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From: Marcus M. <me...@gm...> - 2022-04-28 03:15:13
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Howdy Amanda, Looks like two issues. I emailed you directly about the problem in your towhee_parallel file as you need different directories. However, looking at your error message it seems very likely something has gone wrong compiling your code in parallel. Are you sure you have the mpi compilers installed properly on this machine? Could be that the Makefile is not finding them. Might need to see the output from the compilation itself to get an idea why MPI is disabled. Marcus On Mon, Apr 18, 2022 at 6:01 PM Amanda Chen via Towhee-bugs < tow...@li...> wrote: > Dear TOWHEE management team, > > Good afternoon, this is Amanda, a user of Towhee software (version > 8.2.3). > I encounter some issues while running the parallel jobs on a remote system > and hope to have some instructions from you. > > Currently, I compiled towhee (version 8.2.3) on a remote system via " ./configure > --enable-mpi". The software was able to be compiled without > error codes. > However, a job was ended up with the following error message while running > it: > "Warning: MPI not supported, parstyle JOBFARM disabled. > Doing nothing." > > I'm wondering if you have any suggestions on resolving this issue. Any > suggestions will be much appreciated. Thank you for your time and > assistance. > p.s. The attached files were run with n=16. (srun -n 16 > ~/towhee-8.2.3/Source/towhee -p jobfarm towhee_input ) > > Sincerely, > Amanda > > -- > Advanced Thermodynamics, Light-Matter-Interactions and Simulations Lab > Department of NanoEngineering > Email: aa...@en... > University of California - San Diego > _______________________________________________ > Towhee-bugs mailing list > Tow...@li... > https://lists.sourceforge.net/lists/listinfo/towhee-bugs > -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Amanda C. <aa...@en...> - 2022-04-18 22:08:49
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Dear TOWHEE management team, Good afternoon, this is Amanda, a user of Towhee software (version 8.2.3). I encounter some issues while running the parallel jobs on a remote system and hope to have some instructions from you. Currently, I compiled towhee (version 8.2.3) on a remote system via " ./configure --enable-mpi". The software was able to be compiled without error codes. However, a job was ended up with the following error message while running it: "Warning: MPI not supported, parstyle JOBFARM disabled. Doing nothing." I'm wondering if you have any suggestions on resolving this issue. Any suggestions will be much appreciated. Thank you for your time and assistance. p.s. The attached files were run with n=16. (srun -n 16 ~/towhee-8.2.3/Source/towhee -p jobfarm towhee_input ) Sincerely, Amanda -- Advanced Thermodynamics, Light-Matter-Interactions and Simulations Lab Department of NanoEngineering Email: aa...@en... University of California - San Diego |
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From: Marcus M. <me...@gm...> - 2021-06-03 18:34:43
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Howdy, Looks like this was also previously submitted as Bug 17. A fix was implemented in version 8.2.2 (released today). Marcus On Thu, Jun 3, 2021 at 9:16 AM Rosie Wood <ros...@gm...> wrote: > Hello, > > I am trying to compile Towhee-8.2.1 on my laptop (macbook pro, big sur) > and am getting a mismatch error when running the make towhee command. > > make towhee > *❯**❯**❯* > gfortran -DPACKAGE_NAME=\"towhee\" -DPACKAGE_TARNAME=\"towhee\" > -DPACKAGE_VERSION=\"8.2.1\" -DPACKAGE_STRING=\"towhee-8.2.1\" > -DPACKAGE_BUGREPORT=\"tow...@li...\" > -DPACKAGE_URL=\"\" -DPACKAGE=\"towhee\" -DVERSION=\"8.2.1\" > -DPACKAGE=\"towhee\" -DVERSION=\"8.2.1\" -DHAVE_STRSTR=1 -I. > -fno-second-underscore -g -O2 -c -o checkstruc.o checkstruc.F > *checkstruc.F:668:52:* > > 651 | call twh_bencoeff(GLB_GET,itemp,0,theta) > | 2 > ...... > 668 | call twh_bencoeff(GLB_GET,itemp,1,thetatwo) > | *1* > *Error:* Type mismatch between actual argument at *(1)* and actual > argument at (2) (INTEGER(4)/REAL(8)). > make: *** [checkstruc.o] Error 1 > (base) *-> [2]* > > Could you give me some advice as to how to fix this? > > Thanks in advance, > Rosie Wood > _______________________________________________ > Towhee-bugs mailing list > Tow...@li... > https://lists.sourceforge.net/lists/listinfo/towhee-bugs > -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com towhee.sourceforge.net |
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From: Rosie W. <ros...@gm...> - 2021-06-03 15:11:15
|
Hello,
I am trying to compile Towhee-8.2.1 on my laptop (macbook pro, big sur) and am getting a mismatch error when running the make towhee command.
make towhee ❯❯❯
gfortran -DPACKAGE_NAME=\"towhee\" -DPACKAGE_TARNAME=\"towhee\" -DPACKAGE_VERSION=\"8.2.1\" -DPACKAGE_STRING=\"towhee-8.2.1\" -DPACKAGE_BUGREPORT=\"tow...@li...\" -DPACKAGE_URL=\"\" -DPACKAGE=\"towhee\" -DVERSION=\"8.2.1\" -DPACKAGE=\"towhee\" -DVERSION=\"8.2.1\" -DHAVE_STRSTR=1 -I. -fno-second-underscore -g -O2 -c -o checkstruc.o checkstruc.F
checkstruc.F:668:52:
651 | call twh_bencoeff(GLB_GET,itemp,0,theta)
| 2
......
668 | call twh_bencoeff(GLB_GET,itemp,1,thetatwo)
| 1
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)).
make: *** [checkstruc.o] Error 1
(base) -> [2]
Could you give me some advice as to how to fix this?
Thanks in advance,
Rosie Wood |
|
From: Rashid K. <ras...@tu...> - 2017-06-30 12:43:21
|
Hi,
I am trying to build towhee 7.2.0 with a intel studio 2017 compiler.
Towhee does not compile at all. There are two bugs:
System:
Redhat Linux Based System
gcc 6.3.0
intel studio 2017
towhee-7.2.0
First:
./configure F77='ifort' CC='icc' CXX='icpc'
your configure script tests always if the test program works with the
gcc, no matter what compiler you provide. So you need to have a gcc
installed to run configure, even if the Makefile which is generated
clearly uses icc (icc -g -o towhee accumulateaverages.o ...). If
you don't have a gcc installed, it can find the icc but tells you, that
it can't compile with it and it is not working (even if it is). So far,
so annoying. I changed the $CC Variable by hand and made sure it realy
uses icc in the Makefile.
Second, Game Breaking Bug with some of your fortran code:
./configure F77='ifort' CC='icc' CXX='icpc'
ifort -DPACKAGE_NAME=\"towhee\" -DPACKAGE_TARNAME=\"towhee\"
-DPACKAGE_VERSION=\"7.2.0\" -DPACKAGE_STRING=\"towhee-7.2.0\"
-DPACKAGE_BUGREPORT=\"tow...@li...\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"towhee\" -DVERSION=\"7.2.0\"
-DHAVE_STRSTR=1 -I. -g -c -o ffding1986.o ffding1986.F
ifort -DPACKAGE_NAME=\"towhee\" -DPACKAGE_TARNAME=\"towhee\"
-DPACKAGE_VERSION=\"7.2.0\" -DPACKAGE_STRING=\"towhee-7.2.0\"
-DPACKAGE_BUGREPORT=\"tow...@li...\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"towhee\" -DVERSION=\"7.2.0\"
-DHAVE_STRSTR=1 -I. -g -c -o ffdreiding.o ffdreiding.F
ffdreiding.F(1208): error #5082: Syntax error, found END-OF-STATEMENT
when expecting one of: = .EQV. .NEQV. .XOR. .OR. .AND. .LT. < .LE. <=
.EQ. == .NE. /= .GT. > ...
call twh_torstyle(2001,type,TOR_STYLE_DREIDIN
---------------------------------------------------------------------^
ffdreiding.F(1208): error #6404: This name does not have a type, and
must have an explicit type. [TOR_STYLE_DREIDIN]
call twh_torstyle(2001,type,TOR_STYLE_DREIDIN
----------------------------------------------------^
compilation aborted for ffdreiding.F (code 1)
make[1]: *** [ffdreiding.o] Fehler 1
make[1]: Leaving directory `/root/rash/towhee/towhee-7.2.0/Source'
make: *** [all-recursive] Fehler 1
It works with gfortran but not with ifort which is stricter. We would
love to use the intel compiler to get a bit better performance. Btw. is
there a reason, why you compile with -O3 instead -O2? -O3 could provide
a speed boost with good compilers.
Kind regards
--
Rashid Kratou
M. Sc. Informatik
Gauß-IT-Zentrum
Technische Universität Braunschweig
0531 39163749
|
|
From: Jianying Hu <jx...@ca...> - 2015-04-22 19:40:00
|
Dear Dr. Martin, I am trying to create lammps data file under OPLS-AA force field usingTowhee 7.1.0. After running, it shows "invalid dihedral style 2, which has nothing similar in lammps". I tried other types 11 and 13, they also did not work. Compared with expression for dihedral in lammps using opls-aa, I found one term is missing in Towhee program. Could you help modify the expression for dihedral torsion or give me a suggestion to solve it? Thanks! Jane |
|
From: Nic K. <nk...@gm...> - 2013-11-19 20:32:16
|
Hello, I am trying to compile the program on a Mac OSX 10.9. If I simply configure the package without LDFLAGS=-lcc_dynamic, it works but runs into an error when I am compiling. However, when I configure with LDFLAGS=-lcc_dynamic, it fails with an "error: C compiler cannot create executables" message. I am not sure how to proceed. Thank you. -- Nicholas Kuon Department of Physics Colorado State University (720)877-1984 |
|
From: Wesley E. <Wes...@oi...> - 2013-04-23 11:12:02
|
Background: I am a systems programmer helping a user run towhee on RHEL6.
Occasionally (20-30% of the time), towhee would get hung in an apparent
infinite loop during the twh_mimage() routine here:
do while ( twh_cmp_gt(rxuij, hbx) )
rxuij = rxuij - hmvalue
Running the code in a debugger showed me that rxuij was sometimes really
large value (-3e100 or 3e100).
I eventually narrowed this down to the xcmi, ycmi, and zcmi variables being
used before they were initialized (these variables were allocated, but not
set to anything).
The following patch has made the problem disappear:
--- towhee-7.0.4/Source/globalinfo.c 2011-08-17 13:58:27.000000000 -0400
+++ towhee-7.0.4.modified/Source/globalinfo.c 2013-04-23 06:23:09.419902042
-0400
@@ -71,7 +71,14 @@
void *twh_allocateVector(size_t size, int M) {
void *x;
- if (!(x = malloc(size * M))) {
+
+
+ /*It appears that sometimes memory is used before being set.
+ twh_com(GLB_GET, ..., xcmi, ycmi, zcmi) in initconf.F appears
+ to be one such case. Towhee expects that memory will be zeroed before
use.
+ calloc() zeroes memory.
+ */
+ if (!(x = calloc(M,size))) {
fprintf(stderr, "Fatal memory allocation error\n");
exit(1);
}
@@ -111,8 +118,11 @@
exit(1);
}
+ /*Towhee expects that memory will be zeroed before use.
+ calloc() zeroes memory
+ */
for (i = 0; i < M; i++)
- if (!(x[i] = (void*) malloc(size * N))) {
+ if (!(x[i] = (void*) calloc(N,size))) {
fprintf(stderr, "Fatal memory allocation error\n");
exit(1);
}
This patch uses calloc to initialize memory to zero when it is first
allocated.
Wesley
--
Wesley Emeneker, Research Scientist
The Partnership for an Advanced Computing Environment
Georgia Institute of Technology
404.385.2303
Wes...@oi...
http://pace.gatech.edu
|
|
From: Marcus M. <me...@gm...> - 2013-04-22 14:27:31
|
It looks like you are attempting to make all of the routines using a parallel compiler. Right now the only software package that is set up for use with MPI is the main towhee one. Starting in the home directory of the Towhee package you should type something like the following ./configure --enable-mpi cd Source make towhee You will need something other than mpi to compile the utility routines or the forcefield routine. Marcus > MAKE ERROR with Intel-MPI: > > x86_64-k1om-linux-ld: warning: libintlc.so.5, needed by > /opt/intel/composer_xe_2013.0.079/compiler/lib/mic/libifport.so.5, not > found (try using -rpath or -rpath-link) > /usr/linux-k1om-4.7/linux-k1om/usr/lib64/crt1.o: In function `_start': > (.text+0x20): undefined reference to `main' > make[1]: *** [forcefield] Error 1 > make[1]: Leaving directory > > `/home/shraddha/APPLI/TOWHEE/native/Comp-XE-2013/IMPI-410018/towhee-7.0.4/Source' > make: *** [all-recursive] Error 1 > > Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com |
|
From: <shr...@cd...> - 2013-04-19 06:11:10
|
Dear User, I have successfully installed towhee with gnu-446 + MPICH2-141p1. I have also tried to install it with Intel-MPI. MAKE ERROR with Intel-MPI: x86_64-k1om-linux-ld: warning: libintlc.so.5, needed by /opt/intel/composer_xe_2013.0.079/compiler/lib/mic/libifport.so.5, not found (try using -rpath or -rpath-link) /usr/linux-k1om-4.7/linux-k1om/usr/lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' make[1]: *** [forcefield] Error 1 make[1]: Leaving directory `/home/shraddha/APPLI/TOWHEE/native/Comp-XE-2013/IMPI-410018/towhee-7.0.4/Source' make: *** [all-recursive] Error 1 Can you please help me in resolving this issue. Regards, Shraddha S.Desai Senior Technical Officer, HPC Solutions Group C-DAC R&D,Pune Website: www.cdac.in ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------------------------- |
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From: Marcus M. <me...@gm...> - 2013-03-29 15:37:18
|
So, I'm assuming that Intel-MPI means a parallel compiler so in that case you would need to turn on the parallel options in your configure script. Something like ./configure --enable-mpi should compile a parallel version of Towhee. Of course, the parallel version of Towhee is mainly just a job launcher, but hopefully this sorts out the issue you are having. Marcus On Thu, Feb 28, 2013 at 10:20 PM, <shr...@cd...> wrote: > Dear Sir, > I am trying to compile Towhee with Intel-MPI version 4.0.3.008 and > 4.1.0.018, but it is giving error me at last of installation process of > make. > > mpiicc -g -o forcefield arccos.o averages.o compare.o crossproduct.o > distance.o dotproduct.o ffackl2004.o ffalavi2005.o ffamber96.o ffaqvist.o > ffc19eef1.o ffc19sasa.o ffc27rigid.o ffcatlowfaux.o ffcharmm19.o > ffcharmm22.o ffcharmm22fe.o ffcharmm27.o ffcharmm27x.o ffcheck.o > ffclayff.o ffcompass.o ffcoon1987.o ffcreate.o ffcui1998.o ffcui2002.o > ffdacnisua.o ffdevel.o ffdick1994.o ffding1986.o ffdreiding.o ffdubb2004.o > ffdws2001.o ffelli2002.o ffepm.o ffgala1994.o ffgordon.o ffgromos43a1.o > fffris2003.o fffris2008.o ffhardsphere.o ffjaramillo.o ffkfvbvs.o > fflast1993.o fflgm.o ffljium.o ffmcy1976.o ffmend2003.o ffmgmstereo.o > ffmm2.o ffmmff94.o ffmorrow2002.o ffnerdv1.o ffnerdv2.o ffnerdv3.o > ffoplsaa.o ffoplsua.o ffopls1996.o ffopls2001.o ffpana1989.o ffpmf.o > ffpotter1997.o ffqmff_viii.o ffreadcharmmfile.o ffreadsetflfile.o > ffrichar1995.o ffshah2004.o ffshukla1987.o ffsks.o ffsmith1994.o > ffsmmkmain.o ffsmmknaip.o ffspce.o ffsquarewell.o ffstil1985.o ffsum2003.o > fftele1987.o fftip3p.o fftip4p.o fftip5p.o fftrappeeh.o fftrappeua.o > fftrappeuaf.o ffuff.o ffunlu2004.o ffvahid2010.o ffvega1992.o ffvink2001.o > ffwalt2001.o ffweiner1984.o ffweiner1986.o ffwielop1985.o getelement.o > getnbtype.o globalaccess.o globaldata.o initialize.o inverthmatrix.o > openfile.o readutils.o rwforcefield.o scaled_potential.o globalinfo.o > -L/share/apps/intelcs/impi/4.0.3.008/intel64/lib > -L/share/apps/intelcs/composer_xe_2011_sp1.6.233/compiler/lib/intel64 > -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6 > -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64 -L/lib/../lib64 > -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../.. > -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -ldl -lmpi_dbg -lmpigf -lmpigi > -lpthread -lrt -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lgcc_s > -lirc_s > /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In > function `_start': > (.text+0x20): undefined reference to `main' > make[1]: *** [forcefield] Error 1 > make[1]: Leaving directory > > `/home/shraddha/APPLI/TOWHEE/intel/Intel-12-1-0/IMPI-403008/towhee-7.0.4/Source' > make: *** [all-recursive] Error 1 > > Can you please provide me proper configure option to be used to compile > Towhee sucessfully with Intel-MPI. > > Regards, > Shraddha > Senior Technical Officer, HPC Solutions Group > C-DAC R&D,Pune > Website: www.cdac.in > > > > > ------------------------------------------------------------------------------------------------------------------------------- > > This e-mail is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. If you are not the > intended recipient, please contact the sender by reply e-mail and destroy > all copies and the original message. Any unauthorized review, use, > disclosure, dissemination, forwarding, printing or copying of this email > is strictly prohibited and appropriate legal action will be taken. > > ------------------------------------------------------------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------------ > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > _______________________________________________ > Towhee-bugs mailing list > Tow...@li... > https://lists.sourceforge.net/lists/listinfo/towhee-bugs > -- Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.photobirder.com |
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From: <shr...@cd...> - 2013-03-01 05:28:16
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Dear Sir, I am trying to compile Towhee with Intel-MPI version 4.0.3.008 and 4.1.0.018, but it is giving error me at last of installation process of make. mpiicc -g -o forcefield arccos.o averages.o compare.o crossproduct.o distance.o dotproduct.o ffackl2004.o ffalavi2005.o ffamber96.o ffaqvist.o ffc19eef1.o ffc19sasa.o ffc27rigid.o ffcatlowfaux.o ffcharmm19.o ffcharmm22.o ffcharmm22fe.o ffcharmm27.o ffcharmm27x.o ffcheck.o ffclayff.o ffcompass.o ffcoon1987.o ffcreate.o ffcui1998.o ffcui2002.o ffdacnisua.o ffdevel.o ffdick1994.o ffding1986.o ffdreiding.o ffdubb2004.o ffdws2001.o ffelli2002.o ffepm.o ffgala1994.o ffgordon.o ffgromos43a1.o fffris2003.o fffris2008.o ffhardsphere.o ffjaramillo.o ffkfvbvs.o fflast1993.o fflgm.o ffljium.o ffmcy1976.o ffmend2003.o ffmgmstereo.o ffmm2.o ffmmff94.o ffmorrow2002.o ffnerdv1.o ffnerdv2.o ffnerdv3.o ffoplsaa.o ffoplsua.o ffopls1996.o ffopls2001.o ffpana1989.o ffpmf.o ffpotter1997.o ffqmff_viii.o ffreadcharmmfile.o ffreadsetflfile.o ffrichar1995.o ffshah2004.o ffshukla1987.o ffsks.o ffsmith1994.o ffsmmkmain.o ffsmmknaip.o ffspce.o ffsquarewell.o ffstil1985.o ffsum2003.o fftele1987.o fftip3p.o fftip4p.o fftip5p.o fftrappeeh.o fftrappeua.o fftrappeuaf.o ffuff.o ffunlu2004.o ffvahid2010.o ffvega1992.o ffvink2001.o ffwalt2001.o ffweiner1984.o ffweiner1986.o ffwielop1985.o getelement.o getnbtype.o globalaccess.o globaldata.o initialize.o inverthmatrix.o openfile.o readutils.o rwforcefield.o scaled_potential.o globalinfo.o -L/share/apps/intelcs/impi/4.0.3.008/intel64/lib -L/share/apps/intelcs/composer_xe_2011_sp1.6.233/compiler/lib/intel64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../.. -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -ldl -lmpi_dbg -lmpigf -lmpigi -lpthread -lrt -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lgcc_s -lirc_s /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' make[1]: *** [forcefield] Error 1 make[1]: Leaving directory `/home/shraddha/APPLI/TOWHEE/intel/Intel-12-1-0/IMPI-403008/towhee-7.0.4/Source' make: *** [all-recursive] Error 1 Can you please provide me proper configure option to be used to compile Towhee sucessfully with Intel-MPI. Regards, Shraddha Senior Technical Officer, HPC Solutions Group C-DAC R&D,Pune Website: www.cdac.in ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. ------------------------------------------------------------------------------------------------------------------------------- |
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From: Marcus M. <mar...@us...> - 2011-08-18 14:45:25
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On Mon, Aug 15, 2011 at 9:10 PM, Fatemesadat Emami <fe...@zi...> wrote: > I was wondering of you found out the bug in Energy baising that I was > involved with. Could you please advise me if there is anything in my input > file that causes this problem? Looks like that was an out of bounds array error related to the atom not being in the central simulation box. Fixed that up with version 7.01. Let me know if that solves your problem. Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.usefulbias.com www.photobirder.com |
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From: Marcus M. <mar...@us...> - 2011-08-16 16:00:46
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On Mon, Aug 15, 2011 at 9:10 PM, Fatemesadat Emami <fe...@zi...> wrote: > I was wondering of you found out the bug in Energy baising that I was > involved with. Could you please advise me if there is anything in my input > file that causes this problem? Yes I have found the bug. There was a change I was not aware of in the rwconf file starting with version 6.2.16 and persisting for the rest of the 6.2.x run that makes it incompatible with the previous 6 style towhee_initial files (and will in fact be incompatible with the fixed versions starting with 7.0.0). The fix has required me to reveal the Random number generator work that has been going on in Towhee and that means I need to test it quite a bit first as changing random number generators makes it much trickier to validate that things are still working. Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.usefulbias.com www.photobirder.com |
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From: Marcus M. <mar...@us...> - 2011-08-06 04:48:54
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On Thu, Jun 2, 2011 at 2:08 PM, Oloriegbe, Suleiman <olo...@mi...> wrote: > To those who may be using LAMMPS and towhee and needs to convert LAMMPS setfl file to towhee forcefiled format. There is a bug you need to clean up before getting the correct forcefield file for towhee. > > In the file ffreadsetflfile.F subroutine ffreadsetflfile, some arguments of the to the subroutine twh_table_pair were not properly set, making forcefield to print the wrong bond distances for the embedding fundtion. Going back deep into the old CVS archives it appears this mistake was introduced back in 9-2008 during one of the data structure rewrites, and then fixed incorrectly later in 10-2008. > The original code look like this from line 148 to line 175. > call twh_table_pair(GLB_SET,1,cross,ir,dtemp) ------> Correction call twh_table_pair(GLB_GET,1,cross,ir,dtemp) I agree with this change and have incorporated it into the next release (6.2.18). Should be out this week. > dvalue = CON_EVTOK*tableread(ir) / dtemp > call twh_table_pair(GLB_SET,2,cross,ir-1,dvalue) > c --- shift the value down one slot for the first index > call twh_table_pair(GLB_SET,1,cross,ir-1,dtemp) ------> Correction call twh_table_pair(GLB_GET,1,cross,ir-1,dtemp) I believe this one is correct as a GLB_SET when looking back at the older files. Welcome to the list of 2011 code contributors. thanks, Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 land (505) 286 4457 cell (505) 363 3179 www.usefulbias.com www.photobirder.com |
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From: Oloriegbe, S. <olo...@mi...> - 2011-06-02 20:08:28
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To those who may be using LAMMPS and towhee and needs to convert LAMMPS setfl file to towhee forcefiled format. There is a bug you need to clean up before getting the correct forcefield file for towhee.
In the file ffreadsetflfile.F subroutine ffreadsetflfile, some arguments of the to the subroutine twh_table_pair were not properly set, making forcefield to print the wrong bond distances for the embedding fundtion.
The original code look like this from line 148 to line 175.
do itype = 1,nbtype
do jtype= 1,itype
cross = twh_getnbtype(itype,jtype)
read(10,9902) (tableread(ir),ir=1,nr)
c --- need to convert this by dividing out the distance
c --- this is not valid for the first point, which we are
c --- going to remove
do ir = 2,nr
c --- set the second index of table_pair
call twh_table_pair(GLB_SET,1,cross,ir,dtemp) ------> Correction call twh_table_pair(GLB_GET,1,cross,ir,dtemp)
dvalue = CON_EVTOK*tableread(ir) / dtemp
call twh_table_pair(GLB_SET,2,cross,ir-1,dvalue)
c --- shift the value down one slot for the first index
call twh_table_pair(GLB_SET,1,cross,ir-1,dtemp) ------> Correction call twh_table_pair(GLB_GET,1,cross,ir-1,dtemp)
if ( itype .eq. 1 .and. jtype .eq. 1 ) then
write(12,*) dtemp,dvalue/CON_EVTOK
elseif ( itype .eq. 2 .and. jtype .eq. 1 ) then
write(13,*) dtemp,dvalue/CON_EVTOK
else
write(14,*) dtemp,dvalue/CON_EVTOK
endif
enddo
c --- reduce table_npair by 1
call twh_table_npair(GLB_GET,cross,ipair)
ipair = ipair - 1
call twh_table_npair(GLB_SET,cross,ipair)
enddo
enddo
The correction to this is to set the argument of twh_table_pair correctly as shown above (with arrows) and recompile forcefield.
Suleiman.
________________________________________
From: Oloriegbe, Suleiman
Sent: Friday, May 27, 2011 11:07 AM
To: mar...@us...
Cc: tow...@li...
Subject: Incorect Setfl file from towhee forcefield
Hello,
Please could anyone help me figure out why towhee forcefiled routine ffreadsetflfile.F is printing out incorrect distances after converting from setfl EAM file to tohwee_ff_* file. I check the code and the read format is
***** ignore line
***** ignore line
***** ignore line
number_of_atom_type
nrho, drho, nr, dr, rcutall
atomic_number atomic_mass
----- from here down it reads the data files for F(rho), V(r) and rho(r)
The current setfl files looks like this. Even after changing my setfl to conform to towhee read input, I still have alll the bond lengths coming out as the same ,in fact it is printing the atomic mass of the atoms, instead of incremental bond distance from zero to the cutoff distance.
I don't want to modify and recompile the forcefield code if there is no need for it, but towhee read format doesn't seems to conform to the current version of the EAM setfl files. Any help would be appreciated.
Suleiman.
___________________________________________________________________________________________________________________
#Potential generated by PoCo (FE) on 12/05/97 at 10.59.13
#Traj. : 2 C|2 C|2 C|2 C|1 C|1 C|sig|sig|sig|sig|Al |Al |Al |the|the|thet
#Aluminum (Z= 13)Copper (Z= 29)
2 Al Cu
500 0.1202404809619238E-01 500 0.1139742685370741E-01 0.5687316000000000E+01
13 26.982 4.0320 FCC
0.0000000000000000E+00 -0.1955308516385325E+00 -0.3709428419507702E+00 -0.5273976809256672E+00 -0.6660570785521777E+00
-0.7880827448192556E+00 -0.8946363897158549E+00 -0.9868796963197619E+00 -0.1065974238118134E+01 -0.1133082803697506E+01
-0.1189483618538492E+01 -0.1236684804602630E+01 -0.1276221658909149E+01 -0.1309629478477275E+01 -0.1338443547804706E+01
-0.1364199170700185E+01 -0.1388431699193629E+01 -0.1412676430304264E+01 -0.1438433576273574E+01 -0.1466328323264702E+01
-0.1496071075447100E+01 -0.1527329201951728E+01 -0.1559770061755740E+01 -0.1593061001677873E+01 -0.1626869383585991E+01
------------------------------------------- file truncated -------------------------------------------------
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From: Oloriegbe, S. <olo...@mi...> - 2011-05-27 16:07:49
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Hello,
Please could anyone help me figure out why towhee forcefiled routine ffreadsetflfile.F is printing out incorrect distances after converting from setfl EAM file to tohwee_ff_* file. I check the code and the read format is
***** ignore line
***** ignore line
***** ignore line
number_of_atom_type
nrho, drho, nr, dr, rcutall
atomic_number atomic_mass
----- from here down it reads the data files for F(rho), V(r) and rho(r)
The current setfl files looks like this. Even after changing my setfl to conform to towhee read input, I still have alll the bond lengths coming out as the same ,in fact it is printing the atomic mass of the atoms, instead of incremental bond distance from zero to the cutoff distance.
I don't want to modify and recompile the forcefield code if there is no need for it, but towhee read format doesn't seems to conform to the current version of the EAM setfl files. Any help would be appreciated.
Suleiman.
___________________________________________________________________________________________________________________
#Potential generated by PoCo (FE) on 12/05/97 at 10.59.13
#Traj. : 2 C|2 C|2 C|2 C|1 C|1 C|sig|sig|sig|sig|Al |Al |Al |the|the|thet
#Aluminum (Z= 13)Copper (Z= 29)
2 Al Cu
500 0.1202404809619238E-01 500 0.1139742685370741E-01 0.5687316000000000E+01
13 26.982 4.0320 FCC
0.0000000000000000E+00 -0.1955308516385325E+00 -0.3709428419507702E+00 -0.5273976809256672E+00 -0.6660570785521777E+00
-0.7880827448192556E+00 -0.8946363897158549E+00 -0.9868796963197619E+00 -0.1065974238118134E+01 -0.1133082803697506E+01
-0.1189483618538492E+01 -0.1236684804602630E+01 -0.1276221658909149E+01 -0.1309629478477275E+01 -0.1338443547804706E+01
-0.1364199170700185E+01 -0.1388431699193629E+01 -0.1412676430304264E+01 -0.1438433576273574E+01 -0.1466328323264702E+01
-0.1496071075447100E+01 -0.1527329201951728E+01 -0.1559770061755740E+01 -0.1593061001677873E+01 -0.1626869383585991E+01
------------------------------------------- file truncated -------------------------------------------------
|
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From: Marcus M. <mar...@us...> - 2010-05-19 23:31:32
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On Tue, Mar 2, 2010 at 6:09 AM, Eva G. Noya <eva...@iq...> wrote: > I send you attached the towhee_input files that I used to learn how to > use the towhee_map. The first one (towhee_input) is taken directly form > the Examples/Energy_bias directory and the second one > (towhee_input.read) is a modification of the first one, following the > manual of towhee, to read the towhee_map previously created. > > As I said, it is while reading the towhee_map when the program gives a > "Segmentation fault". Version 6.2.9 is now available and it should have addressed this error. Thank you for your bug report. Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 ph. (505) 286-4457 fax (505) 286-0987 www.usefulbias.com www.photobirder.com |
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From: Marcus M. <mar...@us...> - 2010-05-19 22:22:12
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On Thu, Nov 12, 2009 at 12:27 PM, swapnil chandratre <smc...@uh...> wrote: > I am trying to install the software Towhee . I am trying to compile it on > Windows O.S. using cygwin. I am following the instructions and according to > them, when I enter ./configure. It gives me the following errors. > ./configure: line 13: $'\r' : command not found > ./configure: line 21: syntax error near expected token 'elif' > ./configure: line 21: elif test -n "$<BASH_VERSION+set>" && <set -o posix> > > /de'/null 2>&1; then > Can u tell what steps I should take to get the errors removed. If you are still having problems with the current version of the code please let me know. I'm afraid that at the moment I do not have a windows machine set up to test upon, but if this is still and issue I'll track down a machine to try to resolve it. thanks, Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 ph. (505) 286-4457 fax (505) 286-0987 www.usefulbias.com www.photobirder.com |
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From: Marcus M. <mar...@us...> - 2010-05-18 22:09:41
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On Sun, Apr 11, 2010 at 10:30 PM, varun gopal <var...@gm...> wrote: > I have downloaded the tar file for the Towhee software. I have unzipped > it. Is the software exclusively for linux??? How can i get the windows > version??? Please help me out. This is described in the Towhee code manual. http://towhee.sourceforge.net/code/code_manual.html To sum up, it has been run on many platforms, but requires a Unix-style shell for compilation. Cygwin is the suggested method on Windows and a link to that software is provided on the manual page listed above. Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 ph. (505) 286-4457 www.usefulbias.com www.photobirder.com |
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From: Marcus M. <mar...@us...> - 2010-05-18 22:07:00
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On Tue, Apr 13, 2010 at 1:00 PM, Erik Santiso <esa...@mi...> wrote: > I'm trying to make towhee in a late 2009 MacBook Pro running Mac OS X > 10.6. It all goes well until I reach the linking stage, then I get the > following error: > > ld: duplicate symbol _main in towhee.o and allocate.o > > which is odd since I didn't find any main() function in allocate.F... > > Any idea what may be causing this? I'm using gcc and gfortran. Let me > know if you need any more details. Thanks! That is a very strange error. However, there was a duplicate return and end statement in allocate.F that was causing some other problems and could be related to your issue. Version 6.2.8 has resolved that problem and it is possible that it has also fixed your issue as well so give it a try at your convenience and let me know if the problem still exists. thanks, Marcus -- Marcus G. Martin Director, Useful Bias Incorporated 88 Martinez Road Edgewood NM 87015-8222 ph. (505) 286-4457 www.usefulbias.com www.photobirder.com |
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From: Eva G. N. <eva...@iq...> - 2010-04-28 15:16:41
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Dear Prof Marcus, I was wondering if you could find the origin of the bug on reading the towhee map I ask about in the forum. I would be very grateful if you could report me on any news on this topic. Thank you very much. Yours sincerely Eva G Noya |
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From: Erik S. <esantiso@MIT.EDU> - 2010-04-13 19:01:03
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Hi, I'm trying to make towhee in a late 2009 MacBook Pro running Mac OS X 10.6. It all goes well until I reach the linking stage, then I get the following error: ld: duplicate symbol _main in towhee.o and allocate.o which is odd since I didn't find any main() function in allocate.F... Any idea what may be causing this? I'm using gcc and gfortran. Let me know if you need any more details. Thanks! Best, Erik Santiso. |
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From: varun g. <var...@gm...> - 2010-04-12 04:30:54
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Dear sir,
I have downloaded the tar file for the Towhee software. I have unzipped
it. Is the software exclusively for linux??? How can i get the windows
version??? Please help me out.
Regards
--
Varun Gopal.K
Biomedical Engineering
Dept of Electronics and Communication Engineering
Amrita School of Engineering
Amrita Vishwa Vidyapeetham
Coimbatore
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From: Eva G. N. <eva...@iq...> - 2010-03-02 13:27:03
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Dear Prof. Martin, I send you attached the towhee_input files that I used to learn how to use the towhee_map. The first one (towhee_input) is taken directly form the Examples/Energy_bias directory and the second one (towhee_input.read) is a modification of the first one, following the manual of towhee, to read the towhee_map previously created. As I said, it is while reading the towhee_map when the program gives a "Segmentation fault". Thank you very much in advance for your help Eva G Noya |
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