Re: [Apbs-users] apbs-1.3-source make fails
Biomolecular electrostatics software
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From: Ilyas Y. <i-y...@no...> - 2011-06-29 20:17:50
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Hi Robert - I've attached the config.log file to this email. Thanks. Ilyas Yildirim, Ph.D. ----------------------------------------------------------- = Department of Chemistry - 2145 Sheridan Road = = Northwestern University - Evanston, IL 60208 = = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 = = http://www.pas.rochester.edu/~yildirim/ = ----------------------------------------------------------- On Wed, 29 Jun 2011, Robert Konecny wrote: > Hi Ilyas, > > ./contrib/include is created and populated during the configure step. Can > you send us the full output of your "./configure" after you do "make clean" > in your apbs source directory? > > Best, > > Robert > > On Wed, Jun 29, 2011 at 02:48:33PM -0500, Ilyas Yildirim wrote: >> Hi Robert - >> >> There is no /fantom/softwares/apbs-1.3-source/contrib/include >> directory in my version of apbs-1.3-source. >> >> [iyi803@rnanano apbs-1.3-source]$ ls -l /fantom/softwares/apbs-1.3-source/contrib >> total 60 >> drwxr-xr-x 3 iyi803 schatz 4096 Jun 29 13:24 aqua >> drwxr-xr-x 3 iyi803 schatz 4096 Jun 29 13:23 blas >> -rw-r--r-- 1 iyi803 schatz 16246 Jun 29 13:22 Makefile >> -rw-r--r-- 1 iyi803 schatz 468 May 11 2010 Makefile.am >> -rw-r--r-- 1 iyi803 schatz 15774 May 19 2010 Makefile.in >> drwxr-xr-x 8 iyi803 schatz 4096 Jun 29 13:22 maloc >> drwxr-xr-x 4 iyi803 schatz 4096 Jun 29 13:22 opal >> drwxr-xr-x 3 iyi803 schatz 4096 Jun 29 13:23 pmgZ >> drwxr-xr-x 13 iyi803 schatz 4096 Jun 29 13:24 zlib >> >> There is also no 'include' directory in any place in apbs-1.3-source >> directory tree. >> >> [iyi803@rnanano apbs-1.3-source]$ pwd >> /fantom/softwares/apbs-1.3-source >> [iyi803@rnanano apbs-1.3-source]$ find ./ -name "include" >> [iyi803@rnanano apbs-1.3-source]$ >> >> The way I configure is as follows: first I set the CC and F77 >> environments. >> >> setenv CC gcc >> setenv F77 gfortran >> >> Then >> >> ./configure --prefix=/programs/apbs >> >> My machine type is as follows: >> >> [iyi803@rnanano apbs-1.3-source]$ uname -a >> Linux ***.northwestern.edu 2.6.18-238.5.1.el5 #1 SMP Mon Feb 21 >> 05:52:39 EST 2011 x86_64 x86_64 x86_64 GNU/Linux >> >> Do I need to specify the machine architecture? Thanks. >> >> Best regards, >> >> Ilyas Yildirim, Ph.D. >> ----------------------------------------------------------- >> = Department of Chemistry - 2145 Sheridan Road = >> = Northwestern University - Evanston, IL 60208 = >> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 = >> = http://www.pas.rochester.edu/~yildirim/ = >> ----------------------------------------------------------- >> >> >> On Wed, 29 Jun 2011, Robert Konecny wrote: >> >>> Hi Ilyas, >>> >>> you should have maloc/maloc.h in >>> /fantom/softwares/apbs-1.3-source/contrib/include. This path is being >>> included as one of the compiler options. >>> >>> What are your configure arguments? >>> >>> Best, >>> >>> Robert >>> >>> On Wed, Jun 29, 2011 at 01:37:55PM -0500, Ilyas Yildirim wrote: >>>> Hi Robert - >>>> >>>> I set the CC and F77 environment variables to use gcc and gfortran. >>>> Configure did not give any error message but when I start the make using >>>> 'sudo make all', it gives the following error message: >>>> >>>> . >>>> . >>>> . >>>> make[4]: Leaving directory `/fantom/softwares/apbs-1.3-source' >>>> /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. >>>> -I../../src/aaa_inc -I../../src/fem -I../../src/mg -I../../src/aaa_inc -I. >>>> -I/fantom/softwares/apbs-1.3-source/contrib/include -g -O2 -g -O2 -c >>>> -o nosh.lo nosh.c >>>> gcc -DHAVE_CONFIG_H -I. -I../../src/aaa_inc -I../../src/fem >>>> -I../../src/mg -I../../src/aaa_inc -I. >>>> -I/fantom/softwares/apbs-1.3-source/contrib/include -g -O2 -g -O2 -c >>>> nosh.c -o nosh.o >>>> In file included from nosh.c:51: >>>> apbs/nosh.h:58:25: error: maloc/maloc.h: No such file or directory >>>> In file included from apbs/nosh.h:62, >>>> from nosh.c:51: >>>> ./apbs/pbeparm.h:58:25: error: maloc/maloc.h: No such file or directory >>>> In file included from apbs/nosh.h:62, >>>> from nosh.c:51: >>>> ./apbs/pbeparm.h:177: error: 'VMAX_ARGLEN' undeclared here (not in a >>>> function) >>>> ./apbs/pbeparm.h:211: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'double' >>>> ./apbs/pbeparm.h:221: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'double' >>>> ./apbs/pbeparm.h:231: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'double' >>>> ./apbs/pbeparm.h:242: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'PBEparm' >>>> ./apbs/pbeparm.h:249: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'int' >>>> ./apbs/pbeparm.h:257: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'void' >>>> ./apbs/pbeparm.h:265: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'void' >>>> ./apbs/pbeparm.h:274: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'int' >>>> ./apbs/pbeparm.h:282: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'void' >>>> ./apbs/pbeparm.h:293: error: expected '=', ',', ';', 'asm' or >>>> '__attribute__' before 'int' >>>> In file included from apbs/nosh.h:63, >>>> . >>>> . >>>> . >>>> >>>> In nosh.h file, there is the following generic headers defined: >>>> >>>> /* Generic headers */ >>>> #include "maloc/maloc.h" >>>> #include "apbs/vhal.h" >>>> >>>> and nosh.h is located at >>>> >>>> ./src/generic/apbs/nosh.h >>>> >>>> There is no maloc directory under >>>> >>>> ./src/generic >>>> >>>> This is just one of the problems. When I copy the directory >>>> >>>> ./contrib/maloc/src/aaa_inc/maloc >>>> >>>> to >>>> >>>> ./src/generic >>>> ./src/aaa_inc >>>> >>>> I bypass the error messages, but at the end, I end up with the following >>>> error message: >>>> >>>> . >>>> . >>>> . >>>> gcc -DHAVE_CONFIG_H -I. -I../src/aaa_inc -I. >>>> -I/fantom/softwares/apbs-1.3-source/contrib/include -g -O2 -c main.c >>>> /bin/sh ../libtool --tag=CC --mode=link gfortran -g -O2 -g -O2 -g -O2 >>>> -o apbs main.o >>>> /fantom/softwares/apbs-1.3-source/bin/libapbsmainroutines.la >>>> /fantom/softwares/apbs-1.3-source/src/aaa_lib/libapbs.la >>>> -L/fantom/softwares/apbs-1.3-source/contrib/lib -lmaloc -lm >>>> /fantom/softwares/apbs-1.3-source/contrib/blas/.libs/libapbsblas.a >>>> /fantom/softwares/apbs-1.3-source/contrib/zlib/.libs/libz.a >>>> gfortran -g -O2 -g -O2 -g -O2 -o apbs main.o >>>> /fantom/softwares/apbs-1.3-source/bin/.libs/libapbsmainroutines.a >>>> /fantom/softwares/apbs-1.3-source/src/aaa_lib/.libs/libapbs.a >>>> -L/fantom/softwares/apbs-1.3-source/contrib/lib -lmaloc -lm >>>> /fantom/softwares/apbs-1.3-source/contrib/blas/.libs/libapbsblas.a >>>> /fantom/softwares/apbs-1.3-source/contrib/zlib/.libs/libz.a >>>> /usr/bin/ld: cannot find -lmaloc >>>> collect2: ld returned 1 exit status >>>> make[2]: *** [apbs] Error 1 >>>> make[2]: Leaving directory `/fantom/softwares/apbs-1.3-source/bin' >>>> make[1]: *** [all] Error 2 >>>> make[1]: Leaving directory `/fantom/softwares/apbs-1.3-source/bin' >>>> make: *** [all-recursive] Error 1 >>>> . >>>> . >>>> . >>>> >>>> At this point I am unable to solve the problem/issue. There is no >>>> >>>> /fantom/softwares/apbs-1.3-source/contrib/lib >>>> >>>> directory by the way (after I extract the gzipped source file; >>>> apbs-1.3-source.tar.gz). >>>> >>>> Maybe I am making a mistake somewhere. If you have any suggestion, I would >>>> like to hear it. Thanks in advance. >>>> >>>> Best regards, >>>> >>>> Ilyas Yildirim, Ph.D. >>>> ----------------------------------------------------------- >>>> = Department of Chemistry - 2145 Sheridan Road = >>>> = Northwestern University - Evanston, IL 60208 = >>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 = >>>> = http://www.pas.rochester.edu/~yildirim/ = >>>> ----------------------------------------------------------- >>>> >>>> >>>> On Wed, 29 Jun 2011, Robert Konecny wrote: >>>> >>>>> Hi, >>>>> >>>>> 1.3 works for me just fine on Ubuntu 10.04 x86_64 with both gcc/gfortran >>>>> and intel compilers. >>>>> >>>>> Are you sure you are not mixing GNU and Intel compiled objects? >>>>> >>>>> Best, >>>>> >>>>> Robert >>>>> >>>>> On Wed, Jun 29, 2011 at 09:18:44AM -0500, Ilyas Yildirim wrote: >>>>>> Hi - I also had issues installing the version 1.3 yesterday. It gave a lot >>>>>> of error messages. Installing version 1.2, however, did not give any >>>>>> issues (after deciding that ver. 1.3 would not be possible to install). >>>>>> You might want to download and install 1.2. >>>>>> >>>>>> Best, >>>>>> >>>>>> Ilyas Yildirim, Ph.D. >>>>>> ----------------------------------------------------------- >>>>>> = Department of Chemistry - 2145 Sheridan Road = >>>>>> = Northwestern University - Evanston, IL 60208 = >>>>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 = >>>>>> = http://www.pas.rochester.edu/~yildirim/ = >>>>>> ----------------------------------------------------------- >>>>>> >>>>>> >>>>>> On Wed, 29 Jun 2011, Daniel Aiello wrote: >>>>>> >>>>>>> Hello, >>>>>>> Make of APBS 1.3 on x86_64 GNU/Linux machine fails. The configuration completes with no errors. I am then prompted to do a make followed by make install. The make fails with below errors. Any insight as to why APBS might not be compiling would be appreciated. Thanks, >>>>>>> Dan >>>>>>> >>>>>>> ...... >>>>>>> /home/soft/src/apbs/contrib/zlib/.libs/libz.a(deflate.o): In function `fill_window': >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:1426: undefined reference to `_intel_fast_memset' >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:1415: undefined reference to `_intel_fast_memset' >>>>>>> /home/soft/src/apbs/contrib/zlib/.libs/libz.a(deflate.o): In function `deflateReset': >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:383: undefined reference to `_intel_fast_memset' >>>>>>> /home/soft/src/apbs/contrib/zlib/.libs/libz.a(deflate.o): In function `deflateSetDictionary': >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:335: undefined reference to `_intel_fast_memcpy' >>>>>>> /home/soft/src/apbs/contrib/zlib/.libs/libz.a(deflate.o): In function `deflateInit_': >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:204: undefined reference to `_intel_fast_memset' >>>>>>> /home/soft/src/apbs/contrib/zlib/.libs/libz.a(deflate.o): In function `deflateInit2_': >>>>>>> /home/soft/src/apbs/contrib/zlib/deflate.c:307: undefined reference to `_intel_fast_memset' >>>>>>> >>>>>>> make[2]: *** [apbs] Error 1 >>>>>>> make[2]: Leaving directory `/home/soft/src/apbs/bin' >>>>>>> make[1]: *** [all] Error 2 >>>>>>> make[1]: Leaving directory `/home/soft/src/apbs/bin' >>>>>>> make: *** [all-recursive] Error 1 >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> All of the data generated in your IT infrastructure is seriously valuable. >>>>>>> Why? It contains a definitive record of application performance, security >>>>>>> threats, fraudulent activity, and more. Splunk takes this data and makes >>>>>>> sense of it. IT sense. And common sense. >>>>>>> http://p.sf.net/sfu/splunk-d2d-c2 >>>>>>> _______________________________________________ >>>>>>> apbs-users mailing list >>>>>>> apb...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> All of the data generated in your IT infrastructure is seriously valuable. >>>>>> Why? It contains a definitive record of application performance, security >>>>>> threats, fraudulent activity, and more. Splunk takes this data and makes >>>>>> sense of it. IT sense. And common sense. >>>>>> http://p.sf.net/sfu/splunk-d2d-c2 >>>>>> _______________________________________________ >>>>>> apbs-users mailing list >>>>>> apb...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> All of the data generated in your IT infrastructure is seriously valuable. >>>> Why? It contains a definitive record of application performance, security >>>> threats, fraudulent activity, and more. Splunk takes this data and makes >>>> sense of it. IT sense. And common sense. >>>> http://p.sf.net/sfu/splunk-d2d-c2 >>>> _______________________________________________ >>>> apbs-users mailing list >>>> apb...@li... >>>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>> >>> ------------------------------------------------------------------------------ >>> All of the data generated in your IT infrastructure is seriously valuable. >>> Why? It contains a definitive record of application performance, security >>> threats, fraudulent activity, and more. Splunk takes this data and makes >>> sense of it. IT sense. And common sense. >>> http://p.sf.net/sfu/splunk-d2d-c2 >>> _______________________________________________ >>> apbs-users mailing list >>> apb...@li... >>> https://lists.sourceforge.net/lists/listinfo/apbs-users >>> > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |