Re: [gmx-users] Making Commands Non-Interactive
I once wrote some lines of adventurous C-code to get an observable of choice from g_energy without typing the observable index myself... this may also be applied to trjconv I think. string genergyCall = g_energy -f + myEdrFile + -o + myXvgFile + /dev/null; string energyObs = 8; // e.g. potential FILE *fpipe; fpipe = popen(genergyCall.c_str(),w); fwrite(energyObs.data(), 1, 1, fpipe); // tell g_energy what to write pclose(fpipe); If you want to pipe more stuff to the program you are calling, the buffer size of fwrite has to be increased. So you might put this into a minimal C-program and start that non-interactive with qsub or whatever. Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. Thank you again for your help ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alexander Bujotzek Zuse Institute Berlin Computational Drug Design Group Tel. : +49 30 84185-234 eMail: bujot...@zib.de ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
Have you tried: echo 0 zero trjconv bla bla bla zero You could put more arguments in the file, for example - use the -center option, and then echo another 0 into the zero file. --Omer. On Sun, Oct 4, 2009 at 18:22, ABEL Stephane 175950 stephane.a...@cea.frwrote: Dear GMX Users, echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
Cool. You can also write a python script to generate and execute your C-code, which you then wrap with Java to be executed through Ruby... etc. Erik, can you maybe give the assembly solution? :p Tsjerk On Mon, Oct 5, 2009 at 10:15 AM, Alexander Bujotzek bujot...@zib.de wrote: I once wrote some lines of adventurous C-code to get an observable of choice from g_energy without typing the observable index myself... this may also be applied to trjconv I think. string genergyCall = g_energy -f + myEdrFile + -o + myXvgFile + /dev/null; string energyObs = 8; // e.g. potential FILE *fpipe; fpipe = popen(genergyCall.c_str(),w); fwrite(energyObs.data(), 1, 1, fpipe); // tell g_energy what to write pclose(fpipe); If you want to pipe more stuff to the program you are calling, the buffer size of fwrite has to be increased. So you might put this into a minimal C-program and start that non-interactive with qsub or whatever. Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. Thank you again for your help ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Alexander Bujotzek Zuse Institute Berlin Computational Drug Design Group Tel. : +49 30 84185-234 eMail: bujot...@zib.de ___ gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Making Commands Non-Interactive
Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. Thank you again for your help winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
ABEL Stephane 175950 wrote: Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. I routinely use a text file for scripted jobs. Odd that yours isn't working. Is it just that the command still exits before finishing? In any case, you can make an .ndx file with only an entry for [System]. When presented with one choice, trjconv has to choose it. -Justin Thank you again for your help ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
Hi, Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... Well, the most interesting part in that regard is probably the I/O. But that's the hardest bit to parallelize. How to pass the choice 0 in the script Just as you would on the command line...: #!/bin/bash echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact Didn't you try? There may be a problem, as the script is probably executed in the home directory. So you need to add a line changing to the right directory; just as you have done in interactive mode. Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Making Commands Non-Interactive
Justin A. Lemkul wrote: ABEL Stephane 175950 wrote: Dear GMX Users, I ask this question in this mailing list since probably a user have already encountered this similar problem. I would like to post-process my trajectory with the command trjconv (in mpi mode). For this I use the following shell command: Is trjconv parallelizable? This is nowhere in the documentation, but if it is, that would be very interesting... No. There are no 4.0.x tools that use MPI. Hence the wiki advice not to bother compiling tools in parallel, and the old website installation guide directing the use of only make mdrun after reconfiguring with --enable-mpi. echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0 (System) It works but since my simulations is very long ( 300ns) the command stops in the middle of the trajectory before to finish the process ( i suspect a time limit for using the interactive mode). So i would like to use a script to do the task. How to pass the choice 0 in the script (i.e. equivalent to the echo 0). I use a bash shell and the command qsub to launch a mpi job. I have tried to adapt the examples available in the GMX website with a text file as suggested by the author in GROMACS site with no success. I routinely use a text file for scripted jobs. Odd that yours isn't working. Is it just that the command still exits before finishing? In any case, you can make an .ndx file with only an entry for [System]. When presented with one choice, trjconv has to choose it. Recompiling without mpi, and doing non-mdrun operations on your local machine / cluster login node is usually the approach simplest to use. Yes, it's more work when you configure and compile, but you only do that every once in a while right? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
