >> configure:12664: result: GNU/Linux ld.so >> configure:12766: checking how to hardcode library paths into programs >> configure:12791: result: immediate >> configure:13604: checking whether stripping libraries is possible >> configure:13609: result: yes >> configure:13644: checking if libtool supports shared libraries >> configure:13646: result: yes >> configure:13649: checking whether to build shared libraries >> configure:13670: result: no >> configure:13673: checking whether to build static libraries >> configure:13677: result: yes >> configure:13827: checking for ld used by g++ >> configure:13894: result: /usr/bin/ld >> configure:13903: checking if the linker (/usr/bin/ld) is GNU ld >> configure:13918: result: yes >> configure:13973: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >> configure:14935: result: yes >> configure:14963: g++ -c -g -O2 conftest.cpp >&5 >> configure:14966: $? = 0 >> configure:15148: checking for g++ option to produce PIC >> configure:15457: result: -fPIC -DPIC >> configure:15466: checking if g++ PIC flag -fPIC -DPIC works >> configure:15487: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5 >> configure:15491: $? = 0 >> configure:15501: result: yes >> configure:15522: checking if g++ static flag -static works >> configure:15550: result: yes >> configure:15562: checking if g++ supports -c -o file.o >> configure:15586: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 >> configure:15590: $? = 0 >> configure:15609: result: yes >> configure:15614: checking if g++ supports -c -o file.o >> configure:15661: result: yes >> configure:15691: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >> configure:15717: result: yes >> configure:15854: checking dynamic linker characteristics >> configure:16245: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5 >> configure:16251: $? = 0 >> configure:16481: result: GNU/Linux ld.so >> configure:16532: checking how to hardcode library paths into programs >> configure:16557: result: immediate >> configure:16698: checking if libtool supports shared libraries >> configure:16700: result: yes >> configure:16703: checking whether to build shared libraries >> configure:16723: result: no >> configure:16726: checking whether to build static libraries >> configure:16730: result: yes >> configure:16744: checking for ifort option to produce PIC >> configure:17001: result: -KPIC >> configure:17010: checking if ifort PIC flag -KPIC works >> configure:17031: ifort -c -g -nofor_main -KPIC conftest.f >&5 >> configure:17035: $? = 0 >> configure:17045: result: yes >> configure:17066: checking if ifort static flag -static works >> configure:17094: result: yes >> configure:17106: checking if ifort supports -c -o file.o >> configure:17130: ifort -c -g -nofor_main -o out/conftest2.o conftest.f >&5 >> configure:17134: $? = 0 >> configure:17153: result: yes >> configure:17158: checking if ifort supports -c -o file.o >> configure:17205: result: yes >> configure:17235: checking whether the ifort linker (/usr/bin/ld) supports shared libraries >> configure:18269: result: yes >> configure:18406: checking dynamic linker characteristics >> configure:18787: ifort -o conftest -g -nofor_main -Wl,-rpath -Wl,/foo conftest.f >&5 >> configure:18793: $? = 0 >> configure:19023: result: GNU/Linux ld.so >> configure:19074: checking how to hardcode library paths into programs >> configure:19099: result: immediate >> configure:19155: checking for pow in -lm >> configure:19190: icc -o conftest -g -O2 conftest.c -lm >&5 >> conftest.c(35): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "pow" >> >> configure:19196: $? = 0 >> configure:19214: result: yes >> configure:19229: checking for strerrno in -liberty >> configure:19264: icc -o conftest -g -O2 conftest.c -liberty >&5 >> /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/../../..//libiberty.a(strerror.o)(.text+0x240): In function `errno_max': >> : `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead >> configure:19270: $? = 0 >> configure:19288: result: yes >> configure:19304: checking for gethostbyname >> configure:19360: icc -o conftest -g -O2 conftest.c >&5 >> configure:19366: $? = 0 >> configure:19383: result: yes >> configure:19468: checking for connect >> configure:19524: icc -o conftest -g -O2 conftest.c >&5 >> configure:19530: $? = 0 >> configure:19547: result: yes >> configure:19632: checking for thr_create >> configure:19688: icc -o conftest -g -O2 conftest.c >&5 >> /tmp/iccv8SYca.o(.text+0x12): In function `main': >> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:58: undefined reference to `thr_create' >> configure:19694: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | /* end confdefs.h. */ >> | /* Define thr_create to an innocuous variant, in case <limits.h> declares thr_create. >> | For example, HP-UX 11i <limits.h> declares gettimeofday. */ >> | #define thr_create innocuous_thr_create >> | >> | /* System header to define __stub macros and hopefully few prototypes, >> | which can conflict with char thr_create (); below. >> | Prefer <limits.h> to <assert.h> if __STDC__ is defined, since >> | <limits.h> exists even on freestanding compilers. */ >> | >> | #ifdef __STDC__ >> | # include <limits.h> >> | #else >> | # include <assert.h> >> | #endif >> | >> | #undef thr_create >> | >> | /* Override any GCC internal prototype to avoid an error. >> | Use char because int might match the return type of a GCC >> | builtin and then its argument prototype would still apply. */ >> | #ifdef __cplusplus >> | extern "C" >> | #endif >> | char thr_create (); >> | /* The GNU C library defines this for functions which it implements >> | to always fail with ENOSYS. Some functions are actually named >> | something starting with __ and the normal name is an alias. */ >> | #if defined __stub_thr_create || defined __stub___thr_create >> | choke me >> | #endif >> | >> | int >> | main () >> | { >> | return thr_create (); >> | ; >> | return 0; >> | } >> configure:19711: result: no >> configure:19720: checking for thr_create in -lthread >> configure:19755: icc -o conftest -g -O2 conftest.c -lthread >&5 >> ld: cannot find -lthread >> configure:19761: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | /* end confdefs.h. */ >> | >> | /* Override any GCC internal prototype to avoid an error. >> | Use char because int might match the return type of a GCC >> | builtin and then its argument prototype would still apply. */ >> | #ifdef __cplusplus >> | extern "C" >> | #endif >> | char thr_create (); >> | int >> | main () >> | { >> | return thr_create (); >> | ; >> | return 0; >> | } >> configure:19779: result: no >> configure:19796: checking for time >> configure:19852: icc -o conftest -g -O2 conftest.c >&5 >> conftest.c(58): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "time" >> >> configure:19858: $? = 0 >> configure:19875: result: yes >> configure:19892: checking for rand >> configure:19948: icc -o conftest -g -O2 conftest.c >&5 >> configure:19954: $? = 0 >> configure:19971: result: yes >> configure:19988: checking for srand >> configure:20044: icc -o conftest -g -O2 conftest.c >&5 >> conftest.c(60): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "srand" >> >> configure:20050: $? = 0 >> configure:20067: result: yes >> configure:20085: checking the machine epsilon for VFLOOR >> configure:20111: icc -g -O2 -c fperror.c 1>&5 >> configure:20114: $? = 0 >> configure:20123: result: yes >> configure:20167: ----------------------------------------------------------- >> configure:20169: ---------- begin configuring for MALOC linkage ------------ >> configure:20171: ----------------------------------------------------------- >> configure:20178: WARNING: Error... FETK_INCLUDE is no longer supported. >> configure:20180: WARNING: Use --with-fetk-include=PATH instead. >> configure:20182: WARNING: Ignoring these variables... >> configure:20187: WARNING: Error... FETK_LIBRARY is no longer supported. >> configure:20189: WARNING: Use --with-fetk-library=PATH instead. >> configure:20191: WARNING: Ignoring these variables... >> configure:20195: checking for --with-fetk-include option >> configure:20205: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >> configure:20213: checking for --with-fetk-library option >> configure:20223: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >> configure:20235: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include/maloc/maloc.h >> configure:20251: result: yes >> configure:20267: Using MALOC headers in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >> configure:20273: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib/libmaloc.a >> configure:20289: result: yes >> configure:20306: Using MALOC libraries in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >> configure:20316: checking for --with-mpich option >> configure:20331: result: no >> configure:20337: checking for --with-mpich2 option >> configure:20351: result: no >> configure:20358: checking for --with-lam option >> configure:20372: result: no >> configure:20379: checking for --with-openmpi option >> configure:20392: result: no >> configure:20771: --------------------------------------------------------------- >> configure:20773: ---------- begin configuring for Python wrappers -------------- >> configure:20775: --------------------------------------------------------------- >> configure:20779: checking for --enable-python >> configure:21049: result: no >> configure:21058: Python wrappers disabled >> configure:21094: checking for python >> configure:21112: found /usr/bin/python >> configure:21124: result: /usr/bin/python >> configure:21214: Skipping MALOC installation; will use MALOC provided with FEtk >> configure:21225: checking for maloc_needs_rl in -lmaloc >> configure:21260: icc -o conftest -g -O2 /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmaloc /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -lvf2c -liberty -lm >&5 >> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include: file not recognized: Is a directory >> configure:21266: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | #define HAVE_TIME_FUNC >> | #define HAVE_RAND_FUNC >> | #define HAVE_SRAND_FUNC >> | #define FLOAT_ERRORS 1 >> | #define MACHINE_EPS 1.19209E-07 >> | /* end confdefs.h. */ >> | >> | /* Override any GCC internal prototype to avoid an error. >> | Use char because int might match the return type of a GCC >> | builtin and then its argument prototype would still apply. */ >> | #ifdef __cplusplus >> | extern "C" >> | #endif >> | char maloc_needs_rl (); >> | int >> | main () >> | { >> | return maloc_needs_rl (); >> | ; >> | return 0; >> | } >> configure:21284: result: no >> configure:21529: ------------------------------------------------------------ >> configure:21531: ---------- begin configuring for FEtk linkage -------------- >> configure:21533: ------------------------------------------------------------ >> configure:21542: checking for --disable-fetk >> configure:21554: result: no >> configure:21556: checking for user-specified FEtk include path >> configure:21559: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >> configure:21567: checking for user-specified FEtk library path >> configure:21570: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >> configure:21593: checking mc/mc.h usability >> configure:21610: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >> configure:21616: $? = 0 >> configure:21630: result: yes >> configure:21634: checking mc/mc.h presence >> configure:21649: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >> configure:21655: $? = 0 >> configure:21669: result: yes >> configure:21702: checking for mc/mc.h >> configure:21709: result: yes >> configure:21720: checking for mc_link in -lmc >> configure:21755: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >> configure:21761: $? = 0 >> configure:21779: result: yes >> configure:21800: checking mcx/mcx.h usability >> configure:21817: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >> conftest.c(62): catastrophic error: could not open source file "mcx/mcx.h" >> #include <mcx/mcx.h> >> ^ >> >> compilation aborted for conftest.c (code 4) >> configure:21823: $? = 4 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | #define HAVE_TIME_FUNC >> | #define HAVE_RAND_FUNC >> | #define HAVE_SRAND_FUNC >> | #define FLOAT_ERRORS 1 >> | #define MACHINE_EPS 1.19209E-07 >> | /* end confdefs.h. */ >> | #include <stdio.h> >> | #ifdef HAVE_SYS_TYPES_H >> | # include <sys/types.h> >> | #endif >> | #ifdef HAVE_SYS_STAT_H >> | # include <sys/stat.h> >> | #endif >> | #ifdef STDC_HEADERS >> | # include <stdlib.h> >> | # include <stddef.h> >> | #else >> | # ifdef HAVE_STDLIB_H >> | # include <stdlib.h> >> | # endif >> | #endif >> | #ifdef HAVE_STRING_H >> | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H >> | # include <memory.h> >> | # endif >> | # include <string.h> >> | #endif >> | #ifdef HAVE_STRINGS_H >> | # include <strings.h> >> | #endif >> | #ifdef HAVE_INTTYPES_H >> | # include <inttypes.h> >> | #endif >> | #ifdef HAVE_STDINT_H >> | # include <stdint.h> >> | #endif >> | #ifdef HAVE_UNISTD_H >> | # include <unistd.h> >> | #endif >> | #include <mcx/mcx.h> >> configure:21837: result: no >> configure:21841: checking mcx/mcx.h presence >> configure:21856: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >> conftest.c(29): error #5: could not open source file "mcx/mcx.h" >> #include <mcx/mcx.h> >> ^ >> >> configure:21862: $? = 2 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | #define HAVE_TIME_FUNC >> | #define HAVE_RAND_FUNC >> | #define HAVE_SRAND_FUNC >> | #define FLOAT_ERRORS 1 >> | #define MACHINE_EPS 1.19209E-07 >> | /* end confdefs.h. */ >> | #include <mcx/mcx.h> >> configure:21876: result: no >> configure:21909: checking for mcx/mcx.h >> configure:21916: result: no >> configure:21927: checking for mcx_link in -lmcx >> configure:21962: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmcx -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >> ld: cannot find -lmcx >> configure:21968: $? = 1 >> configure: failed program was: >> | /* confdefs.h. */ >> | #define PACKAGE_NAME "APBS" >> | #define PACKAGE_TARNAME "apbs" >> | #define PACKAGE_VERSION "1.2.1" >> | #define PACKAGE_STRING "APBS 1.2.1" >> | #define PACKAGE_BUGREPORT "ba...@bi..." >> | #define PACKAGE "apbs" >> | #define VERSION "1.2.1" >> | #define VF77_ONEUNDERSCORE >> | #define VF77_LOWERCASE >> | #define STDC_HEADERS 1 >> | #define HAVE_SYS_TYPES_H 1 >> | #define HAVE_SYS_STAT_H 1 >> | #define HAVE_STDLIB_H 1 >> | #define HAVE_STRING_H 1 >> | #define HAVE_MEMORY_H 1 >> | #define HAVE_STRINGS_H 1 >> | #define HAVE_INTTYPES_H 1 >> | #define HAVE_STDINT_H 1 >> | #define HAVE_UNISTD_H 1 >> | #define HAVE_DLFCN_H 1 >> | #define LT_OBJDIR ".libs/" >> | #define HAVE_TIME_FUNC >> | #define HAVE_RAND_FUNC >> | #define HAVE_SRAND_FUNC >> | #define FLOAT_ERRORS 1 >> | #define MACHINE_EPS 1.19209E-07 >> | /* end confdefs.h. */ >> | >> | /* Override any GCC internal prototype to avoid an error. >> | Use char because int might match the return type of a GCC >> | builtin and then its argument prototype would still apply. */ >> | #ifdef __cplusplus >> | extern "C" >> | #endif >> | char mcx_link (); >> | int >> | main () >> | { >> | return mcx_link (); >> | ; >> | return 0; >> | } >> configure:21986: result: no >> configure:22000: FEtk component MC found: enabled. >> configure:22025: WARNING: FEtk component MCX not found: hierarchical basis methods disabled. >> configure:22039: --------------------------------------------------------------- >> configure:22041: ------------ begin processing APBS configure options ---------- >> configure:22043: --------------------------------------------------------------- >> configure:22046: checking for EMBED macro can be used >> configure:22070: icc -c -g -O2 conftest.c >&5 >> configure:22076: $? = 0 >> configure:22094: result: yes >> configure:22098: checking --enable-pansi >> configure:22116: result: no >> configure:22123: checking for strcasecmp >> configure:22179: icc -o conftest -g -O2 conftest.c >&5 >> conftest.c(65): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "strcasecmp" >> >> configure:22185: $? = 0 >> configure:22202: result: yes >> configure:22225: checking for --disable-tools >> configure:22237: result: no >> configure:22239: tools will be compiled >> configure:22258: checking for --with-blas >> configure:22353: result: no >> configure:22383: checking for --with-arpack >> configure:22399: result: no >> configure:22405: checking for --disable-inline >> configure:22416: result: no >> configure:22418: inline functions will be used >> configure:22432: checking for --enable-tinker >> configure:22456: result: no >> configure:22460: checking for --enable-abps-quiet >> configure:22479: result: no >> configure:22483: checking for --disable-openmp >> configure:22497: result: no >> configure:22876: creating ./config.status >> >> ## ---------------------- ## >> ## Running config.status. ## >> ## ---------------------- ## >> >> This file was extended by APBS config.status 1.2.1, which was >> generated by GNU Autoconf 2.61. Invocation command line was >> >> CONFIG_FILES = >> CONFIG_HEADERS = >> CONFIG_LINKS = >> CONFIG_COMMANDS = >> $ ./config.status >> >> on osiris >> >> config.status:1044: creating Makefile >> config.status:1044: creating contrib/Makefile >> config.status:1044: creating contrib/blas/Makefile >> config.status:1044: creating contrib/pmgZ/Makefile >> config.status:1044: creating contrib/aqua/Makefile >> config.status:1044: creating contrib/opal/Makefile >> config.status:1044: creating contrib/opal/ZSI/Makefile >> config.status:1044: creating tools/Makefile >> config.status:1044: creating tools/mesh/Makefile >> config.status:1044: creating tools/manip/Makefile >> config.status:1044: creating tools/python/Makefile >> config.status:1044: creating tools/arpack/Makefile >> config.status:1044: creating tools/python/vgrid/Makefile >> config.status:1044: creating src/Makefile >> config.status:1044: creating src/generic/Makefile >> config.status:1044: creating src/mg/Makefile >> config.status:1044: creating src/fem/Makefile >> config.status:1044: creating src/aaa_inc/Makefile >> config.status:1044: creating src/aaa_inc/apbs/Makefile >> config.status:1044: creating src/aaa_lib/Makefile >> config.status:1044: creating examples/Makefile >> config.status:1044: creating examples/actin-dimer/Makefile >> config.status:1044: creating examples/alkanes/Makefile >> config.status:1044: creating examples/born/Makefile >> config.status:1044: creating examples/FKBP/Makefile >> config.status:1044: creating examples/hca-bind/Makefile >> config.status:1044: creating examples/ion-pmf/Makefile >> config.status:1044: creating examples/ion-protein/Makefile >> config.status:1044: creating examples/ionize/Makefile >> config.status:1044: creating examples/pka-lig/Makefile >> config.status:1044: creating examples/point-pmf/Makefile >> config.status:1044: creating examples/protein-rna/Makefile >> config.status:1044: creating examples/smpbe/Makefile >> config.status:1044: creating examples/solv/Makefile >> config.status:1044: creating examples/opal/Makefile >> config.status:1044: creating bin/Makefile >> config.status:1044: creating src/aaa_inc/apbscfg.h >> config.status:1327: executing depfiles commands >> config.status:1327: executing libtool commands >> configure:25486: >> >> APBS to be compiled with following settings: icc -g -O2 -openmp >> APBS to be compiled with following settings: ifort -g -nofor_main -nofor_main -openmp -assume cc_omp >> APBS to be linked with following libraries : -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas >> APBS to be compiled with following includes: -I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >> >> Please type "make; make install" >> >> >> ## ---------------- ## >> ## Cache variables. ## >> ## ---------------- ## >> >> ac_cv_build=ia64-unknown-linux-gnu >> ac_cv_c_compiler_gnu=yes >> ac_cv_cxx_compiler_gnu=yes >> ac_cv_env_CCC_set= >> ac_cv_env_CCC_value= >> ac_cv_env_CC_set= >> ac_cv_env_CC_value= >> ac_cv_env_CFLAGS_set= >> ac_cv_env_CFLAGS_value= >> ac_cv_env_CPPFLAGS_set= >> ac_cv_env_CPPFLAGS_value= >> ac_cv_env_CPP_set= >> ac_cv_env_CPP_value= >> ac_cv_env_CXXCPP_set= >> ac_cv_env_CXXCPP_value= >> ac_cv_env_CXXFLAGS_set= >> ac_cv_env_CXXFLAGS_value= >> ac_cv_env_CXX_set= >> ac_cv_env_CXX_value= >> ac_cv_env_F77_set= >> ac_cv_env_F77_value= >> ac_cv_env_FFLAGS_set= >> ac_cv_env_FFLAGS_value= >> ac_cv_env_LDFLAGS_set= >> ac_cv_env_LDFLAGS_value= >> ac_cv_env_LIBS_set= >> ac_cv_env_LIBS_value= >> ac_cv_env_build_alias_set= >> ac_cv_env_build_alias_value= >> ac_cv_env_host_alias_set= >> ac_cv_env_host_alias_value= >> ac_cv_env_target_alias_set= >> ac_cv_env_target_alias_value= >> ac_cv_f77_compiler_gnu=no >> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__include_maloc_maloc_h=yes >> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__lib_libmaloc_a=yes >> ac_cv_func_connect=yes >> ac_cv_func_gethostbyname=yes >> ac_cv_func_rand=yes >> ac_cv_func_srand=yes >> ac_cv_func_strcasecmp=yes >> ac_cv_func_thr_create=no >> ac_cv_func_time=yes >> ac_cv_header_dlfcn_h=yes >> ac_cv_header_inttypes_h=yes >> ac_cv_header_mc_mc_h=yes >> ac_cv_header_mcx_mcx_h=no >> ac_cv_header_memory_h=yes >> ac_cv_header_stdc=yes >> ac_cv_header_stdint_h=yes >> ac_cv_header_stdlib_h=yes >> ac_cv_header_string_h=yes >> ac_cv_header_strings_h=yes >> ac_cv_header_sys_stat_h=yes >> ac_cv_header_sys_types_h=yes >> ac_cv_header_unistd_h=yes >> ac_cv_host=ia64-unknown-linux-gnu >> ac_cv_lib_iberty_strerrno=yes >> ac_cv_lib_m_pow=yes >> ac_cv_lib_maloc_maloc_needs_rl=no >> ac_cv_lib_mc_mc_link=yes >> ac_cv_lib_mcx_mcx_link=no >> ac_cv_lib_thread_thr_create=no >> ac_cv_objext=o >> ac_cv_path_EGREP='/bin/grep -E' >> ac_cv_path_FGREP='/bin/grep -F' >> ac_cv_path_GREP=/bin/grep >> ac_cv_path_SED=/bin/sed >> ac_cv_path_install='/usr/bin/install -c' >> ac_cv_path_mkdir=/bin/mkdir >> ac_cv_path_py_path=/usr/bin/python >> ac_cv_prog_AWK=gawk >> ac_cv_prog_CPP='icc -E' >> ac_cv_prog_CXXCPP='g++ -E' >> ac_cv_prog_ac_ct_AR=ar >> ac_cv_prog_ac_ct_CC=icc >> ac_cv_prog_ac_ct_CXX=g++ >> ac_cv_prog_ac_ct_F77=ifort >> ac_cv_prog_ac_ct_RANLIB=ranlib >> ac_cv_prog_ac_ct_STRIP=strip >> ac_cv_prog_cc_c89= >> ac_cv_prog_cc_g=yes >> ac_cv_prog_cxx_g=yes >> ac_cv_prog_f77_g=yes >> ac_cv_prog_make_make_set=yes >> ac_cv_target=ia64-unknown-linux-gnu >> am_cv_CC_dependencies_compiler_type=none >> am_cv_CXX_dependencies_compiler_type=none >> am_cv_prog_cc_stdc= >> lt_cv_deplibs_check_method=pass_all >> lt_cv_file_magic_cmd='$MAGIC_CMD' >> lt_cv_file_magic_test_file= >> lt_cv_ld_reload_flag=-r >> lt_cv_nm_interface='BSD nm' >> lt_cv_objdir=.libs >> lt_cv_path_LD=/usr/bin/ld >> lt_cv_path_LDCXX=/usr/bin/ld >> lt_cv_path_NM='/usr/bin/nm -B' >> lt_cv_prog_compiler_c_o=yes >> lt_cv_prog_compiler_c_o_CXX=yes >> lt_cv_prog_compiler_c_o_F77=yes >> lt_cv_prog_compiler_pic_works=yes >> lt_cv_prog_compiler_pic_works_CXX=yes >> lt_cv_prog_compiler_pic_works_F77=yes >> lt_cv_prog_compiler_rtti_exceptions=yes >> lt_cv_prog_compiler_static_works=yes >> lt_cv_prog_compiler_static_works_CXX=yes >> lt_cv_prog_compiler_static_works_F77=yes >> lt_cv_prog_gnu_ld=yes >> lt_cv_prog_gnu_ldcxx=yes >> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\''' >> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' >> lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' >> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' >> lt_cv_sys_max_cmd_len=98304 >> >> ## ----------------- ## >> ## Output variables. ## >> ## ----------------- ## >> >> ACLOCAL=':' >> AMDEPBACKSLASH='\' >> AMDEP_FALSE='#' >> AMDEP_TRUE='' >> AMTAR='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run tar' >> APBS_VERSION='1:2:1' >> AR='ar' >> AUTOCONF=':' >> AUTOHEADER=':' >> AUTOMAKE=':' >> AWK='gawk' >> CC='icc' >> CCDEPMODE='depmode=none' >> CFLAGS='-g -O2 -openmp' >> CPP='icc -E' >> CPPFLAGS='' >> CXX='g++' >> CXXCPP='g++ -E' >> CXXDEPMODE='depmode=none' >> CXXFLAGS='-g -O2' >> CYGPATH_W='echo' >> DEFS='-DHAVE_CONFIG_H' >> DEPDIR='.deps' >> DSYMUTIL='' >> DUMPBIN='' >> ECHO_C='' >> ECHO_N='-n' >> ECHO_T='' >> EGREP='/bin/grep -E' >> EXEEXT='' >> F77='ifort' >> FFLAGS=' -g -nofor_main -nofor_main -openmp -assume cc_omp' >> FGREP='/bin/grep -F' >> GREP='/bin/grep' >> INSTALL_DATA='${INSTALL} -m 644' >> INSTALL_PROGRAM='${INSTALL}' >> INSTALL_SCRIPT='${INSTALL}' >> INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' >> LD='/usr/bin/ld' >> LDFLAGS=' -static-intel' >> LIBOBJS='' >> LIBS='' >> LIBTOOL='$(SHELL) $(top_builddir)/libtool' >> LIPO='' >> LN_S='ln -s' >> LTLIBOBJS='' >> MAKEINFO='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run makeinfo' >> NM='/usr/bin/nm -B' >> NMEDIT='' >> OBJEXT='o' >> OTOOL64='' >> OTOOL='' >> PACKAGE='apbs' >> PACKAGE_BUGREPORT='ba...@bi...' >> PACKAGE_NAME='APBS' >> PACKAGE_STRING='APBS 1.2.1' >> PACKAGE_TARNAME='apbs' >> PACKAGE_VERSION='1.2.1' >> PATH_SEPARATOR=':' >> PY_CC='' >> PY_CFLAGS='' >> PY_LDFLAGS='' >> PY_LINKFLAGS='' >> PY_PRESENT_FALSE='' >> PY_PRESENT_TRUE='#' >> PY_SHARED='' >> RANLIB='ranlib' >> SED='/bin/sed' >> SET_MAKE='' >> SHELL='/bin/sh' >> SITEPKGS='/home/khelgeo/apbs_fetk//lib/python2.2/site-packages' >> STRIP='strip' >> UHBD_COMPILE_FALSE='#' >> UHBD_COMPILE_TRUE='' >> VERSION='1.2.1' >> ac_ct_CC='icc' >> ac_ct_CXX='g++' >> ac_ct_DUMPBIN='' >> ac_ct_F77='ifort' >> am__fastdepCC_FALSE='' >> am__fastdepCC_TRUE='#' >> am__fastdepCXX_FALSE='' >> am__fastdepCXX_TRUE='#' >> am__include='include' >> am__isrc='' >> am__leading_dot='.' >> am__quote='' >> am__tar='${AMTAR} chof - "$$tardir"' >> am__untar='${AMTAR} xf -' >> apbs_build_libraries='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/bin/libapbsmainroutines.la /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/src/aaa_lib/libapbs.la -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas' >> apbs_do_blas='blas' >> apbs_do_maloc='' >> apbs_do_python='' >> apbs_do_tools='tools' >> arpack_do_tools='' >> arpack_lib='' >> bindir='${exec_prefix}/bin' >> build='ia64-unknown-linux-gnu' >> build_alias='' >> build_cpu='ia64' >> build_os='linux-gnu' >> build_vendor='unknown' >> contrib_path='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib' >> datadir='${datarootdir}' >> datarootdir='${prefix}/share' >> docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' >> dvidir='${docdir}' >> exec_prefix='${prefix}' >> fetk_cpu_vendor_os='' >> host='ia64-unknown-linux-gnu' >> host_alias='' >> host_cpu='ia64' >> host_os='linux-gnu' >> host_vendor='unknown' >> htmldir='${docdir}' >> inc_list='-I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include ' >> includedir='${prefix}/include' >> infodir='${datarootdir}/info' >> install_sh='$(SHELL) /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/install-sh' >> lib_list=' -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas' >> libdir='${exec_prefix}/lib' >> liberty_lib='-liberty' >> libexecdir='${exec_prefix}/libexec' >> localedir='${datarootdir}/locale' >> localstatedir='${prefix}/var' >> lt_ECHO='echo' >> maloc_inc='-I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include' >> maloc_lib='-L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc' >> mandir='${datarootdir}/man' >> math_lib='-lm' >> mc_inc='' >> mc_lib='-L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc' >> mcx_inc='' >> mcx_lib='' >> mkdir_p='/bin/mkdir -p' >> mpi_inc='' >> mpi_lib='' >> nsl_lib='' >> oldincludedir='/usr/include' >> pdfdir='${docdir}' >> pedantic_ansi='' >> prefix='/home/khelgeo/apbs_fetk/' >> program_transform_name='s,x,x,' >> psdir='${docdir}' >> py_path='/usr/bin/python' >> rl_lib='' >> sbindir='${exec_prefix}/sbin' >> sharedstatedir='${prefix}/com' >> socket_lib='' >> sysconfdir='${prefix}/etc' >> target='ia64-unknown-linux-gnu' >> target_alias='' >> target_cpu='ia64' >> target_os='linux-gnu' >> target_vendor='unknown' >> thread_lib='' >> top_apbsdir='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source' >> wall='' >> wall_pedantic='' >> wall_pedantic_ansi='' >> >> ## ----------- ## >> ## confdefs.h. ## >> ## ----------- ## >> >> #defin... [truncated message content] |
From: Michael H. <mh...@ma...> - 2010-07-23 18:25:47
|
Hi George, That should do it as far as FETK being built correctly. You can check this by trying to build one of the MC examples (for example: cd into ./fetk/mc/examples/simpleMCsh). You will have to edit the very simple makefile in the example directory to make sure that it finds the headers and libraries in the "build" directory that was created by the "./fetk-build all". If a "make" in the simpleMCsh directory completes and creates an "mcsh" binary in the simpleMCsh directory, then it is finding all of the FETK libraries and linking correctly. If the step above works, then the problem is only in the linkage between APBS and the FETK libraries. It is likely that this is the problem, since we have just released FETK in the last two weeks, and have possibly broken some of the linkage with APBS. We want to know about any problems you and others have in building things so that we can quickly fix them. thanks, -mike George Khelashvili <ge...@me...> (07-23-2010 14:13:25-0400): >Dear Michael, > >Thank you for your comment. I used fetk_build script to build the entire >fetk by running "./fetk-build all". Are there any other options that I >missed? It looks like that both maloc and mc are in place. > >Sincerely, >George > >Michael Holst wrote: >> Nathan and all, >> >> A quick look at the make.log indicates that MALOC calls within MC >> are not being resolved, so MALOC (via libmaloc.a) was either not >> built or not being found. >> >> best, -mike >> >> George Khelashvili <ge...@me...> (07-23-2010 12:25:07-0400): >> >>> Hi Nathan, >>> >>> The listing of >>> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ >>> directory is "bin doc fetk-env include lib". By the way, I >>> realized that I sent you wrong log files, which did not exactly >>> correspond to the versions of APBS and FETK I used (I played with >>> several combinations and I accidentally mixed them up). Sorry for >>> that. Here are the corrected log files which were obtained by >>> installing Fetk version 1.1 first, and then installing APBS 1.2.1. >>> The log files were generated during the APBS installation. This log >>> file produced somewhat different error message. >>> I do realize that APBS-FETK link is in the beginning stages so I will >>> be glad to contribute as I can to resolve this issue so that the >>> community can use this what I think will be a wonderful tool. >>> >>> Sincerely, >>> George >>> >>> Baker, Nathan wrote: >>> >>>> Hi George -- >>>> >>>> This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? >>>> >>>> All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. >>>> >>>> Thanks, >>>> >>>> __________________________________________________ Nathan Baker >>>> Chief Scientist for Signature Science >>>> Pacific Northwest National Laboratory >>>> >>>> >>>> >>>>> -----Original Message----- >>>>> From: George Khelashvili [mailto:ge...@me...] >>>>> Sent: Wednesday, July 21, 2010 11:31 AM >>>>> To: apb...@li... >>>>> Subject: Re: [Apbs-users] FeTK support in APBS >>>>> >>>>> Dear APBS users, >>>>> >>>>> I am trying to compile APBS version 1.2 with Fetk support (Fetk version >>>>> 1.1). I have downloaded and installed the entire Fetk package, and now >>>>> I moved on to installing APBS itself. While configuring apparently >>>>> worked since all the necessary Fetk library and header files where >>>>> found, the compilation crushed when I run "make". I have attached log >>>>> files from configuration step as well as "make" step. Obviously there >>>>> is a problem while compiling fetk.c file. I would appreciate if >>>>> somebody can take a look at the attached files and suggest what is >>>>> missing. >>>>> >>>>> Thank you, >>>>> George >>>>> >>>>> Baker, Nathan wrote: >>>>> >>>>>> Hello - >>>>>> >>>>>> Yes, FEtk is available for download at >>>>>> http://fetk.org/codes/download/. I will be updating the documentation >>>>>> in the next few weeks with revised instructions on how to compile, >>>>>> >>>>> etc. >>>>> >>>>>> Thanks, >>>>>> >>>>>> Nathan >>>>>> >>>>>> __________________________________________________ >>>>>> *Nathan Baker* >>>>>> Chief Scientist for Signature Science >>>>>> Pacific Northwest National Laboratory >>>>>> >>>>>> *From:* patrizio ansalone [mailto:p.a...@in...] >>>>>> *Sent:* Wednesday, July 21, 2010 12:39 AM >>>>>> *To:* apb...@li... >>>>>> *Subject:* [Apbs-users] FeTK support in APBS >>>>>> >>>>>> >>>>>> Is it possibile to compile apbs with fetk support? I have understod >>>>>> that FeTk must be installed >>>>>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>>>>> >>>>> avil >>>>> >>>>>> /source-installation) but I can't find a repository where I can >>>>>> download it. Any sugestion how to fix this problem ? >>>>>> thanks in advance >>>>>> Patrizio >>>>>> >>>>>> --------------------------------------------------------------------- >>>>>> >>>>> - >>>>> >>>>>> -- >>>>>> >>>>>> --------------------------------------------------------------------- >>>>>> >>>>> - >>>>> >>>>>> -------- This SF.net email is sponsored by Sprint What will you do >>>>>> first with EVO, the first 4G phone? >>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>>>>> --------------------------------------------------------------------- >>>>>> >>>>> - >>>>> >>>>>> -- >>>>>> >>>>>> _______________________________________________ >>>>>> apbs-users mailing list >>>>>> apb...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>>> >>>>>> >>>>> -- >>>>> George Khelashvili, Ph.D. >>>>> Department of Physiology and Biophysics >>>>> Weill Medical College of Cornell University 1300 York Avenue, Room >>>>> LC501 New York, NY, 10065, USA ge...@me... >>>>> Phone: 1-212-746-6539 >>>>> Fax: 1-212-746-6226 >>>>> >>>>> >>> -- >>> George Khelashvili, Ph.D. >>> Department of Physiology and Biophysics >>> Weill Medical College of Cornell University >>> 1300 York Avenue, Room LC501 >>> New York, NY, 10065, USA >>> ge...@me... >>> Phone: 1-212-746-6539 >>> Fax: 1-212-746-6226 >>> >>> >> >> >>> This file contains any messages produced by compilers while >>> running configure, to aid debugging if configure makes a mistake. >>> >>> It was created by APBS configure 1.2.1, which was >>> generated by GNU Autoconf 2.61. Invocation command line was >>> >>> $ ./configure --with-fetk-include=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include --with-fetk-library=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib --prefix=/home/khelgeo/apbs_fetk/ >>> >>> ## --------- ## >>> ## Platform. ## >>> ## --------- ## >>> >>> hostname = osiris >>> uname -m = ia64 >>> uname -r = 2.4.21-sgi301rp04091014_10105 >>> uname -s = Linux >>> uname -v = #1 SMP Fri Sep 10 15:02:03 PDT 2004 >>> >>> /usr/bin/uname -p = unknown >>> /bin/uname -X = unknown >>> >>> /bin/arch = ia64 >>> /usr/bin/arch -k = unknown >>> /usr/convex/getsysinfo = unknown >>> /usr/bin/hostinfo = unknown >>> /bin/machine = unknown >>> /usr/bin/oslevel = unknown >>> /bin/universe = unknown >>> >>> PATH: /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin >>> PATH: /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin >>> PATH: /softlib/exe/osiris/bin >>> PATH: /softlib/exe/ia64/bin >>> PATH: /softlib/exe/linux/bin >>> PATH: /softlib/exe/all/bin >>> PATH: /usr/kerberos/bin >>> PATH: /usr/local/bin >>> PATH: /bin >>> PATH: /usr/bin >>> PATH: /usr/X11R6/bin >>> >>> >>> ## ----------- ## >>> ## Core tests. ## >>> ## ----------- ## >>> >>> configure:2051: checking build system type >>> configure:2069: result: ia64-unknown-linux-gnu >>> configure:2091: checking host system type >>> configure:2106: result: ia64-unknown-linux-gnu >>> configure:2128: checking target system type >>> configure:2143: result: ia64-unknown-linux-gnu >>> configure:2187: checking for a BSD-compatible install >>> configure:2243: result: /usr/bin/install -c >>> configure:2254: checking whether build environment is sane >>> configure:2297: result: yes >>> configure:2325: checking for a thread-safe mkdir -p >>> configure:2364: result: /bin/mkdir -p >>> configure:2377: checking for gawk >>> configure:2393: found /bin/gawk >>> configure:2404: result: gawk >>> configure:2415: checking whether make sets $(MAKE) >>> configure:2436: result: yes >>> configure:2641: checking for --enable-fast option >>> configure:2661: result: no >>> configure:2669: checking for --enable-python >>> configure:2688: result: no >>> configure:2756: checking for icc >>> configure:2772: found /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin/icc >>> configure:2783: result: icc >>> configure:2819: checking for C compiler version >>> configure:2826: icc --version >&5 >>> icc (ICC) 9.1 20060928 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:2829: $? = 0 >>> configure:2836: icc -v >&5 >>> Version 9.1 >>> configure:2839: $? = 0 >>> configure:2846: icc -V >&5 >>> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >>> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:2849: $? = 0 >>> configure:2872: checking for C compiler default output file name >>> configure:2899: icc conftest.c >&5 >>> configure:2902: $? = 0 >>> configure:2940: result: a.out >>> configure:2957: checking whether the C compiler works >>> configure:2967: ./a.out >>> configure:2970: $? = 0 >>> configure:2987: result: yes >>> configure:2994: checking whether we are cross compiling >>> configure:2996: result: no >>> configure:2999: checking for suffix of executables >>> configure:3006: icc -o conftest conftest.c >&5 >>> configure:3009: $? = 0 >>> configure:3033: result: >>> configure:3039: checking for suffix of object files >>> configure:3065: icc -c conftest.c >&5 >>> configure:3068: $? = 0 >>> configure:3091: result: o >>> configure:3095: checking whether we are using the GNU C compiler >>> configure:3124: icc -c conftest.c >&5 >>> configure:3130: $? = 0 >>> configure:3147: result: yes >>> configure:3152: checking whether icc accepts -g >>> configure:3182: icc -c -g conftest.c >&5 >>> configure:3188: $? = 0 >>> configure:3287: result: yes >>> configure:3304: checking for icc option to accept ISO C89 >>> configure:3378: icc -c -g -O2 conftest.c >&5 >>> configure:3384: $? = 0 >>> configure:3407: result: none needed >>> configure:3436: checking for style of include used by make >>> configure:3464: result: GNU >>> configure:3489: checking dependency style of icc >>> configure:3580: result: none >>> configure:3643: checking for gcc >>> configure:3670: result: icc >>> configure:3908: checking for C compiler version >>> configure:3915: icc --version >&5 >>> icc (ICC) 9.1 20060928 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:3918: $? = 0 >>> configure:3925: icc -v >&5 >>> Version 9.1 >>> configure:3928: $? = 0 >>> configure:3935: icc -V >&5 >>> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >>> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:3938: $? = 0 >>> configure:3941: checking whether we are using the GNU C compiler >>> configure:3993: result: yes >>> configure:3998: checking whether icc accepts -g >>> configure:4133: result: yes >>> configure:4150: checking for icc option to accept ISO C89 >>> configure:4253: result: none needed >>> configure:4273: checking dependency style of icc >>> configure:4364: result: none >>> configure:4440: checking for g++ >>> configure:4456: found /usr/bin/g++ >>> configure:4467: result: g++ >>> configure:4498: checking for C++ compiler version >>> configure:4505: g++ --version >&5 >>> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>> Copyright (C) 2002 Free Software Foundation, Inc. >>> This is free software; see the source for copying conditions. There is NO >>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>> >>> configure:4508: $? = 0 >>> configure:4515: g++ -v >&5 >>> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >>> Thread model: posix >>> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>> configure:4518: $? = 0 >>> configure:4525: g++ -V >&5 >>> g++: argument to `-V' missing >>> >>> configure:4528: $? = 1 >>> configure:4531: checking whether we are using the GNU C++ compiler >>> configure:4560: g++ -c conftest.cpp >&5 >>> configure:4566: $? = 0 >>> configure:4583: result: yes >>> configure:4588: checking whether g++ accepts -g >>> configure:4618: g++ -c -g conftest.cpp >&5 >>> configure:4624: $? = 0 > >>> configure:4723: result: yes >>> configure:4748: checking dependency style of g++ >>> configure:4839: result: none >>> configure:4907: checking for ifort >>> configure:4923: found /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin/ifort >>> configure:4934: result: ifort >>> configure:4964: checking for Fortran 77 compiler version >>> configure:4971: ifort --version >&5 >>> ifort (IFORT) 9.1 20060928 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:4974: $? = 0 >>> configure:4981: ifort -v >&5 >>> Version 9.1 >>> configure:4984: $? = 0 >>> configure:4991: ifort -V >&5 >>> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >>> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:4994: $? = 0 >>> configure:5002: checking whether we are using the GNU Fortran 77 compiler >>> configure:5021: ifort -c conftest.F >&5 >>> fortcom: Error: conftest.F, line 3: Syntax error, found END-OF-STATEMENT when expecting one of: => = . ( : % >>> choke me >>> ---------------^ >>> fortcom: Error: conftest.F, line 3: This statement is positioned incorrectly and/or has syntax errors. >>> choke me >>> ---------------^ >>> compilation aborted for conftest.F (code 1) >>> configure:5027: $? = 1 >>> configure: failed program was: >>> | program main >>> | #ifndef __GNUC__ >>> | choke me >>> | #endif >>> | >>> | end >>> configure:5044: result: no >>> configure:5050: checking whether ifort accepts -g >>> configure:5067: ifort -c -g conftest.f >&5 >>> configure:5073: $? = 0 >>> configure:5089: result: yes >>> configure:5180: icc -c -g -O2 noformain.c 1>&5 >>> configure:5183: $? = 0 >>> configure:5194: checking if Fortran 77 compiler accepts -nofor_main >>> configure:5203: ifort -nofor_main -g noformain.o -o noformain 1>&5 >>> configure:5206: $? = 0 >>> configure:5209: result: yes >>> configure:5211: checking if Fortran 77 compilers requires -nofor_main >>> configure:5221: ifort -g noformain.o -o noformain >>> 1>&5 >>> noformain.o(.text+0x0): In function `main': >>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/noformain.c:1: multiple definition of `main' >>> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0x0): first defined here >>> ld: Warning: size of symbol `main' changed from 384 in /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o to 32 in noformain.o >>> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0xf2): In function `main': >>> : undefined reference to `MAIN__' >>> configure:5224: $? = 1 >>> configure:5230: result: yes >>> configure:5253: checking how f77 mangles function names >>> configure:5264: ifort -c -g -nofor_main mangle-func.f 1>&5 >>> configure:5267: $? = 0 >>> configure:5310: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >>> conftest.c(14): warning #266: function declared implicitly >>> foobar(); >>> ^ >>> >>> /tmp/iccqc5Wny.o(.text+0x12): In function `main': >>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:14: undefined reference to `foobar' >>> configure:5316: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | /* end confdefs.h. */ >>> | >>> | int >>> | main () >>> | { >>> | foobar(); >>> | ; >>> | return 0; >>> | } >>> configure:5348: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >>> conftest.c(14): warning #266: function declared implicitly >>> foobar_(); >>> ^ >>> >>> configure:5354: $? = 0 >>> configure:5466: result: lowercase-underscore >>> configure:5542: checking how to run the C preprocessor >>> configure:5582: icc -E conftest.c >>> configure:5588: $? = 0 >>> configure:5619: icc -E conftest.c >>> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >>> #include <ac_nonexistent.h> >>> ^ >>> >>> configure:5625: $? = 2 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | /* end confdefs.h. */ >>> | #include <ac_nonexistent.h> >>> configure:5658: result: icc -E >>> configure:5687: icc -E conftest.c >>> configure:5693: $? = 0 >>> configure:5724: icc -E conftest.c >>> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >>> #include <ac_nonexistent.h> >>> ^ >>> >>> configure:5730: $? = 2 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | /* end confdefs.h. */ >>> | #include <ac_nonexistent.h> >>> configure:5823: checking for a sed that does not truncate output >>> configure:5902: result: /bin/sed >>> configure:5920: checking for grep that handles long lines and -e >>> configure:5994: result: /bin/grep >>> configure:5999: checking for egrep >>> configure:6077: result: /bin/grep -E >>> configure:6082: checking for fgrep >>> configure:6160: result: /bin/grep -F >>> configure:6195: checking for ld used by icc >>> configure:6262: result: /usr/bin/ld >>> configure:6271: checking if the linker (/usr/bin/ld) is GNU ld >>> configure:6286: result: yes >>> configure:6298: checking for BSD- or MS-compatible name lister (nm) >>> configure:6347: result: /usr/bin/nm -B >>> configure:6469: checking the name lister (/usr/bin/nm -B) interface >>> configure:6476: icc -c -g -O2 conftest.c >&5 >>> configure:6479: /usr/bin/nm -B "conftest.o" >>> configure:6482: output >>> 0000000000000000 N .debug_info_seg >>> 0000000000000000 S some_variable >>> configure:6489: result: BSD nm >>> configure:6492: checking whether ln -s works >>> configure:6496: result: yes >>> configure:6504: checking the maximum length of command line arguments >>> configure:6624: result: 98304 >>> configure:6641: checking whether the shell understands some XSI constructs >>> configure:6651: result: yes >>> configure:6655: checking whether the shell understands "+=" >>> configure:6661: result: no >>> configure:6696: checking for /usr/bin/ld option to reload object files >>> configure:6703: result: -r >>> configure:6730: checking how to recognize dependent libraries >>> configure:6920: result: pass_all >>> configure:6980: checking for ar >>> configure:6996: found /usr/bin/ar >>> configure:7007: result: ar >>> configure:7089: checking for strip >>> configure:7105: found /usr/bin/strip >>> configure:7116: result: strip >>> configure:7192: checking for ranlib >>> configure:7208: found /usr/bin/ranlib >>> configure:7219: result: ranlib >>> configure:7313: checking command to parse /usr/bin/nm -B output from icc object >>> configure:7431: icc -c -g -O2 conftest.c >&5 >>> configure:7434: $? = 0 >>> configure:7438: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm >>> configure:7441: $? = 0 >>> configure:7495: icc -o conftest -g -O2 conftest.c conftstm.o >&5 >>> configure:7498: $? = 0 >>> configure:7536: result: ok >>> configure:8410: checking for ANSI C header files >>> configure:8440: icc -c -g -O2 conftest.c >&5 >>> configure:8446: $? = 0 >>> configure:8542: icc -o conftest -g -O2 conftest.c >&5 >>> configure:8545: $? = 0 >>> configure:8551: ./conftest >>> configure:8554: $? = 0 >>> configure:8571: result: yes >>> configure:8595: checking for sys/types.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for sys/stat.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for stdlib.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for string.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for memory.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for strings.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for inttypes.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for stdint.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8595: checking for unistd.h >>> configure:8616: icc -c -g -O2 conftest.c >&5 >>> configure:8622: $? = 0 >>> configure:8638: result: yes >>> configure:8654: checking for dlfcn.h >>> configure:8675: icc -c -g -O2 conftest.c >&5 >>> configure:8681: $? = 0 >>> configure:8697: result: yes >>> configure:8826: checking for C++ compiler version >>> configure:8833: g++ --version >&5 >>> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>> Copyright (C) 2002 Free Software Foundation, Inc. >>> This is free software; see the source for copying conditions. There is NO >>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>> >>> configure:8836: $? = 0 >>> configure:8843: g++ -v >&5 >>> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >>> Thread model: posix >>> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>> configure:8846: $? = 0 >>> configure:8853: g++ -V >&5 >>> g++: argument to `-V' missing >>> >>> configure:8856: $? = 1 >>> configure:8859: checking whether we are using the GNU C++ compiler >>> configure:8911: result: yes >>> configure:8916: checking whether g++ accepts -g >>> configure:9051: result: yes >>> configure:9076: checking dependency style of g++ >>> configure:9167: result: none >>> configure:9190: checking how to run the C++ preprocessor >>> configure:9226: g++ -E conftest.cpp >>> configure:9232: $? = 0 >>> configure:9263: g++ -E conftest.cpp >>> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >>> configure:9269: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | /* end confdefs.h. */ >>> | #include <ac_nonexistent.h> >>> configure:9302: result: g++ -E >>> configure:9331: g++ -E conftest.cpp >>> configure:9337: $? = 0 >>> configure:9368: g++ -E conftest.cpp >>> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >>> configure:9374: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | /* end confdefs.h. */ >>> | #include <ac_nonexistent.h> >>> configure:9525: checking for Fortran 77 compiler version >>> configure:9532: ifort --version >&5 >>> ifort (IFORT) 9.1 20060928 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:9535: $? = 0 >>> configure:9542: ifort -v >&5 >>> Version 9.1 >>> configure:9545: $? = 0 >>> configure:9552: ifort -V >&5 >>> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >>> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>> >>> configure:9555: $? = 0 >>> configure:9563: checking whether we are using the GNU Fortran 77 compiler >>> configure:9605: result: no >>> configure:9611: checking whether ifort accepts -g >>> configure:9650: result: yes >>> configure:9824: checking for objdir >>> configure:9839: result: .libs >>> configure:10131: checking if icc supports -fno-rtti -fno-exceptions >>> configure:10152: icc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 >>> configure:10156: $? = 0 >>> configure:10166: result: yes >>> configure:10186: checking for icc option to produce PIC >>> configure:10443: result: -fPIC -DPIC >>> configure:10455: checking if icc PIC flag -fPIC -DPIC works >>> configure:10476: icc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5 >>> configure:10480: $? = 0 >>> configure:10490: result: yes >>> configure:10514: checking if icc static flag -static works >>> configure:10542: result: yes >>> configure:10557: checking if icc supports -c -o file.o >>> configure:10581: icc -c -g -O2 -o out/conftest2.o conftest.c >&5 >>> configure:10585: $? = 0 >>> configure:10604: result: yes >>> configure:10612: checking if icc supports -c -o file.o >>> configure:10659: result: yes >>> configure:10692: checking whether the icc linker (/usr/bin/ld) supports shared libraries >>> configure:11746: result: yes >>> configure:11985: checking dynamic linker characteristics >>> configure:12428: icc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5 >>> configure:12434: $? = 0 >>> configure:12664: result: GNU/Linux ld.so >>> configure:12766: checking how to hardcode library paths into programs >>> configure:12791: result: immediate >>> configure:13604: checking whether stripping libraries is possible >>> configure:13609: result: yes >>> configure:13644: checking if libtool supports shared libraries >>> configure:13646: result: yes >>> configure:13649: checking whether to build shared libraries >>> configure:13670: result: no >>> configure:13673: checking whether to build static libraries >>> configure:13677: result: yes >>> configure:13827: checking for ld used by g++ >>> configure:13894: result: /usr/bin/ld >>> configure:13903: checking if the linker (/usr/bin/ld) is GNU ld >>> configure:13918: result: yes >>> configure:13973: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >>> configure:14935: result: yes >>> configure:14963: g++ -c -g -O2 conftest.cpp >&5 >>> configure:14966: $? = 0 >>> configure:15148: checking for g++ option to produce PIC >>> configure:15457: result: -fPIC -DPIC >>> configure:15466: checking if g++ PIC flag -fPIC -DPIC works >>> configure:15487: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5 >>> configure:15491: $? = 0 >>> configure:15501: result: yes >>> configure:15522: checking if g++ static flag -static works >>> configure:15550: result: yes >>> configure:15562: checking if g++ supports -c -o file.o >>> configure:15586: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 >>> configure:15590: $? = 0 >>> configure:15609: result: yes >>> configure:15614: checking if g++ supports -c -o file.o >>> configure:15661: result: yes >>> configure:15691: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >>> configure:15717: result: yes >>> configure:15854: checking dynamic linker characteristics >>> configure:16245: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5 >>> configure:16251: $? = 0 >>> configure:16481: result: GNU/Linux ld.so >>> configure:16532: checking how to hardcode library paths into programs >>> configure:16557: result: immediate >>> configure:16698: checking if libtool supports shared libraries >>> configure:16700: result: yes >>> configure:16703: checking whether to build shared libraries >>> configure:16723: result: no >>> configure:16726: checking whether to build static libraries >>> configure:16730: result: yes >>> configure:16744: checking for ifort option to produce PIC >>> configure:17001: result: -KPIC >>> configure:17010: checking if ifort PIC flag -KPIC works >>> configure:17031: ifort -c -g -nofor_main -KPIC conftest.f >&5 >>> configure:17035: $? = 0 >>> configure:17045: result: yes >>> configure:17066: checking if ifort static flag -static works >>> configure:17094: result: yes >>> configure:17106: checking if ifort supports -c -o file.o >>> configure:17130: ifort -c -g -nofor_main -o out/conftest2.o conftest.f >&5 >>> configure:17134: $? = 0 >>> configure:17153: result: yes >>> configure:17158: checking if ifort supports -c -o file.o >>> configure:17205: result: yes >>> configure:17235: checking whether the ifort linker (/usr/bin/ld) supports shared libraries >>> configure:18269: result: yes >>> configure:18406: checking dynamic linker characteristics >>> configure:18787: ifort -o conftest -g -nofor_main -Wl,-rpath -Wl,/foo conftest.f >&5 >>> configure:18793: $? = 0 >>> configure:19023: result: GNU/Linux ld.so >>> configure:19074: checking how to hardcode library paths into programs >>> configure:19099: result: immediate >>> configure:19155: checking for pow in -lm >>> configure:19190: icc -o conftest -g -O2 conftest.c -lm >&5 >>> conftest.c(35): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "pow" >>> >>> configure:19196: $? = 0 >>> configure:19214: result: yes >>> configure:19229: checking for strerrno in -liberty >>> configure:19264: icc -o conftest -g -O2 conftest.c -liberty >&5 >>> /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/../../..//libiberty.a(strerror.o)(.text+0x240): In function `errno_max': >>> : `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead >>> configure:19270: $? = 0 >>> configure:19288: result: yes >>> configure:19304: checking for gethostbyname >>> configure:19360: icc -o conftest -g -O2 conftest.c >&5 >>> configure:19366: $? = 0 >>> configure:19383: result: yes >>> configure:19468: checking for connect >>> configure:19524: icc -o conftest -g -O2 conftest.c >&5 >>> configure:19530: $? = 0 >>> configure:19547: result: yes >>> configure:19632: checking for thr_create >>> configure:19688: icc -o conftest -g -O2 conftest.c >&5 >>> /tmp/iccv8SYca.o(.text+0x12): In function `main': >>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:58: undefined reference to `thr_create' >>> configure:19694: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | /* end confdefs.h. */ >>> | /* Define thr_create to an innocuous variant, in case <limits.h> declares thr_create. >>> | For example, HP-UX 11i <limits.h> declares gettimeofday. */ >>> | #define thr_create innocuous_thr_create >>> | >>> | /* System header to define __stub macros and hopefully few prototypes, >>> | which can conflict with char thr_create (); below. >>> | Prefer <limits.h> to <assert.h> if __STDC__ is defined, since >>> | <limits.h> exists even on freestanding compilers. */ >>> | >>> | #ifdef __STDC__ >>> | # include <limits.h> >>> | #else >>> | # include <assert.h> >>> | #endif >>> | >>> | #undef thr_create >>> | >>> | /* Override any GCC internal prototype to avoid an error. >>> | Use char because int might match the return type of a GCC >>> | builtin and then its argument prototype would still apply. */ >>> | #ifdef __cplusplus >>> | extern "C" >>> | #endif >>> | char thr_create (); >>> | /* The GNU C library defines this for functions which it implements >>> | to always fail with ENOSYS. Some functions are actually named >>> | something starting with __ and the normal name is an alias. */ >>> | #if defined __stub_thr_create || defined __stub___thr_create >>> | choke me >>> | #endif >>> | >>> | int >>> | main () >>> | { >>> | return thr_create (); >>> | ; >>> | return 0; >>> | } >>> configure:19711: result: no >>> configure:19720: checking for thr_create in -lthread >>> configure:19755: icc -o conftest -g -O2 conftest.c -lthread >&5 >>> ld: cannot find -lthread >>> configure:19761: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | /* end confdefs.h. */ >>> | >>> | /* Override any GCC internal prototype to avoid an error. >>> | Use char because int might match the return type of a GCC >>> | builtin and then its argument prototype would still apply. */ >>> | #ifdef __cplusplus >>> | extern "C" >>> | #endif >>> | char thr_create (); >>> | int >>> | main () >>> | { >>> | return thr_create (); >>> | ; >>> | return 0; >>> | } >>> configure:19779: result: no >>> configure:19796: checking for time >>> configure:19852: icc -o conftest -g -O2 conftest.c >&5 >>> conftest.c(58): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "time" >>> >>> configure:19858: $? = 0 >>> configure:19875: result: yes >>> configure:19892: checking for rand >>> configure:19948: icc -o conftest -g -O2 conftest.c >&5 >>> configure:19954: $? = 0 >>> configure:19971: result: yes >>> configure:19988: checking for srand >>> configure:20044: icc -o conftest -g -O2 conftest.c >&5 >>> conftest.c(60): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "srand" >>> >>> configure:20050: $? = 0 >>> configure:20067: result: yes >>> configure:20085: checking the machine epsilon for VFLOOR >>> configure:20111: icc -g -O2 -c fperror.c 1>&5 >>> configure:20114: $? = 0 >>> configure:20123: result: yes >>> configure:20167: ----------------------------------------------------------- >>> configure:20169: ---------- begin configuring for MALOC linkage ------------ >>> configure:20171: ----------------------------------------------------------- >>> configure:20178: WARNING: Error... FETK_INCLUDE is no longer supported. >>> configure:20180: WARNING: Use --with-fetk-include=PATH instead. >>> configure:20182: WARNING: Ignoring these variables... >>> configure:20187: WARNING: Error... FETK_LIBRARY is no longer supported. >>> configure:20189: WARNING: Use --with-fetk-library=PATH instead. >>> configure:20191: WARNING: Ignoring these variables... >>> configure:20195: checking for --with-fetk-include option >>> configure:20205: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>> configure:20213: checking for --with-fetk-library option >>> configure:20223: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>> configure:20235: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include/maloc/maloc.h >>> configure:20251: result: yes >>> configure:20267: Using MALOC headers in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>> configure:20273: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib/libmaloc.a >>> configure:20289: result: yes >>> configure:20306: Using MALOC libraries in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>> configure:20316: checking for --with-mpich option >>> configure:20331: result: no >>> configure:20337: checking for --with-mpich2 option >>> configure:20351: result: no >>> configure:20358: checking for --with-lam option >>> configure:20372: result: no >>> configure:20379: checking for --with-openmpi option >>> configure:20392: result: no >>> configure:20771: --------------------------------------------------------------- >>> configure:20773: ---------- begin configuring for Python wrappers -------------- >>> configure:20775: --------------------------------------------------------------- >>> configure:20779: checking for --enable-python >>> configure:21049: result: no >>> configure:21058: Python wrappers disabled >>> configure:21094: checking for python >>> configure:21112: found /usr/bin/python >>> configure:21124: result: /usr/bin/python >>> configure:21214: Skipping MALOC installation; will use MALOC provided with FEtk >>> configure:21225: checking for maloc_needs_rl in -lmaloc >>> configure:21260: icc -o conftest -g -O2 /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmaloc /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -lvf2c -liberty -lm >&5 >>> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include: file not recognized: Is a directory >>> configure:21266: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | #define HAVE_TIME_FUNC >>> | #define HAVE_RAND_FUNC >>> | #define HAVE_SRAND_FUNC >>> | #define FLOAT_ERRORS 1 >>> | #define MACHINE_EPS 1.19209E-07 >>> | /* end confdefs.h. */ >>> | >>> | /* Override any GCC internal prototype to avoid an error. >>> | Use char because int might match the return type of a GCC >>> | builtin and then its argument prototype would still apply. */ >>> | #ifdef __cplusplus >>> | extern "C" >>> | #endif >>> | char maloc_needs_rl (); >>> | int >>> | main () >>> | { >>> | return maloc_needs_rl (); >>> | ; >>> | return 0; >>> | } >>> configure:21284: result: no >>> configure:21529: ------------------------------------------------------------ >>> configure:21531: ---------- begin configuring for FEtk linkage -------------- >>> configure:21533: ------------------------------------------------------------ >>> configure:21542: checking for --disable-fetk >>> configure:21554: result: no >>> configure:21556: checking for user-specified FEtk include path >>> configure:21559: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>> configure:21567: checking for user-specified FEtk library path >>> configure:21570: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>> configure:21593: checking mc/mc.h usability >>> configure:21610: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >>> configure:21616: $? = 0 >>> configure:21630: result: yes >>> configure:21634: checking mc/mc.h presence >>> configure:21649: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >>> configure:21655: $? = 0 >>> configure:21669: result: yes >>> configure:21702: checking for mc/mc.h >>> configure:21709: result: yes >>> configure:21720: checking for mc_link in -lmc >>> configure:21755: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >>> configure:21761: $? = 0 >>> configure:21779: result: yes >>> configure:21800: checking mcx/mcx.h usability >>> configure:21817: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >>> conftest.c(62): catastrophic error: could not open source file "mcx/mcx.h" >>> #include <mcx/mcx.h> >>> ^ >>> >>> compilation aborted for conftest.c (code 4) >>> configure:21823: $? = 4 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | #define HAVE_TIME_FUNC >>> | #define HAVE_RAND_FUNC >>> | #define HAVE_SRAND_FUNC >>> | #define FLOAT_ERRORS 1 >>> | #define MACHINE_EPS 1.19209E-07 >>> | /* end confdefs.h. */ >>> | #include <stdio.h> >>> | #ifdef HAVE_SYS_TYPES_H >>> | # include <sys/types.h> >>> | #endif >>> | #ifdef HAVE_SYS_STAT_H >>> | # include <sys/stat.h> >>> | #endif >>> | #ifdef STDC_HEADERS >>> | # include <stdlib.h> >>> | # include <stddef.h> >>> | #else >>> | # ifdef HAVE_STDLIB_H >>> | # include <stdlib.h> >>> | # endif >>> | #endif >>> | #ifdef HAVE_STRING_H >>> | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H >>> | # include <memory.h> >>> | # endif >>> | # include <string.h> >>> | #endif >>> | #ifdef HAVE_STRINGS_H >>> | # include <strings.h> >>> | #endif >>> | #ifdef HAVE_INTTYPES_H >>> | # include <inttypes.h> >>> | #endif >>> | #ifdef HAVE_STDINT_H >>> | # include <stdint.h> >>> | #endif >>> | #ifdef HAVE_UNISTD_H >>> | # include <unistd.h> >>> | #endif >>> | #include <mcx/mcx.h> >>> configure:21837: result: no >>> configure:21841: checking mcx/mcx.h presence >>> configure:21856: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >>> conftest.c(29): error #5: could not open source file "mcx/mcx.h" >>> #include <mcx/mcx.h> >>> ^ >>> >>> configure:21862: $? = 2 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | #define HAVE_TIME_FUNC >>> | #define HAVE_RAND_FUNC >>> | #define HAVE_SRAND_FUNC >>> | #define FLOAT_ERRORS 1 >>> | #define MACHINE_EPS 1.19209E-07 >>> | /* end confdefs.h. */ >>> | #include <mcx/mcx.h> >>> configure:21876: result: no >>> configure:21909: checking for mcx/mcx.h >>> configure:21916: result: no >>> configure:21927: checking for mcx_link in -lmcx >>> configure:21962: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmcx -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >>> ld: cannot find -lmcx >>> configure:21968: $? = 1 >>> configure: failed program was: >>> | /* confdefs.h. */ >>> | #define PACKAGE_NAME "APBS" >>> | #define PACKAGE_TARNAME "apbs" >>> | #define PACKAGE_VERSION "1.2.1" >>> | #define PACKAGE_STRING "APBS 1.2.1" >>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>> | #define PACKAGE "apbs" >>> | #define VERSION "1.2.1" >>> | #define VF77_ONEUNDERSCORE >>> | #define VF77_LOWERCASE >>> | #define STDC_HEADERS 1 >>> | #define HAVE_SYS_TYPES_H 1 >>> | #define HAVE_SYS_STAT_H 1 >>> | #define HAVE_STDLIB_H 1 >>> | #define HAVE_STRING_H 1 >>> | #define HAVE_MEMORY_H 1 >>> | #define HAVE_STRINGS_H 1 >>> | #define HAVE_INTTYPES_H 1 >>> | #define HAVE_STDINT_H 1 >>> | #define HAVE_UNISTD_H 1 >>> | #define HAVE_DLFCN_H 1 >>> | #define LT_OBJDIR ".libs/" >>> | #define HAVE_TIME_FUNC >>> | #define HAVE_RAND_FUNC >>> | #define HAVE_SRAND_FUNC >>> | #define FLOAT_ERRORS 1 >>> | #define MACHINE_EPS 1.19209E-07 >>> | /* end confdefs.h. */ >>> | >>> | /* Override any GCC internal prototype to avoid an error. >>> | Use char because int might match the return type of a GCC >>> | builtin and then its argument prototype would still apply. */ >>> | #ifdef __cplusplus >>> | extern "C" >>> | #endif >>> | char mcx_link (); >>> | int >>> | main () >>> | { >>> | return mcx_link (); >>> | ; >>> | return 0; >>> | } >>> configure:21986: result: no >>> configure:22000: FEtk component MC found: enabled. >>> configure:22025: WARNING: FEtk component MCX not found: hierarchical basis methods disabled. >>> configure:22039: --------------------------------------------------------------- >>> configure:22041: ------------ begin processing APBS configure options ---------- >>> configure:22043: --------------------------------------------------------------- >>> configure:22046: checking for EMBED macro can be used >>> configure:22070: icc -c -g -O2 conftest.c >&5 >>> configure:22076: $? = 0 >>> configure:22094: result: yes >>> configure:22098: checking --enable-pansi >>> configure:22116: result: no >>> configure:22123: checking for strcasecmp >>> configure:22179: icc -o conftest -g -O2 conftest.c >&5 >>> conftest.c(65): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "strcasecmp" >>> >>> configure:22185: $? = 0 >>> configure:22202: result: yes >>> configure:22225: checking for --disable-tools >>> configure:22237: result: no >>> configure:22239: tools will be compiled >>> configure:22258: checking for --with-blas >>> configure:22353: result: no >>> configure:22383: checking for --with-arpack >>> configure:22399: result: no >>> configure:22405: checking for --disable-inline >>> configure:22416: result: no >>> configure:22418: inline functions will be used >>> configure:22432: checking for --enable-tinker >>> configure:22456: result: no >>> configure:22460: checking for --enable-abps-quiet >>> configure:22479: result: no >>> configure:22483: checking for --disable-openmp >>> configure:22497: result: no >>> configure:22876: creating ./config.status >>> >>> ## ---------------------- ## >>> ## Running config.status. ## >>> ## ---------------------- ## >>> >>> This file was extended by APBS config.status 1.2.1, which was >>> generated by GNU Autoconf 2.61. Invocation command line was >>> >>> CONFIG_FILES = >>> CONFIG_HEADERS = >>> CONFIG_LINKS = >>> CONFIG_COMMANDS = >>> $ ./config.status >>> >>> on osiris >>> >>> config.status:1044: creating Makefile >>> config.status:1044: creating contrib/Makefile >>> config.status:1044: creating contrib/blas/Makefile >>> config.status:1044: creating contrib/pmgZ/Makefile >>> config.status:1044: creating contrib/aqua/Makefile >>> config.status:1044: creating contrib/opal/Makefile >>> config.status:1044: creating contrib/opal/ZSI/Makefile >>> config.status:1044: creating tools/Makefile >>> config.status:1044: creating tools/mesh/Makefile >>> config.status:1044: creating tools/manip/Makefile >>> config.status:1044: creating tools/python/Makefile >>> config.status:1044: creating tools/arpack/Makefile >>> config.status:1044: creating tools/python/vgrid/Makefile >>> config.status:1044: creating src/Makefile >>> config.status:1044: creating src/generic/Makefile >>> config.status:1044: creating src/mg/Makefile >>> config.status:1044: creating src/fem/Makefile >>> config.status:1044: creating src/aaa_inc/Makefile >>> config.status:1044: creating src/aaa_inc/apbs/Makefile >>> config.status:1044: creating src/aaa_lib/Makefile >>> config.status:1044: creating examples/Makefile >>> config.status:1044: creating examples/actin-dimer/Makefile >>> config.status:1044: creating examples/alkanes/Makefile >>> config.status:1044: creating examples/born/Makefile >>> config.status:1044: creating examples/FKBP/Makefile >>> config.status:1044: creating examples/hca-bind/Makefile >>> config.status:1044: creating examples/ion-pmf/Makefile >>> config.status:1044: creating examples/ion-protein/Makefile >>> config.status:1044: creating examples/ionize/Makefile >>> config.status:1044: creating examples/pka-lig/Makefile >>> config.status:1044: creating examples/point-pmf/Makefile >>> config.status:1044: creating examples/protein-rna/Makefile >>> config.status:1044: creating examples/smpbe/Makefile >>> config.status:1044: creating examples/solv/Makefile >>> config.status:1044: creating examples/opal/Makefile >>> config.status:1044: creating bin/Makefile >>> config.status:1044: creating src/aaa_inc/apbscfg.h >>> config.status:1327: executing depfiles commands >>> config.status:1327: executing libtool commands >>> configure:25486: >>> >>> APBS to be compiled with following settings: icc -g -O2 -openmp >>> APBS to be compiled with following settings: ifort -g -nofor_main -nofor_main -openmp -assume cc_omp >>> APBS to be linked with following libraries : -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas >>> APBS to be compiled with following includes: -I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>> >>> Please type "make; make install" >>> >>> >>> ## ---------------- ## >>> ## Cache variables. ## >>> ## ---------------- ## >>> >>> ac_cv_build=ia64-unknown-linux-gnu >>> ac_cv_c_compiler_gnu=yes >>> ac_cv_cxx_compiler_gnu=yes >>> ac_cv_env_CCC_set= >>> ac_cv_env_CCC_value= >>> ac_cv_env_CC_set= >>> ac_cv_env_CC_value= >>> ac_cv_env_CFLAGS_set= >>> ac_cv_env_CFLAGS_value= >>> ac_cv_env_CPPFLAGS_set= >>> ac_cv_env_CPPFLAGS_value= >>> ac_cv_env_CPP_set= >>> ac_cv_env_CPP_value= >>> ac_cv_env_CXXCPP_set= >>> ac_cv_env_CXXCPP_value= >>> ac_cv_env_CXXFLAGS_set= >>> ac_cv_env_CXXFLAGS_value= >>> ac_cv_env_CXX_set= >>> ac_cv_env_CXX_value= >>> ac_cv_env_F77_set= >>> ac_cv_env_F77_value= >>> ac_cv_env_FFLAGS_set= >>> ac_cv_env_FFLAGS_value= >>> ac_cv_env_LDFLAGS_set= >>> ac_cv_env_LDFLAGS_value= >>> ac_cv_env_LIBS_set= >>> ac_cv_env_LIBS_value= >>> ac_cv_env_build_alias_set= >>> ac_cv_env_build_alias_value= >>> ac_cv_env_host_alias_set= >>> ac_cv_env_host_alias_value= >>> ac_cv_env_target_alias_set= >>> ac_cv_env_target_alias_value= >>> ac_cv_f77_compiler_gnu=no >>> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__include_maloc_maloc_h=yes >>> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__lib_libmaloc_a=yes >>> ac_cv_func_connect=yes >>> ac_cv_func_gethostbyname=yes >>> ac_cv_func_rand=yes >>> ac_cv_func_srand=yes >>> ac_cv_func_strcasecmp=yes >>> ac_cv_func_thr_create=no >>> ac_cv_func_time=yes >>> ac_cv_header_dlfcn_h=yes >>> ac_cv_header_inttypes_h=yes >>> ac_cv_header_mc_mc_h=yes >>> ac_cv_header_mcx_mcx_h=no >>> ac_cv_header_memory_h=yes >>> ac_cv_header_stdc=yes >>> ac_cv_header_stdint_h=yes >>> ac_cv_header_stdlib_h=yes >>> ac_cv_header_string_h=yes >>> ac_cv_header_strings_h=yes >>> ac_cv_header_sys_stat_h=yes >>> ac_cv_header_sys_types_h=yes >>> ac_cv_header_unistd_h=yes >>> ac_cv_host=ia64-unknown-linux-gnu >>> ac_cv_lib_iberty_strerrno=yes >>> ac_cv_lib_m_pow=yes >>> ac_cv_lib_maloc_maloc_needs_rl=no >>> ac_cv_lib_mc_mc_link=yes >>> ac_cv_lib_mcx_mcx_link=no >>> ac_cv_lib_thread_thr_create=no >>> ac_cv_objext=o >>> ac_cv_path_EGREP='/bin/grep -E' >>> ac_cv_path_FGREP='/bin/grep -F' >>> ac_cv_path_GREP=/bin/grep >>> ac_cv_path_SED=/bin/sed >>> ac_cv_path_install='/usr/bin/install -c' >>> ac_cv_path_mkdir=/bin/mkdir >>> ac_cv_path_py_path=/usr/bin/python >>> ac_cv_prog_AWK=gawk >>> ac_cv_prog_CPP='icc -E' >>> ac_cv_prog_CXXCPP='g++ -E' >>> ac_cv_prog_ac_ct_AR=ar >>> ac_cv_prog_ac_ct_CC=icc >>> ac_cv_prog_ac_ct_CXX=g++ >>> ac_cv_prog_ac_ct_F77=ifort >>> ac_cv_prog_ac_ct_RANLIB=ranlib >>> ac_cv_prog_ac_ct_STRIP=strip >>> ac_cv_prog_cc_c89= >>> ac_cv_prog_cc_g=yes >>> ac_cv_prog_cxx_g=yes >>> ac_cv_prog_f77_g=yes >>> ac_cv_prog_make_make_set=yes >>> ac_cv_target=ia64-unknown-linux-gnu >>> am_cv_CC_dependencies_compiler_type=none >>> am_cv_CXX_dependencies_compiler_type=none >>> am_cv_prog_cc_stdc= >>> lt_cv_deplibs_check_method=pass_all >>> lt_cv_file_magic_cmd='$MAGIC_CMD' >>> lt_cv_file_magic_test_file= >>> lt_cv_ld_reload_flag=-r >>> lt_cv_nm_interface='BSD nm' >>> lt_cv_objdir=.libs >>> lt_cv_path_LD=/usr/bin/ld >>> lt_cv_path_LDCXX=/usr/bin/ld >>> lt_cv_path_NM='/usr/bin/nm -B' >>> lt_cv_prog_compiler_c_o=yes >>> lt_cv_prog_compiler_c_o_CXX=yes >>> lt_cv_prog_compiler_c_o_F77=yes >>> lt_cv_prog_compiler_pic_works=yes >>> lt_cv_prog_compiler_pic_works_CXX=yes >>> lt_cv_prog_compiler_pic_works_F77=yes >>> lt_cv_prog_compiler_rtti_exceptions=yes >>> lt_cv_prog_compiler_static_works=yes >>> lt_cv_prog_compiler_static_works_CXX=yes >>> lt_cv_prog_compiler_static_works_F77=yes >>> lt_cv_prog_gnu_ld=yes >>> lt_cv_prog_gnu_ldcxx=yes >>> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\''' >>> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' >>> lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' >>> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' >>> lt_cv_sys_max_cmd_len=98304 >>> >>> ## ----------------- ## >>> ## Output variables. ## >>> ## ----------------- ## >>> >>> ACLOCAL=':' >>> AMDEPBACKSLASH='\' >>> AMDEP_FALSE='#' >>> AMDEP_TRUE='' >>> AMTAR='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run tar' >>> APBS_VERSION='1:2:1' >>> AR='ar' >>> AUTOCONF=':' >>> AUTOHEADER=':' >>> AUTOMAKE=':' >>> AWK='gawk' >>> CC='icc' >>> CCDEPMODE='depmode=none' >>> CFLAGS='-g -O2 -openmp' >>> CPP='icc -E' >>> CPPFLAGS='' >>> CXX='g++' >>> CXXCPP='g++ -E' >>> CXXDEPMODE='depmode=none' >>> CXXFLAGS='-g -O2' >>> CYGPATH_W='echo' >>> DEFS='-DHAVE_CONFIG_H' >>> DEPDIR='.deps' >>> DSYMUTIL='' >>> DUMPBIN='' >>> ECHO_C='' >>> ECHO_N='-n' >>> ECHO_T='' >>> EGREP='/bin/grep -E' >>> EXEEXT='' >>> F77='ifort' >>> FFLAGS=' -g -nofor_main -nofor_main -openmp -assume cc_omp' >>> FGREP='/bin/grep -F' >>> GREP='/bin/grep' >>> INSTALL_DATA='${INSTALL} -m 644' >>> INSTALL_PROGRAM='${INSTALL}' >>> INSTALL_SCRIPT='${INSTALL}' >>> INSTALL_STRIP_PROGRAM='$(install_sh) -c -s' >>> LD='/usr/bin/ld' >>> LDFLAGS=' -static-intel' >>> LIBOBJS='' >>> LIBS='' >>> LIBTOOL='$(SHELL) $(top_builddir)/libtool' >>> LIPO='' >>> LN_S='ln -s' >>> LTLIBOBJS='' >>> MAKEINFO='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run makeinfo' >>> NM='/usr/bin/nm -B' >>> NMEDIT='' >>> OBJEXT='o' >>> OTOOL64='' >>> OTOOL='' >>> PACKAGE='apbs' >>> PACKAGE_BUGREPORT='ba...@bi...' >>> PACKAGE_NAME='APBS' >>> PACKAGE_STRING='APBS 1.2.1' >>> PACKAGE_TARNAME='apbs' >>> PACKAGE_VERSION='1.2.1' >>> PATH_SEPARATOR=':' >>> PY_CC='' >>> PY_CFLAGS='' >>> PY_LDFLAGS='' >>> PY_LINKFLAGS='' >>> PY_PRESENT_FALSE='' >>> PY_PRESENT_TRUE='#' >>> PY_SHARED='' >>> RANLIB='ranlib' >>> SED='/bin/sed' >>> SET_MAKE='' >>> SHELL='/bin/sh' >>> SITEPKGS='/home/khelgeo/apbs_fetk//lib/python2.2/site-packages' >>> STRIP='strip' >>> UHBD_COMPILE_FALSE='#' >>> UHBD_COMPILE_TRUE='' >>> VERSION='1.2.1' >>> ac_ct_CC='icc' >>> ac_ct_CXX='g++' >>> ac_ct_DUMPBIN='' >>> ac_ct_F77='ifort' >>> am__fastdepCC_FALSE='' >>> am__fastdepCC_TRUE='#' >>> am__fastdepCXX_FALSE='' >>> am__fastdepCXX_TRUE='#' >>> am__include='include' >>> am__isrc='' >>> am__leading_dot='.' >>> am__quote='' >>> am__tar='${AMTAR} chof - "$$tardir"' >>> am__untar='${AMTAR} xf -' >>> apbs_build_libraries='/home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/bin/libapbsmainroutines.la /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/src/aaa_lib/libapbs.la -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-... [truncated message content] |
From: George K. <ge...@me...> - 2010-07-23 18:44:39
|
Hello all, I just ran the sample script that Michael has suggested and it worked, producing "mcsh" executable. So I guess Fetk library itself has been successfully built, and the problem is with the linkage between APBS and Fetk. Sincerely, George Michael Holst wrote: > Hi George, > > That should do it as far as FETK being built correctly. > > You can check this by trying to build one of the MC examples > (for example: cd into ./fetk/mc/examples/simpleMCsh). You will > have to edit the very simple makefile in the example directory > to make sure that it finds the headers and libraries in the > "build" directory that was created by the "./fetk-build all". > If a "make" in the simpleMCsh directory completes and creates an > "mcsh" binary in the simpleMCsh directory, then it is finding > all of the FETK libraries and linking correctly. > > If the step above works, then the problem is only in the > linkage between APBS and the FETK libraries. It is likely that > this is the problem, since we have just released FETK in the last > two weeks, and have possibly broken some of the linkage with APBS. > We want to know about any problems you and others have in building > things so that we can quickly fix them. > > thanks, -mike > > George Khelashvili <ge...@me...> (07-23-2010 14:13:25-0400): > >> Dear Michael, >> >> Thank you for your comment. I used fetk_build script to build the entire >> fetk by running "./fetk-build all". Are there any other options that I >> missed? It looks like that both maloc and mc are in place. >> >> Sincerely, >> George >> >> Michael Holst wrote: >> >>> Nathan and all, >>> >>> A quick look at the make.log indicates that MALOC calls within MC >>> are not being resolved, so MALOC (via libmaloc.a) was either not >>> built or not being found. >>> >>> best, -mike >>> >>> George Khelashvili <ge...@me...> (07-23-2010 12:25:07-0400): >>> >>> >>>> Hi Nathan, >>>> >>>> The listing of >>>> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ >>>> directory is "bin doc fetk-env include lib". By the way, I >>>> realized that I sent you wrong log files, which did not exactly >>>> correspond to the versions of APBS and FETK I used (I played with >>>> several combinations and I accidentally mixed them up). Sorry for >>>> that. Here are the corrected log files which were obtained by >>>> installing Fetk version 1.1 first, and then installing APBS 1.2.1. >>>> The log files were generated during the APBS installation. This log >>>> file produced somewhat different error message. >>>> I do realize that APBS-FETK link is in the beginning stages so I will >>>> be glad to contribute as I can to resolve this issue so that the >>>> community can use this what I think will be a wonderful tool. >>>> >>>> Sincerely, >>>> George >>>> >>>> Baker, Nathan wrote: >>>> >>>> >>>>> Hi George -- >>>>> >>>>> This is very strange. Can you send me a listing of your /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? >>>>> >>>>> All: please note that FEtk has just been released and the APBS/FEtk interface is very much in a "beta" state. >>>>> >>>>> Thanks, >>>>> >>>>> __________________________________________________ Nathan Baker >>>>> Chief Scientist for Signature Science >>>>> Pacific Northwest National Laboratory >>>>> >>>>> >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: George Khelashvili [mailto:ge...@me...] >>>>>> Sent: Wednesday, July 21, 2010 11:31 AM >>>>>> To: apb...@li... >>>>>> Subject: Re: [Apbs-users] FeTK support in APBS >>>>>> >>>>>> Dear APBS users, >>>>>> >>>>>> I am trying to compile APBS version 1.2 with Fetk support (Fetk version >>>>>> 1.1). I have downloaded and installed the entire Fetk package, and now >>>>>> I moved on to installing APBS itself. While configuring apparently >>>>>> worked since all the necessary Fetk library and header files where >>>>>> found, the compilation crushed when I run "make". I have attached log >>>>>> files from configuration step as well as "make" step. Obviously there >>>>>> is a problem while compiling fetk.c file. I would appreciate if >>>>>> somebody can take a look at the attached files and suggest what is >>>>>> missing. >>>>>> >>>>>> Thank you, >>>>>> George >>>>>> >>>>>> Baker, Nathan wrote: >>>>>> >>>>>> >>>>>>> Hello - >>>>>>> >>>>>>> Yes, FEtk is available for download at >>>>>>> http://fetk.org/codes/download/. I will be updating the documentation >>>>>>> in the next few weeks with revised instructions on how to compile, >>>>>>> >>>>>>> >>>>>> etc. >>>>>> >>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Nathan >>>>>>> >>>>>>> __________________________________________________ >>>>>>> *Nathan Baker* >>>>>>> Chief Scientist for Signature Science >>>>>>> Pacific Northwest National Laboratory >>>>>>> >>>>>>> *From:* patrizio ansalone [mailto:p.a...@in...] >>>>>>> *Sent:* Wednesday, July 21, 2010 12:39 AM >>>>>>> *To:* apb...@li... >>>>>>> *Subject:* [Apbs-users] FeTK support in APBS >>>>>>> >>>>>>> >>>>>>> Is it possibile to compile apbs with fetk support? I have understod >>>>>>> that FeTk must be installed >>>>>>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>>>>>> >>>>>>> >>>>>> avil >>>>>> >>>>>> >>>>>>> /source-installation) but I can't find a repository where I can >>>>>>> download it. Any sugestion how to fix this problem ? >>>>>>> thanks in advance >>>>>>> Patrizio >>>>>>> >>>>>>> --------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>> - >>>>>> >>>>>> >>>>>>> -- >>>>>>> >>>>>>> --------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>> - >>>>>> >>>>>> >>>>>>> -------- This SF.net email is sponsored by Sprint What will you do >>>>>>> first with EVO, the first 4G phone? >>>>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>>>>>> --------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>> - >>>>>> >>>>>> >>>>>>> -- >>>>>>> >>>>>>> _______________________________________________ >>>>>>> apbs-users mailing list >>>>>>> apb...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> George Khelashvili, Ph.D. >>>>>> Department of Physiology and Biophysics >>>>>> Weill Medical College of Cornell University 1300 York Avenue, Room >>>>>> LC501 New York, NY, 10065, USA ge...@me... >>>>>> Phone: 1-212-746-6539 >>>>>> Fax: 1-212-746-6226 >>>>>> >>>>>> >>>>>> >>>> -- >>>> George Khelashvili, Ph.D. >>>> Department of Physiology and Biophysics >>>> Weill Medical College of Cornell University >>>> 1300 York Avenue, Room LC501 >>>> New York, NY, 10065, USA >>>> ge...@me... >>>> Phone: 1-212-746-6539 >>>> Fax: 1-212-746-6226 >>>> >>>> >>>> >>> >>> >>>> This file contains any messages produced by compilers while >>>> running configure, to aid debugging if configure makes a mistake. >>>> >>>> It was created by APBS configure 1.2.1, which was >>>> generated by GNU Autoconf 2.61. Invocation command line was >>>> >>>> $ ./configure --with-fetk-include=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include --with-fetk-library=/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib --prefix=/home/khelgeo/apbs_fetk/ >>>> >>>> ## --------- ## >>>> ## Platform. ## >>>> ## --------- ## >>>> >>>> hostname = osiris >>>> uname -m = ia64 >>>> uname -r = 2.4.21-sgi301rp04091014_10105 >>>> uname -s = Linux >>>> uname -v = #1 SMP Fri Sep 10 15:02:03 PDT 2004 >>>> >>>> /usr/bin/uname -p = unknown >>>> /bin/uname -X = unknown >>>> >>>> /bin/arch = ia64 >>>> /usr/bin/arch -k = unknown >>>> /usr/convex/getsysinfo = unknown >>>> /usr/bin/hostinfo = unknown >>>> /bin/machine = unknown >>>> /usr/bin/oslevel = unknown >>>> /bin/universe = unknown >>>> >>>> PATH: /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin >>>> PATH: /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin >>>> PATH: /softlib/exe/osiris/bin >>>> PATH: /softlib/exe/ia64/bin >>>> PATH: /softlib/exe/linux/bin >>>> PATH: /softlib/exe/all/bin >>>> PATH: /usr/kerberos/bin >>>> PATH: /usr/local/bin >>>> PATH: /bin >>>> PATH: /usr/bin >>>> PATH: /usr/X11R6/bin >>>> >>>> >>>> ## ----------- ## >>>> ## Core tests. ## >>>> ## ----------- ## >>>> >>>> configure:2051: checking build system type >>>> configure:2069: result: ia64-unknown-linux-gnu >>>> configure:2091: checking host system type >>>> configure:2106: result: ia64-unknown-linux-gnu >>>> configure:2128: checking target system type >>>> configure:2143: result: ia64-unknown-linux-gnu >>>> configure:2187: checking for a BSD-compatible install >>>> configure:2243: result: /usr/bin/install -c >>>> configure:2254: checking whether build environment is sane >>>> configure:2297: result: yes >>>> configure:2325: checking for a thread-safe mkdir -p >>>> configure:2364: result: /bin/mkdir -p >>>> configure:2377: checking for gawk >>>> configure:2393: found /bin/gawk >>>> configure:2404: result: gawk >>>> configure:2415: checking whether make sets $(MAKE) >>>> configure:2436: result: yes >>>> configure:2641: checking for --enable-fast option >>>> configure:2661: result: no >>>> configure:2669: checking for --enable-python >>>> configure:2688: result: no >>>> configure:2756: checking for icc >>>> configure:2772: found /softlib/exe/ia64/pkg/icc/9.1.044/dist/bin/icc >>>> configure:2783: result: icc >>>> configure:2819: checking for C compiler version >>>> configure:2826: icc --version >&5 >>>> icc (ICC) 9.1 20060928 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:2829: $? = 0 >>>> configure:2836: icc -v >&5 >>>> Version 9.1 >>>> configure:2839: $? = 0 >>>> configure:2846: icc -V >&5 >>>> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >>>> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:2849: $? = 0 >>>> configure:2872: checking for C compiler default output file name >>>> configure:2899: icc conftest.c >&5 >>>> configure:2902: $? = 0 >>>> configure:2940: result: a.out >>>> configure:2957: checking whether the C compiler works >>>> configure:2967: ./a.out >>>> configure:2970: $? = 0 >>>> configure:2987: result: yes >>>> configure:2994: checking whether we are cross compiling >>>> configure:2996: result: no >>>> configure:2999: checking for suffix of executables >>>> configure:3006: icc -o conftest conftest.c >&5 >>>> configure:3009: $? = 0 >>>> configure:3033: result: >>>> configure:3039: checking for suffix of object files >>>> configure:3065: icc -c conftest.c >&5 >>>> configure:3068: $? = 0 >>>> configure:3091: result: o >>>> configure:3095: checking whether we are using the GNU C compiler >>>> configure:3124: icc -c conftest.c >&5 >>>> configure:3130: $? = 0 >>>> configure:3147: result: yes >>>> configure:3152: checking whether icc accepts -g >>>> configure:3182: icc -c -g conftest.c >&5 >>>> configure:3188: $? = 0 >>>> configure:3287: result: yes >>>> configure:3304: checking for icc option to accept ISO C89 >>>> configure:3378: icc -c -g -O2 conftest.c >&5 >>>> configure:3384: $? = 0 >>>> configure:3407: result: none needed >>>> configure:3436: checking for style of include used by make >>>> configure:3464: result: GNU >>>> configure:3489: checking dependency style of icc >>>> configure:3580: result: none >>>> configure:3643: checking for gcc >>>> configure:3670: result: icc >>>> configure:3908: checking for C compiler version >>>> configure:3915: icc --version >&5 >>>> icc (ICC) 9.1 20060928 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:3918: $? = 0 >>>> configure:3925: icc -v >&5 >>>> Version 9.1 >>>> configure:3928: $? = 0 >>>> configure:3935: icc -V >&5 >>>> Intel(R) C Itanium(R) Compiler for Itanium(R)-based applications >>>> Version 9.1 Build 20060928 Package ID: l_cc_c_9.1.044 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:3938: $? = 0 >>>> configure:3941: checking whether we are using the GNU C compiler >>>> configure:3993: result: yes >>>> configure:3998: checking whether icc accepts -g >>>> configure:4133: result: yes >>>> configure:4150: checking for icc option to accept ISO C89 >>>> configure:4253: result: none needed >>>> configure:4273: checking dependency style of icc >>>> configure:4364: result: none >>>> configure:4440: checking for g++ >>>> configure:4456: found /usr/bin/g++ >>>> configure:4467: result: g++ >>>> configure:4498: checking for C++ compiler version >>>> configure:4505: g++ --version >&5 >>>> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>>> Copyright (C) 2002 Free Software Foundation, Inc. >>>> This is free software; see the source for copying conditions. There is NO >>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>>> >>>> configure:4508: $? = 0 >>>> configure:4515: g++ -v >&5 >>>> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >>>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >>>> Thread model: posix >>>> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>>> configure:4518: $? = 0 >>>> configure:4525: g++ -V >&5 >>>> g++: argument to `-V' missing >>>> >>>> configure:4528: $? = 1 >>>> configure:4531: checking whether we are using the GNU C++ compiler >>>> configure:4560: g++ -c conftest.cpp >&5 >>>> configure:4566: $? = 0 >>>> configure:4583: result: yes >>>> configure:4588: checking whether g++ accepts -g >>>> configure:4618: g++ -c -g conftest.cpp >&5 >>>> configure:4624: $? = 0 >>>> >>>> configure:4723: result: yes >>>> configure:4748: checking dependency style of g++ >>>> configure:4839: result: none >>>> configure:4907: checking for ifort >>>> configure:4923: found /softlib/exe/ia64/pkg/ifort/9.1.039/dist/bin/ifort >>>> configure:4934: result: ifort >>>> configure:4964: checking for Fortran 77 compiler version >>>> configure:4971: ifort --version >&5 >>>> ifort (IFORT) 9.1 20060928 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:4974: $? = 0 >>>> configure:4981: ifort -v >&5 >>>> Version 9.1 >>>> configure:4984: $? = 0 >>>> configure:4991: ifort -V >&5 >>>> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >>>> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:4994: $? = 0 >>>> configure:5002: checking whether we are using the GNU Fortran 77 compiler >>>> configure:5021: ifort -c conftest.F >&5 >>>> fortcom: Error: conftest.F, line 3: Syntax error, found END-OF-STATEMENT when expecting one of: => = . ( : % >>>> choke me >>>> ---------------^ >>>> fortcom: Error: conftest.F, line 3: This statement is positioned incorrectly and/or has syntax errors. >>>> choke me >>>> ---------------^ >>>> compilation aborted for conftest.F (code 1) >>>> configure:5027: $? = 1 >>>> configure: failed program was: >>>> | program main >>>> | #ifndef __GNUC__ >>>> | choke me >>>> | #endif >>>> | >>>> | end >>>> configure:5044: result: no >>>> configure:5050: checking whether ifort accepts -g >>>> configure:5067: ifort -c -g conftest.f >&5 >>>> configure:5073: $? = 0 >>>> configure:5089: result: yes >>>> configure:5180: icc -c -g -O2 noformain.c 1>&5 >>>> configure:5183: $? = 0 >>>> configure:5194: checking if Fortran 77 compiler accepts -nofor_main >>>> configure:5203: ifort -nofor_main -g noformain.o -o noformain 1>&5 >>>> configure:5206: $? = 0 >>>> configure:5209: result: yes >>>> configure:5211: checking if Fortran 77 compilers requires -nofor_main >>>> configure:5221: ifort -g noformain.o -o noformain >>>> 1>&5 >>>> noformain.o(.text+0x0): In function `main': >>>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/noformain.c:1: multiple definition of `main' >>>> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0x0): first defined here >>>> ld: Warning: size of symbol `main' changed from 384 in /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o to 32 in noformain.o >>>> /softlib/exe/ia64/pkg/ifort/9.1.039/dist/lib/for_main.o(.text+0xf2): In function `main': >>>> : undefined reference to `MAIN__' >>>> configure:5224: $? = 1 >>>> configure:5230: result: yes >>>> configure:5253: checking how f77 mangles function names >>>> configure:5264: ifort -c -g -nofor_main mangle-func.f 1>&5 >>>> configure:5267: $? = 0 >>>> configure:5310: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >>>> conftest.c(14): warning #266: function declared implicitly >>>> foobar(); >>>> ^ >>>> >>>> /tmp/iccqc5Wny.o(.text+0x12): In function `main': >>>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:14: undefined reference to `foobar' >>>> configure:5316: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | /* end confdefs.h. */ >>>> | >>>> | int >>>> | main () >>>> | { >>>> | foobar(); >>>> | ; >>>> | return 0; >>>> | } >>>> configure:5348: icc -o conftest -g -O2 conftest.c mangle-func.o >&5 >>>> conftest.c(14): warning #266: function declared implicitly >>>> foobar_(); >>>> ^ >>>> >>>> configure:5354: $? = 0 >>>> configure:5466: result: lowercase-underscore >>>> configure:5542: checking how to run the C preprocessor >>>> configure:5582: icc -E conftest.c >>>> configure:5588: $? = 0 >>>> configure:5619: icc -E conftest.c >>>> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >>>> #include <ac_nonexistent.h> >>>> ^ >>>> >>>> configure:5625: $? = 2 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | /* end confdefs.h. */ >>>> | #include <ac_nonexistent.h> >>>> configure:5658: result: icc -E >>>> configure:5687: icc -E conftest.c >>>> configure:5693: $? = 0 >>>> configure:5724: icc -E conftest.c >>>> conftest.c(12): error #5: could not open source file "ac_nonexistent.h" >>>> #include <ac_nonexistent.h> >>>> ^ >>>> >>>> configure:5730: $? = 2 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | /* end confdefs.h. */ >>>> | #include <ac_nonexistent.h> >>>> configure:5823: checking for a sed that does not truncate output >>>> configure:5902: result: /bin/sed >>>> configure:5920: checking for grep that handles long lines and -e >>>> configure:5994: result: /bin/grep >>>> configure:5999: checking for egrep >>>> configure:6077: result: /bin/grep -E >>>> configure:6082: checking for fgrep >>>> configure:6160: result: /bin/grep -F >>>> configure:6195: checking for ld used by icc >>>> configure:6262: result: /usr/bin/ld >>>> configure:6271: checking if the linker (/usr/bin/ld) is GNU ld >>>> configure:6286: result: yes >>>> configure:6298: checking for BSD- or MS-compatible name lister (nm) >>>> configure:6347: result: /usr/bin/nm -B >>>> configure:6469: checking the name lister (/usr/bin/nm -B) interface >>>> configure:6476: icc -c -g -O2 conftest.c >&5 >>>> configure:6479: /usr/bin/nm -B "conftest.o" >>>> configure:6482: output >>>> 0000000000000000 N .debug_info_seg >>>> 0000000000000000 S some_variable >>>> configure:6489: result: BSD nm >>>> configure:6492: checking whether ln -s works >>>> configure:6496: result: yes >>>> configure:6504: checking the maximum length of command line arguments >>>> configure:6624: result: 98304 >>>> configure:6641: checking whether the shell understands some XSI constructs >>>> configure:6651: result: yes >>>> configure:6655: checking whether the shell understands "+=" >>>> configure:6661: result: no >>>> configure:6696: checking for /usr/bin/ld option to reload object files >>>> configure:6703: result: -r >>>> configure:6730: checking how to recognize dependent libraries >>>> configure:6920: result: pass_all >>>> configure:6980: checking for ar >>>> configure:6996: found /usr/bin/ar >>>> configure:7007: result: ar >>>> configure:7089: checking for strip >>>> configure:7105: found /usr/bin/strip >>>> configure:7116: result: strip >>>> configure:7192: checking for ranlib >>>> configure:7208: found /usr/bin/ranlib >>>> configure:7219: result: ranlib >>>> configure:7313: checking command to parse /usr/bin/nm -B output from icc object >>>> configure:7431: icc -c -g -O2 conftest.c >&5 >>>> configure:7434: $? = 0 >>>> configure:7438: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm >>>> configure:7441: $? = 0 >>>> configure:7495: icc -o conftest -g -O2 conftest.c conftstm.o >&5 >>>> configure:7498: $? = 0 >>>> configure:7536: result: ok >>>> configure:8410: checking for ANSI C header files >>>> configure:8440: icc -c -g -O2 conftest.c >&5 >>>> configure:8446: $? = 0 >>>> configure:8542: icc -o conftest -g -O2 conftest.c >&5 >>>> configure:8545: $? = 0 >>>> configure:8551: ./conftest >>>> configure:8554: $? = 0 >>>> configure:8571: result: yes >>>> configure:8595: checking for sys/types.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for sys/stat.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for stdlib.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for string.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for memory.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for strings.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for inttypes.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for stdint.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8595: checking for unistd.h >>>> configure:8616: icc -c -g -O2 conftest.c >&5 >>>> configure:8622: $? = 0 >>>> configure:8638: result: yes >>>> configure:8654: checking for dlfcn.h >>>> configure:8675: icc -c -g -O2 conftest.c >&5 >>>> configure:8681: $? = 0 >>>> configure:8697: result: yes >>>> configure:8826: checking for C++ compiler version >>>> configure:8833: g++ --version >&5 >>>> g++ (GCC) 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>>> Copyright (C) 2002 Free Software Foundation, Inc. >>>> This is free software; see the source for copying conditions. There is NO >>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>>> >>>> configure:8836: $? = 0 >>>> configure:8843: g++ -v >&5 >>>> Reading specs from /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/specs >>>> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --host=ia64-redhat-linux >>>> Thread model: posix >>>> gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-34) >>>> configure:8846: $? = 0 >>>> configure:8853: g++ -V >&5 >>>> g++: argument to `-V' missing >>>> >>>> configure:8856: $? = 1 >>>> configure:8859: checking whether we are using the GNU C++ compiler >>>> configure:8911: result: yes >>>> configure:8916: checking whether g++ accepts -g >>>> configure:9051: result: yes >>>> configure:9076: checking dependency style of g++ >>>> configure:9167: result: none >>>> configure:9190: checking how to run the C++ preprocessor >>>> configure:9226: g++ -E conftest.cpp >>>> configure:9232: $? = 0 >>>> configure:9263: g++ -E conftest.cpp >>>> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >>>> configure:9269: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | /* end confdefs.h. */ >>>> | #include <ac_nonexistent.h> >>>> configure:9302: result: g++ -E >>>> configure:9331: g++ -E conftest.cpp >>>> configure:9337: $? = 0 >>>> configure:9368: g++ -E conftest.cpp >>>> conftest.cpp:23:28: ac_nonexistent.h: No such file or directory >>>> configure:9374: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | /* end confdefs.h. */ >>>> | #include <ac_nonexistent.h> >>>> configure:9525: checking for Fortran 77 compiler version >>>> configure:9532: ifort --version >&5 >>>> ifort (IFORT) 9.1 20060928 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:9535: $? = 0 >>>> configure:9542: ifort -v >&5 >>>> Version 9.1 >>>> configure:9545: $? = 0 >>>> configure:9552: ifort -V >&5 >>>> Intel(R) Fortran Itanium(R) Compiler for Itanium(R)-based applications >>>> Version 9.1 Build 20060928 Package ID: l_fc_c_9.1.039 >>>> Copyright (C) 1985-2006 Intel Corporation. All rights reserved. >>>> >>>> configure:9555: $? = 0 >>>> configure:9563: checking whether we are using the GNU Fortran 77 compiler >>>> configure:9605: result: no >>>> configure:9611: checking whether ifort accepts -g >>>> configure:9650: result: yes >>>> configure:9824: checking for objdir >>>> configure:9839: result: .libs >>>> configure:10131: checking if icc supports -fno-rtti -fno-exceptions >>>> configure:10152: icc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5 >>>> configure:10156: $? = 0 >>>> configure:10166: result: yes >>>> configure:10186: checking for icc option to produce PIC >>>> configure:10443: result: -fPIC -DPIC >>>> configure:10455: checking if icc PIC flag -fPIC -DPIC works >>>> configure:10476: icc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5 >>>> configure:10480: $? = 0 >>>> configure:10490: result: yes >>>> configure:10514: checking if icc static flag -static works >>>> configure:10542: result: yes >>>> configure:10557: checking if icc supports -c -o file.o >>>> configure:10581: icc -c -g -O2 -o out/conftest2.o conftest.c >&5 >>>> configure:10585: $? = 0 >>>> configure:10604: result: yes >>>> configure:10612: checking if icc supports -c -o file.o >>>> configure:10659: result: yes >>>> configure:10692: checking whether the icc linker (/usr/bin/ld) supports shared libraries >>>> configure:11746: result: yes >>>> configure:11985: checking dynamic linker characteristics >>>> configure:12428: icc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5 >>>> configure:12434: $? = 0 >>>> configure:12664: result: GNU/Linux ld.so >>>> configure:12766: checking how to hardcode library paths into programs >>>> configure:12791: result: immediate >>>> configure:13604: checking whether stripping libraries is possible >>>> configure:13609: result: yes >>>> configure:13644: checking if libtool supports shared libraries >>>> configure:13646: result: yes >>>> configure:13649: checking whether to build shared libraries >>>> configure:13670: result: no >>>> configure:13673: checking whether to build static libraries >>>> configure:13677: result: yes >>>> configure:13827: checking for ld used by g++ >>>> configure:13894: result: /usr/bin/ld >>>> configure:13903: checking if the linker (/usr/bin/ld) is GNU ld >>>> configure:13918: result: yes >>>> configure:13973: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >>>> configure:14935: result: yes >>>> configure:14963: g++ -c -g -O2 conftest.cpp >&5 >>>> configure:14966: $? = 0 >>>> configure:15148: checking for g++ option to produce PIC >>>> configure:15457: result: -fPIC -DPIC >>>> configure:15466: checking if g++ PIC flag -fPIC -DPIC works >>>> configure:15487: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5 >>>> configure:15491: $? = 0 >>>> configure:15501: result: yes >>>> configure:15522: checking if g++ static flag -static works >>>> configure:15550: result: yes >>>> configure:15562: checking if g++ supports -c -o file.o >>>> configure:15586: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5 >>>> configure:15590: $? = 0 >>>> configure:15609: result: yes >>>> configure:15614: checking if g++ supports -c -o file.o >>>> configure:15661: result: yes >>>> configure:15691: checking whether the g++ linker (/usr/bin/ld) supports shared libraries >>>> configure:15717: result: yes >>>> configure:15854: checking dynamic linker characteristics >>>> configure:16245: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5 >>>> configure:16251: $? = 0 >>>> configure:16481: result: GNU/Linux ld.so >>>> configure:16532: checking how to hardcode library paths into programs >>>> configure:16557: result: immediate >>>> configure:16698: checking if libtool supports shared libraries >>>> configure:16700: result: yes >>>> configure:16703: checking whether to build shared libraries >>>> configure:16723: result: no >>>> configure:16726: checking whether to build static libraries >>>> configure:16730: result: yes >>>> configure:16744: checking for ifort option to produce PIC >>>> configure:17001: result: -KPIC >>>> configure:17010: checking if ifort PIC flag -KPIC works >>>> configure:17031: ifort -c -g -nofor_main -KPIC conftest.f >&5 >>>> configure:17035: $? = 0 >>>> configure:17045: result: yes >>>> configure:17066: checking if ifort static flag -static works >>>> configure:17094: result: yes >>>> configure:17106: checking if ifort supports -c -o file.o >>>> configure:17130: ifort -c -g -nofor_main -o out/conftest2.o conftest.f >&5 >>>> configure:17134: $? = 0 >>>> configure:17153: result: yes >>>> configure:17158: checking if ifort supports -c -o file.o >>>> configure:17205: result: yes >>>> configure:17235: checking whether the ifort linker (/usr/bin/ld) supports shared libraries >>>> configure:18269: result: yes >>>> configure:18406: checking dynamic linker characteristics >>>> configure:18787: ifort -o conftest -g -nofor_main -Wl,-rpath -Wl,/foo conftest.f >&5 >>>> configure:18793: $? = 0 >>>> configure:19023: result: GNU/Linux ld.so >>>> configure:19074: checking how to hardcode library paths into programs >>>> configure:19099: result: immediate >>>> configure:19155: checking for pow in -lm >>>> configure:19190: icc -o conftest -g -O2 conftest.c -lm >&5 >>>> conftest.c(35): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "pow" >>>> >>>> configure:19196: $? = 0 >>>> configure:19214: result: yes >>>> configure:19229: checking for strerrno in -liberty >>>> configure:19264: icc -o conftest -g -O2 conftest.c -liberty >&5 >>>> /usr/lib/gcc-lib/ia64-redhat-linux/3.2.3/../../..//libiberty.a(strerror.o)(.text+0x240): In function `errno_max': >>>> : `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead >>>> configure:19270: $? = 0 >>>> configure:19288: result: yes >>>> configure:19304: checking for gethostbyname >>>> configure:19360: icc -o conftest -g -O2 conftest.c >&5 >>>> configure:19366: $? = 0 >>>> configure:19383: result: yes >>>> configure:19468: checking for connect >>>> configure:19524: icc -o conftest -g -O2 conftest.c >&5 >>>> configure:19530: $? = 0 >>>> configure:19547: result: yes >>>> configure:19632: checking for thr_create >>>> configure:19688: icc -o conftest -g -O2 conftest.c >&5 >>>> /tmp/iccv8SYca.o(.text+0x12): In function `main': >>>> /homesN/khelgeo/apbs_fetk/src/apbs-1.2.1-source/conftest.c:58: undefined reference to `thr_create' >>>> configure:19694: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | /* end confdefs.h. */ >>>> | /* Define thr_create to an innocuous variant, in case <limits.h> declares thr_create. >>>> | For example, HP-UX 11i <limits.h> declares gettimeofday. */ >>>> | #define thr_create innocuous_thr_create >>>> | >>>> | /* System header to define __stub macros and hopefully few prototypes, >>>> | which can conflict with char thr_create (); below. >>>> | Prefer <limits.h> to <assert.h> if __STDC__ is defined, since >>>> | <limits.h> exists even on freestanding compilers. */ >>>> | >>>> | #ifdef __STDC__ >>>> | # include <limits.h> >>>> | #else >>>> | # include <assert.h> >>>> | #endif >>>> | >>>> | #undef thr_create >>>> | >>>> | /* Override any GCC internal prototype to avoid an error. >>>> | Use char because int might match the return type of a GCC >>>> | builtin and then its argument prototype would still apply. */ >>>> | #ifdef __cplusplus >>>> | extern "C" >>>> | #endif >>>> | char thr_create (); >>>> | /* The GNU C library defines this for functions which it implements >>>> | to always fail with ENOSYS. Some functions are actually named >>>> | something starting with __ and the normal name is an alias. */ >>>> | #if defined __stub_thr_create || defined __stub___thr_create >>>> | choke me >>>> | #endif >>>> | >>>> | int >>>> | main () >>>> | { >>>> | return thr_create (); >>>> | ; >>>> | return 0; >>>> | } >>>> configure:19711: result: no >>>> configure:19720: checking for thr_create in -lthread >>>> configure:19755: icc -o conftest -g -O2 conftest.c -lthread >&5 >>>> ld: cannot find -lthread >>>> configure:19761: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | /* end confdefs.h. */ >>>> | >>>> | /* Override any GCC internal prototype to avoid an error. >>>> | Use char because int might match the return type of a GCC >>>> | builtin and then its argument prototype would still apply. */ >>>> | #ifdef __cplusplus >>>> | extern "C" >>>> | #endif >>>> | char thr_create (); >>>> | int >>>> | main () >>>> | { >>>> | return thr_create (); >>>> | ; >>>> | return 0; >>>> | } >>>> configure:19779: result: no >>>> configure:19796: checking for time >>>> configure:19852: icc -o conftest -g -O2 conftest.c >&5 >>>> conftest.c(58): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "time" >>>> >>>> configure:19858: $? = 0 >>>> configure:19875: result: yes >>>> configure:19892: checking for rand >>>> configure:19948: icc -o conftest -g -O2 conftest.c >&5 >>>> configure:19954: $? = 0 >>>> configure:19971: result: yes >>>> configure:19988: checking for srand >>>> configure:20044: icc -o conftest -g -O2 conftest.c >&5 >>>> conftest.c(60): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "srand" >>>> >>>> configure:20050: $? = 0 >>>> configure:20067: result: yes >>>> configure:20085: checking the machine epsilon for VFLOOR >>>> configure:20111: icc -g -O2 -c fperror.c 1>&5 >>>> configure:20114: $? = 0 >>>> configure:20123: result: yes >>>> configure:20167: ----------------------------------------------------------- >>>> configure:20169: ---------- begin configuring for MALOC linkage ------------ >>>> configure:20171: ----------------------------------------------------------- >>>> configure:20178: WARNING: Error... FETK_INCLUDE is no longer supported. >>>> configure:20180: WARNING: Use --with-fetk-include=PATH instead. >>>> configure:20182: WARNING: Ignoring these variables... >>>> configure:20187: WARNING: Error... FETK_LIBRARY is no longer supported. >>>> configure:20189: WARNING: Use --with-fetk-library=PATH instead. >>>> configure:20191: WARNING: Ignoring these variables... >>>> configure:20195: checking for --with-fetk-include option >>>> configure:20205: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>>> configure:20213: checking for --with-fetk-library option >>>> configure:20223: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>>> configure:20235: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include/maloc/maloc.h >>>> configure:20251: result: yes >>>> configure:20267: Using MALOC headers in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>>> configure:20273: checking for /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib/libmaloc.a >>>> configure:20289: result: yes >>>> configure:20306: Using MALOC libraries in /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>>> configure:20316: checking for --with-mpich option >>>> configure:20331: result: no >>>> configure:20337: checking for --with-mpich2 option >>>> configure:20351: result: no >>>> configure:20358: checking for --with-lam option >>>> configure:20372: result: no >>>> configure:20379: checking for --with-openmpi option >>>> configure:20392: result: no >>>> configure:20771: --------------------------------------------------------------- >>>> configure:20773: ---------- begin configuring for Python wrappers -------------- >>>> configure:20775: --------------------------------------------------------------- >>>> configure:20779: checking for --enable-python >>>> configure:21049: result: no >>>> configure:21058: Python wrappers disabled >>>> configure:21094: checking for python >>>> configure:21112: found /usr/bin/python >>>> configure:21124: result: /usr/bin/python >>>> configure:21214: Skipping MALOC installation; will use MALOC provided with FEtk >>>> configure:21225: checking for maloc_needs_rl in -lmaloc >>>> configure:21260: icc -o conftest -g -O2 /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmaloc /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -lvf2c -liberty -lm >&5 >>>> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include: file not recognized: Is a directory >>>> configure:21266: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | #define HAVE_TIME_FUNC >>>> | #define HAVE_RAND_FUNC >>>> | #define HAVE_SRAND_FUNC >>>> | #define FLOAT_ERRORS 1 >>>> | #define MACHINE_EPS 1.19209E-07 >>>> | /* end confdefs.h. */ >>>> | >>>> | /* Override any GCC internal prototype to avoid an error. >>>> | Use char because int might match the return type of a GCC >>>> | builtin and then its argument prototype would still apply. */ >>>> | #ifdef __cplusplus >>>> | extern "C" >>>> | #endif >>>> | char maloc_needs_rl (); >>>> | int >>>> | main () >>>> | { >>>> | return maloc_needs_rl (); >>>> | ; >>>> | return 0; >>>> | } >>>> configure:21284: result: no >>>> configure:21529: ------------------------------------------------------------ >>>> configure:21531: ---------- begin configuring for FEtk linkage -------------- >>>> configure:21533: ------------------------------------------------------------ >>>> configure:21542: checking for --disable-fetk >>>> configure:21554: result: no >>>> configure:21556: checking for user-specified FEtk include path >>>> configure:21559: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>>> configure:21567: checking for user-specified FEtk library path >>>> configure:21570: result: /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib >>>> configure:21593: checking mc/mc.h usability >>>> configure:21610: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >>>> configure:21616: $? = 0 >>>> configure:21630: result: yes >>>> configure:21634: checking mc/mc.h presence >>>> configure:21649: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >>>> configure:21655: $? = 0 >>>> configure:21669: result: yes >>>> configure:21702: checking for mc/mc.h >>>> configure:21709: result: yes >>>> configure:21720: checking for mc_link in -lmc >>>> configure:21755: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >>>> configure:21761: $? = 0 >>>> configure:21779: result: yes >>>> configure:21800: checking mcx/mcx.h usability >>>> configure:21817: icc -c -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >&5 >>>> conftest.c(62): catastrophic error: could not open source file "mcx/mcx.h" >>>> #include <mcx/mcx.h> >>>> ^ >>>> >>>> compilation aborted for conftest.c (code 4) >>>> configure:21823: $? = 4 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | #define HAVE_TIME_FUNC >>>> | #define HAVE_RAND_FUNC >>>> | #define HAVE_SRAND_FUNC >>>> | #define FLOAT_ERRORS 1 >>>> | #define MACHINE_EPS 1.19209E-07 >>>> | /* end confdefs.h. */ >>>> | #include <stdio.h> >>>> | #ifdef HAVE_SYS_TYPES_H >>>> | # include <sys/types.h> >>>> | #endif >>>> | #ifdef HAVE_SYS_STAT_H >>>> | # include <sys/stat.h> >>>> | #endif >>>> | #ifdef STDC_HEADERS >>>> | # include <stdlib.h> >>>> | # include <stddef.h> >>>> | #else >>>> | # ifdef HAVE_STDLIB_H >>>> | # include <stdlib.h> >>>> | # endif >>>> | #endif >>>> | #ifdef HAVE_STRING_H >>>> | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H >>>> | # include <memory.h> >>>> | # endif >>>> | # include <string.h> >>>> | #endif >>>> | #ifdef HAVE_STRINGS_H >>>> | # include <strings.h> >>>> | #endif >>>> | #ifdef HAVE_INTTYPES_H >>>> | # include <inttypes.h> >>>> | #endif >>>> | #ifdef HAVE_STDINT_H >>>> | # include <stdint.h> >>>> | #endif >>>> | #ifdef HAVE_UNISTD_H >>>> | # include <unistd.h> >>>> | #endif >>>> | #include <mcx/mcx.h> >>>> configure:21837: result: no >>>> configure:21841: checking mcx/mcx.h presence >>>> configure:21856: icc -E -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include conftest.c >>>> conftest.c(29): error #5: could not open source file "mcx/mcx.h" >>>> #include <mcx/mcx.h> >>>> ^ >>>> >>>> configure:21862: $? = 2 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | #define HAVE_TIME_FUNC >>>> | #define HAVE_RAND_FUNC >>>> | #define HAVE_SRAND_FUNC >>>> | #define FLOAT_ERRORS 1 >>>> | #define MACHINE_EPS 1.19209E-07 >>>> | /* end confdefs.h. */ >>>> | #include <mcx/mcx.h> >>>> configure:21876: result: no >>>> configure:21909: checking for mcx/mcx.h >>>> configure:21916: result: no >>>> configure:21927: checking for mcx_link in -lmcx >>>> configure:21962: icc -o conftest -g -O2 -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib conftest.c -lmcx -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmaloc -liberty -lm >&5 >>>> ld: cannot find -lmcx >>>> configure:21968: $? = 1 >>>> configure: failed program was: >>>> | /* confdefs.h. */ >>>> | #define PACKAGE_NAME "APBS" >>>> | #define PACKAGE_TARNAME "apbs" >>>> | #define PACKAGE_VERSION "1.2.1" >>>> | #define PACKAGE_STRING "APBS 1.2.1" >>>> | #define PACKAGE_BUGREPORT "ba...@bi..." >>>> | #define PACKAGE "apbs" >>>> | #define VERSION "1.2.1" >>>> | #define VF77_ONEUNDERSCORE >>>> | #define VF77_LOWERCASE >>>> | #define STDC_HEADERS 1 >>>> | #define HAVE_SYS_TYPES_H 1 >>>> | #define HAVE_SYS_STAT_H 1 >>>> | #define HAVE_STDLIB_H 1 >>>> | #define HAVE_STRING_H 1 >>>> | #define HAVE_MEMORY_H 1 >>>> | #define HAVE_STRINGS_H 1 >>>> | #define HAVE_INTTYPES_H 1 >>>> | #define HAVE_STDINT_H 1 >>>> | #define HAVE_UNISTD_H 1 >>>> | #define HAVE_DLFCN_H 1 >>>> | #define LT_OBJDIR ".libs/" >>>> | #define HAVE_TIME_FUNC >>>> | #define HAVE_RAND_FUNC >>>> | #define HAVE_SRAND_FUNC >>>> | #define FLOAT_ERRORS 1 >>>> | #define MACHINE_EPS 1.19209E-07 >>>> | /* end confdefs.h. */ >>>> | >>>> | /* Override any GCC internal prototype to avoid an error. >>>> | Use char because int might match the return type of a GCC >>>> | builtin and then its argument prototype would still apply. */ >>>> | #ifdef __cplusplus >>>> | extern "C" >>>> | #endif >>>> | char mcx_link (); >>>> | int >>>> | main () >>>> | { >>>> | return mcx_link (); >>>> | ; >>>> | return 0; >>>> | } >>>> configure:21986: result: no >>>> configure:22000: FEtk component MC found: enabled. >>>> configure:22025: WARNING: FEtk component MCX not found: hierarchical basis methods disabled. >>>> configure:22039: --------------------------------------------------------------- >>>> configure:22041: ------------ begin processing APBS configure options ---------- >>>> configure:22043: --------------------------------------------------------------- >>>> configure:22046: checking for EMBED macro can be used >>>> configure:22070: icc -c -g -O2 conftest.c >&5 >>>> configure:22076: $? = 0 >>>> configure:22094: result: yes >>>> configure:22098: checking --enable-pansi >>>> configure:22116: result: no >>>> configure:22123: checking for strcasecmp >>>> configure:22179: icc -o conftest -g -O2 conftest.c >&5 >>>> conftest.c(65): (col. 8)warning #980: wrong number of actual arguments to intrinsic function "strcasecmp" >>>> >>>> configure:22185: $? = 0 >>>> configure:22202: result: yes >>>> configure:22225: checking for --disable-tools >>>> configure:22237: result: no >>>> configure:22239: tools will be compiled >>>> configure:22258: checking for --with-blas >>>> configure:22353: result: no >>>> configure:22383: checking for --with-arpack >>>> configure:22399: result: no >>>> configure:22405: checking for --disable-inline >>>> configure:22416: result: no >>>> configure:22418: inline functions will be used >>>> configure:22432: checking for --enable-tinker >>>> configure:22456: result: no >>>> configure:22460: checking for --enable-abps-quiet >>>> configure:22479: result: no >>>> configure:22483: checking for --disable-openmp >>>> configure:22497: result: no >>>> configure:22876: creating ./config.status >>>> >>>> ## ---------------------- ## >>>> ## Running config.status. ## >>>> ## ---------------------- ## >>>> >>>> This file was extended by APBS config.status 1.2.1, which was >>>> generated by GNU Autoconf 2.61. Invocation command line was >>>> >>>> CONFIG_FILES = >>>> CONFIG_HEADERS = >>>> CONFIG_LINKS = >>>> CONFIG_COMMANDS = >>>> $ ./config.status >>>> >>>> on osiris >>>> >>>> config.status:1044: creating Makefile >>>> config.status:1044: creating contrib/Makefile >>>> config.status:1044: creating contrib/blas/Makefile >>>> config.status:1044: creating contrib/pmgZ/Makefile >>>> config.status:1044: creating contrib/aqua/Makefile >>>> config.status:1044: creating contrib/opal/Makefile >>>> config.status:1044: creating contrib/opal/ZSI/Makefile >>>> config.status:1044: creating tools/Makefile >>>> config.status:1044: creating tools/mesh/Makefile >>>> config.status:1044: creating tools/manip/Makefile >>>> config.status:1044: creating tools/python/Makefile >>>> config.status:1044: creating tools/arpack/Makefile >>>> config.status:1044: creating tools/python/vgrid/Makefile >>>> config.status:1044: creating src/Makefile >>>> config.status:1044: creating src/generic/Makefile >>>> config.status:1044: creating src/mg/Makefile >>>> config.status:1044: creating src/fem/Makefile >>>> config.status:1044: creating src/aaa_inc/Makefile >>>> config.status:1044: creating src/aaa_inc/apbs/Makefile >>>> config.status:1044: creating src/aaa_lib/Makefile >>>> config.status:1044: creating examples/Makefile >>>> config.status:1044: creating examples/actin-dimer/Makefile >>>> config.status:1044: creating examples/alkanes/Makefile >>>> config.status:1044: creating examples/born/Makefile >>>> config.status:1044: creating examples/FKBP/Makefile >>>> config.status:1044: creating examples/hca-bind/Makefile >>>> config.status:1044: creating examples/ion-pmf/Makefile >>>> config.status:1044: creating examples/ion-protein/Makefile >>>> config.status:1044: creating examples/ionize/Makefile >>>> config.status:1044: creating examples/pka-lig/Makefile >>>> config.status:1044: creating examples/point-pmf/Makefile >>>> config.status:1044: creating examples/protein-rna/Makefile >>>> config.status:1044: creating examples/smpbe/Makefile >>>> config.status:1044: creating examples/solv/Makefile >>>> config.status:1044: creating examples/opal/Makefile >>>> config.status:1044: creating bin/Makefile >>>> config.status:1044: creating src/aaa_inc/apbscfg.h >>>> config.status:1327: executing depfiles commands >>>> config.status:1327: executing libtool commands >>>> configure:25486: >>>> >>>> APBS to be compiled with following settings: icc -g -O2 -openmp >>>> APBS to be compiled with following settings: ifort -g -nofor_main -nofor_main -openmp -assume cc_omp >>>> APBS to be linked with following libraries : -L/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//lib -lmc -lm /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/contrib/blas/.libs/libapbsblas.a -lsuperlu -lumfpack -lamd -lpunc -lblas >>>> APBS to be compiled with following includes: -I. -I/home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu//include >>>> >>>> Please type "make; make install" >>>> >>>> >>>> ## ---------------- ## >>>> ## Cache variables. ## >>>> ## ---------------- ## >>>> >>>> ac_cv_build=ia64-unknown-linux-gnu >>>> ac_cv_c_compiler_gnu=yes >>>> ac_cv_cxx_compiler_gnu=yes >>>> ac_cv_env_CCC_set= >>>> ac_cv_env_CCC_value= >>>> ac_cv_env_CC_set= >>>> ac_cv_env_CC_value= >>>> ac_cv_env_CFLAGS_set= >>>> ac_cv_env_CFLAGS_value= >>>> ac_cv_env_CPPFLAGS_set= >>>> ac_cv_env_CPPFLAGS_value= >>>> ac_cv_env_CPP_set= >>>> ac_cv_env_CPP_value= >>>> ac_cv_env_CXXCPP_set= >>>> ac_cv_env_CXXCPP_value= >>>> ac_cv_env_CXXFLAGS_set= >>>> ac_cv_env_CXXFLAGS_value= >>>> ac_cv_env_CXX_set= >>>> ac_cv_env_CXX_value= >>>> ac_cv_env_F77_set= >>>> ac_cv_env_F77_value= >>>> ac_cv_env_FFLAGS_set= >>>> ac_cv_env_FFLAGS_value= >>>> ac_cv_env_LDFLAGS_set= >>>> ac_cv_env_LDFLAGS_value= >>>> ac_cv_env_LIBS_set= >>>> ac_cv_env_LIBS_value= >>>> ac_cv_env_build_alias_set= >>>> ac_cv_env_build_alias_value= >>>> ac_cv_env_host_alias_set= >>>> ac_cv_env_host_alias_value= >>>> ac_cv_env_target_alias_set= >>>> ac_cv_env_target_alias_value= >>>> ac_cv_f77_compiler_gnu=no >>>> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__include_maloc_maloc_h=yes >>>> ac_cv_file__home_khelgeo_apbs_fetk_src_fetk_build_ia64_unknown_linux_gnu__lib_libmaloc_a=yes >>>> ac_cv_func_connect=yes >>>> ac_cv_func_gethostbyname=yes >>>> ac_cv_func_rand=yes >>>> ac_cv_func_srand=yes >>>> ac_cv_func_strcasecmp=yes >>>> ac_cv_func_thr_create=no >>>> ac_cv_func_time=yes >>>> ac_cv_header_dlfcn_h=yes >>>> ac_cv_header_inttypes_h=yes >>>> ac_cv_header_mc_mc_h=yes >>>> ac_cv_header_mcx_mcx_h=no >>>> ac_cv_header_memory_h=yes >>>> ac_cv_header_stdc=yes >>>> ac_cv_header_stdint_h=yes >>>> ac_cv_header_stdlib_h=yes >>>> ac_cv_header_string_h=yes >>>> ac_cv_header_strings_h=yes >>>> ac_cv_header_sys_stat_h=yes >>>> ac_cv_header_sys_types_h=yes >>>> ac_cv_header_unistd_h=yes >>>> ac_cv_host=ia64-unknown-linux-gnu >>>> ac_cv_lib_iberty_strerrno=yes >>>> ac_cv_lib_m_pow=yes >>>> ac_cv_lib_maloc_maloc_needs_rl=no >>>> ac_cv_lib_mc_mc_link=yes >>>> ac_cv_lib_mcx_mcx_link=no >>>> ac_cv_lib_thread_thr_create=no >>>> ac_cv_objext=o >>>> ac_cv_path_EGREP='/bin/grep -E' >>>> ac_cv_path_FGREP='/bin/grep -F' >>>> ac_cv_path_GREP=/bin/grep >>>> ac_cv_path_SED=/bin/sed >>>> ac_cv_path_install='/usr/bin/install -c' >>>> ac_cv_path_mkdir=/bin/mkdir >>>> ac_cv_path_py_path=/usr/bin/python >>>> ac_cv_prog_AWK=gawk >>>> ac_cv_prog_CPP='icc -E' >>>> ac_cv_prog_CXXCPP='g++ -E' >>>> ac_cv_prog_ac_ct_AR=ar >>>> ac_cv_prog_ac_ct_CC=icc >>>> ac_cv_prog_ac_ct_CXX=g++ >>>> ac_cv_prog_ac_ct_F77=ifort >>>> ac_cv_prog_ac_ct_RANLIB=ranlib >>>> ac_cv_prog_ac_ct_STRIP=strip >>>> ac_cv_prog_cc_c89= >>>> ac_cv_prog_cc_g=yes >>>> ac_cv_prog_cxx_g=yes >>>> ac_cv_prog_f77_g=yes >>>> ac_cv_prog_make_make_set=yes >>>> ac_cv_target=ia64-unknown-linux-gnu >>>> am_cv_CC_dependencies_compiler_type=none >>>> am_cv_CXX_dependencies_compiler_type=none >>>> am_cv_prog_cc_stdc= >>>> lt_cv_deplibs_check_method=pass_all >>>> lt_cv_file_magic_cmd='$MAGIC_CMD' >>>> lt_cv_file_magic_test_file= >>>> lt_cv_ld_reload_flag=-r >>>> lt_cv_nm_interface='BSD nm' >>>> lt_cv_objdir=.libs >>>> lt_cv_path_LD=/usr/bin/ld >>>> lt_cv_path_LDCXX=/usr/bin/ld >>>> lt_cv_path_NM='/usr/bin/nm -B' >>>> lt_cv_prog_compiler_c_o=yes >>>> lt_cv_prog_compiler_c_o_CXX=yes >>>> lt_cv_prog_compiler_c_o_F77=yes >>>> lt_cv_prog_compiler_pic_works=yes >>>> lt_cv_prog_compiler_pic_works_CXX=yes >>>> lt_cv_prog_compiler_pic_works_F77=yes >>>> lt_cv_prog_compiler_rtti_exceptions=yes >>>> lt_cv_prog_compiler_static_works=yes >>>> lt_cv_prog_compiler_static_works_CXX=yes >>>> lt_cv_prog_compiler_static_works_F77=yes >>>> lt_cv_prog_gnu_ld=yes >>>> lt_cv_prog_gnu_ldcxx=yes >>>> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\''' >>>> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\''' >>>> lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\''' >>>> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\''' >>>> lt_cv_sys_max_cmd_len=98304 >>>> >>>> ## ----------------- ## >>>> ## Output variables. ## >>>> ## ----------------- ## >>>> >>>> ACLOCAL=':' >>>> AMDEPBACKSLASH='\' >>>> AMDEP_FALSE='#' >>>> AMDEP_TRUE='' >>>> AMTAR='${SHELL} /home/khelgeo/apbs_fetk/src/apbs-1.2.1-source/config/missing --run tar' >>>> APBS_VERSION='1:2:1' >>>> AR='ar' >>>> AUTOCONF=':' >>>> AUTOHEADER=':' >>>> AUTOMAKE=':' >>>> AWK='gawk' >>>> CC='icc' >>>> CCDEPMODE='depmode=none' >>>> CFLAGS='-g -O2 -openmp' >>>> CPP='icc -E' >>>> CPPFLAGS='' >>>> CXX='g++' >>>> CXXCPP='g++ -E' >>>> CXXDEPMODE='depmode=none' >>>> CX... [truncated message content] |
From: George K. <ge...@me...> - 2010-07-24 15:35:25
|
No problem, Nathan, I hope we can resolve the problem quickly, so that one can start testing Fetk. George On 7/24/2010 10:35 AM, Baker, Nathan wrote: > Thanks, George! > > __________________________________________________ > Nathan Baker > Chief Scientist for Signature Science > Pacific Northwest National Laboratory > >> -----Original Message----- >> From: George Khelashvili [mailto:ge...@me...] >> Sent: Friday, July 23, 2010 9:25 AM >> To: Baker, Nathan >> Cc: apb...@li...; Yong Huang; Dave Gohara >> (sd...@gm...) >> Subject: Re: [Apbs-users] FeTK support in APBS >> >> Hi Nathan, >> >> The listing of >> /home/khelgeo/apbs_fetk/src/fetk/build/ia64-unknown-linux-gnu/ >> directory is "bin doc fetk-env include lib". By the way, I realized >> that I sent you wrong log files, which did not exactly correspond to >> the versions of APBS and FETK I used (I played with several >> combinations and I accidentally mixed them up). Sorry for that. Here >> are the corrected log files which were obtained by installing Fetk >> version 1.1 first, and then installing APBS 1.2.1. The log files were >> generated during the APBS installation. This log file produced somewhat >> different error message. >> I do realize that APBS-FETK link is in the beginning stages so I will >> be glad to contribute as I can to resolve this issue so that the >> community can use this what I think will be a wonderful tool. >> >> Sincerely, >> George >> >> Baker, Nathan wrote: >>> Hi George -- >>> >>> This is very strange. Can you send me a listing of your >> /home/khelgeo/apbs_fetk/src/build/ia64-unknown-linux-gnu/ directory? >>> All: please note that FEtk has just been released and the APBS/FEtk >> interface is very much in a "beta" state. >>> Thanks, >>> >>> __________________________________________________ >>> Nathan Baker >>> Chief Scientist for Signature Science >>> Pacific Northwest National Laboratory >>> >>> >>> >>>> -----Original Message----- >>>> From: George Khelashvili [mailto:ge...@me...] >>>> Sent: Wednesday, July 21, 2010 11:31 AM >>>> To: apb...@li... >>>> Subject: Re: [Apbs-users] FeTK support in APBS >>>> >>>> Dear APBS users, >>>> >>>> I am trying to compile APBS version 1.2 with Fetk support (Fetk >> version >>>> 1.1). I have downloaded and installed the entire Fetk package, and >> now >>>> I moved on to installing APBS itself. While configuring apparently >>>> worked since all the necessary Fetk library and header files where >>>> found, the compilation crushed when I run "make". I have attached >> log >>>> files from configuration step as well as "make" step. Obviously >> there >>>> is a problem while compiling fetk.c file. I would appreciate if >>>> somebody can take a look at the attached files and suggest what is >>>> missing. >>>> >>>> Thank you, >>>> George >>>> >>>> Baker, Nathan wrote: >>>> >>>>> Hello - >>>>> >>>>> Yes, FEtk is available for download at >>>>> http://fetk.org/codes/download/. I will be updating the >> documentation >>>>> in the next few weeks with revised instructions on how to compile, >>>>> >>>> etc. >>>> >>>>> Thanks, >>>>> >>>>> Nathan >>>>> >>>>> __________________________________________________ >>>>> *Nathan Baker* >>>>> Chief Scientist for Signature Science >>>>> Pacific Northwest National Laboratory >>>>> >>>>> *From:* patrizio ansalone [mailto:p.a...@in...] >>>>> *Sent:* Wednesday, July 21, 2010 12:39 AM >>>>> *To:* apb...@li... >>>>> *Subject:* [Apbs-users] FeTK support in APBS >>>>> >>>>> >>>>> Is it possibile to compile apbs with fetk support? I have understod >>>>> that FeTk must be installed >>>>> (http://www.poissonboltzmann.org/apbs/user-guide/installation-and- >>>>> >>>> avil >>>> >>>>> /source-installation) but I can't find a repository where I can >>>>> download it. Any sugestion how to fix this problem ? >>>>> thanks in advance >>>>> Patrizio >>>>> >>>>> ------------------------------------------------------------------- >> -- >>>> - >>>> >>>>> -- >>>>> >>>>> ------------------------------------------------------------------- >> -- >>>> - >>>> >>>>> -------- This SF.net email is sponsored by Sprint What will you do >>>>> first with EVO, the first 4G phone? >>>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >>>>> ------------------------------------------------------------------- >> -- >>>> - >>>> >>>>> -- >>>>> >>>>> _______________________________________________ >>>>> apbs-users mailing list >>>>> apb...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>> >>>>> >>>> -- >>>> George Khelashvili, Ph.D. >>>> Department of Physiology and Biophysics >>>> Weill Medical College of Cornell University 1300 York Avenue, Room >>>> LC501 New York, NY, 10065, USA ge...@me... >>>> Phone: 1-212-746-6539 >>>> Fax: 1-212-746-6226 >>>> >>>> >>> >> >> -- >> George Khelashvili, Ph.D. >> Department of Physiology and Biophysics >> Weill Medical College of Cornell University >> 1300 York Avenue, Room LC501 >> New York, NY, 10065, USA >> ge...@me... >> Phone: 1-212-746-6539 >> Fax: 1-212-746-6226 -- George Khelashvili, Ph.D. Department of Physiology and Biophysics Weill Medical College of Cornell University 1300 York Avenue, Room LC501 New York, NY, 10065, USA ge...@me... Phone: 1-212-746-6539 Fax: 1-212-746-6226 |