Re: [gmx-users] Problem using MPIRUN MDRUN
fpri...@nimr.mrc.ac.uk wrote: I did not stop the simulation manually and it did not give a segmentation fault message, but something else that I have never seen before (and actually, I am still not understanding the error message). Now I'm running the dynamics on my machine, instead of running it on the cluster, and there are no problems at all. This means that the problem is not related to my protein or to the parameters of the dynamic, but it must be somewhere else in the mpirun command line or something like that. OK, so there's probably some problem with file system availability on the cluster, and/or returning output files to the user. We can't help you there. This sort of detail and differential diagnosis would have been a good thing to say the first time you described your problem. See the final link here - http://wiki.gromacs.org/index.php/Support grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_s -s file.tpr -o file.trr -c file.gro -np 32 This looks like asking for trouble, if _s and _d are your suffixes for single and double. Don't mix them. If you've erroneously retyped them, then that's not helpful information for us. Computers are literal, and we can only help you work out what you've told it wrongly if you tell us the same thing - so write a script and/or copy-paste things so that you are reproducible. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problem using MPIRUN MDRUN
Dear users, I'm trying to run gromacs v.3.3.3. on a cluster of 4 machines with 8 CPUs each. I've checked the mailing list and the manual in order to find the correct way to write the command line and I've found that the commands listed below are supposed to be correct and to work. grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file_md.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_d -s file_md.tpr -o file_md.trr -c file_md.gro -np 32 The dynamics starts, but after few minutes it crushes and I've got this message of error: One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 24320 failed on node n0 (195.195.124.134) with exit status 1. Does anyone can help me to sort out this problem?Does anyone know what I'm doing wrong? Thanks a lot, Filippo ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problem using MPIRUN MDRUN
Hi Filippo, Do you have checked your trajectory ( *.trr or *.xtc) and *.log ? You system may have 'exploded'... Osmair Date: Fri, 13 Feb 2009 13:27:09 + From: fpri...@nimr.mrc.ac.uk To: gmx-users@gromacs.org Subject: [gmx-users] Problem using MPIRUN MDRUN Dear users, I'm trying to run gromacs v.3.3.3. on a cluster of 4 machines with 8 CPUs each. I've checked the mailing list and the manual in order to find the correct way to write the command line and I've found that the commands listed below are supposed to be correct and to work. grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file_md.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_d -s file_md.tpr -o file_md.trr -c file_md.gro -np 32 The dynamics starts, but after few minutes it crushes and I've got this message of error: One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a return 0 or exit(0) in your C code before exiting the application. PID 24320 failed on node n0 (195.195.124.134) with exit status 1. Does anyone can help me to sort out this problem?Does anyone know what I'm doing wrong? Thanks a lot, Filippo ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ Windows Live Messenger. O melhor em multitarefa. http://www.microsoft.com/windows/windowslive/products/messenger.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problem using MPIRUN MDRUN
Thanks a lot, I'll check stderr and stdout, because I think that the log file is correct (it looks like a normal dynamic that has been manually interrupted). The system is not exploded cause it does not generate the gro file and step files. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] Problem using MPIRUN MDRUN
fpri...@nimr.mrc.ac.uk wrote: Thanks a lot, I'll check stderr and stdout, because I think that the log file is correct (it looks like a normal dynamic that has been manually interrupted). If you've manually interrupted the simulation, then you cannot expect the buffered I/O to be correctly formed. The system is not exploded cause it does not generate the gro file and step files. If there's no final coordinate file (.gro by default), then the simulation did not complete correctly. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] problem with mpirun
Hi, Gromacs users, This command grompp_ompi -np 6 -f pr_10_200.mdp -c after_em_newton_1000.gro -p all.top -o pr_10_100.tpr -po mdrun_pr_10_100.mdp run normally. But when i run the next command mpirun -np 6 mdrun_ompi -s pr_10_100.tpr -c after_pr_10_100.gro -o after_pr_10_100.trr -e after_pr_10_100.edr -g after_pr_10_100.log -v. It gave out as follows: Wrote pdb files with previous and current coordinates step 0 [node1:13598] *** Process received signal *** [node1:13598] Signal: Segmentation fault (11) [node1:13598] Signal code: Address not mapped (1) [node1:13598] Failing at address: 0x2cc3f38 [node1:13600] *** Process received signal *** [node1:13600] Signal: Segmentation fault (11) [node1:13600] Signal code: Address not mapped (1) [node1:13600] Failing at address: 0x6063518 [node1:13602] *** Process received signal *** [node1:13602] Signal: Segmentation fault (11) [node1:13602] Signal code: Address not mapped (1) [node1:13602] Failing at address: 0xc6519968 [node1:13599] *** Process received signal *** [node1:13599] Signal: Segmentation fault (11) [node1:13599] Signal code: Address not mapped (1) [node1:13599] Failing at address: 0x55dabc8 [node1:13601] *** Process received signal *** [node1:13601] Signal: Segmentation fault (11) [node1:13601] Signal code: Address not mapped (1) [node1:13601] Failing at address: 0x21ae2148 [node1:13598] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13598] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13598] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13598] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13598] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13598] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13598] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13598] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13598] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13598] [ 9] mdrun_ompi [0x412e8a] [node1:13598] *** End of error message *** [node1:13600] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13600] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13600] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13600] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13600] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13600] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13600] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13600] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13600] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13600] [ 9] mdrun_ompi [0x412e8a] [node1:13600] *** End of error message *** [node1:13602] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13602] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13602] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13602] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13602] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13602] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13602] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13602] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13602] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13602] [ 9] mdrun_ompi [0x412e8a] [node1:13602] *** End of error message *** [node1:13599] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13599] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13599] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13599] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13599] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13599] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13599] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13599] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13599] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13599] [ 9] mdrun_ompi [0x412e8a] [node1:13599] *** End of error message *** [node1:13601] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13601] [ 1] mdrun_ompi(inl3120+0x4a7) [0x525bb7] [node1:13601] [ 2] mdrun_ompi(do_fnbf+0xe96) [0x4a3c46] [node1:13601] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13601] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13601] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13601] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc] [node1:13601] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd] [node1:13601] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x307851c3fb] [node1:13601] [ 9] mdrun_ompi [0x412e8a] [node1:13601] *** End of error message *** [node1:13603] *** Process received signal *** [node1:13603] Signal: Segmentation fault (11) [node1:13603] Signal code: Address not mapped (1) [node1:13603] Failing at address: 0x2bb7c08 [node1:13603] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0] [node1:13603] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58] [node1:13603] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97] [node1:13603] [ 3] mdrun_ompi(force+0x120) [0x4432f0] [node1:13603] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb] [node1:13603] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf] [node1:13603] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]
