Re: Re: [gmx-users] mdrun mpi segmentation fault in high load situation
I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing what condition led to the problem. Mark So the only difference is the number of cores I am using. I used -dd but then my system consists only of 4 or slightly more domains which gives me almost no advantage over -pd. The minimum size of a domain is connected to the largest bond length which in my case is half of the box size or more. I will post my .log file but it will probably be next year. So merry christmas and a jolly time. André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] mdrun mpi segmentation fault in high load situation
Dear Gromacs Enthusiasts. I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster. Problem: This runs fine: mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr This produces a segmentation fault: mpiexec -np 128 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr So the only difference is the number of cores I am using. mdrun_mpi was compiled using the intel compiler 11.1.072 with my own fftw3 installation. While configuring and make mdrun / make install-mdrun no errors came up. Is there some issue with threading or mpi? If someone has a clue please give me a hint. integrator = md dt = 0.004 nsteps = 2500 nstxout = 0 nstvout = 0 nstlog = 25 nstenergy = 25 nstxtcout = 12500 xtc_grps = protein energygrps = protein non-protein nstlist = 2 ns_type = grid rlist= 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 rvdw = 0.9 pbc = xyz periodic_molecules = yes tcoupl = nose-hoover nsttcouple = 1 tc-grps = protein non-protein tau_t= 0.1 0.1 ref_t= 310 310 Pcoupl = no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds Error: Getting Loaded... Reading file full031K_mdrun_ions.tpr, VERSION 4.5.3 (single precision) Loaded with Money NOTE: The load imbalance in PME FFT and solve is 48%. For optimal PME load balancing PME grid_x (144) and grid_y (144) should be divisible by #PME_nodes_x (128) and PME grid_y (144) and grid_z (144) should be divisible by #PME_nodes_y (1) Step 0, time 0 (ps) PSIlogger: Child with rank 82 exited on signal 11: Segmentation fault PSIlogger: Child with rank 79 exited on signal 11: Segmentation fault PSIlogger: Child with rank 2 exited on signal 11: Segmentation fault PSIlogger: Child with rank 1 exited on signal 11: Segmentation fault PSIlogger: Child with rank 100 exited on signal 11: Segmentation fault PSIlogger: Child with rank 97 exited on signal 11: Segmentation fault PSIlogger: Child with rank 98 exited on signal 11: Segmentation fault PSIlogger: Child with rank 96 exited on signal 6: Aborted ... Ps, for now I don't care about the imbalanced PME load unless it's independent from my problem. Cheers André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
AW: [gmx-users] mdrun mpi segmentation fault in high load situation
On 23/12/2010 10:01 PM, Wojtyczka, André wrote: Dear Gromacs Enthusiasts. I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster. Problem: This runs fine: mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr This produces a segmentation fault: mpiexec -np 128 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr Unless you know you need it, don't use -pd. DD will be faster and is probably better bug-tested too. Mark Hi Mark thanks for the push into that direction, but I am in the unfortunate situation where I really need -pd because I have long bonds which is the reason why my large system is decomposable just into a little number of domains. So the only difference is the number of cores I am using. mdrun_mpi was compiled using the intel compiler 11.1.072 with my own fftw3 installation. While configuring and make mdrun / make install-mdrun no errors came up. Is there some issue with threading or mpi? If someone has a clue please give me a hint. integrator = md dt = 0.004 nsteps = 2500 nstxout = 0 nstvout = 0 nstlog = 25 nstenergy = 25 nstxtcout = 12500 xtc_grps = protein energygrps = protein non-protein nstlist = 2 ns_type = grid rlist= 0.9 coulombtype = PME rcoulomb = 0.9 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-5 rvdw = 0.9 pbc = xyz periodic_molecules = yes tcoupl = nose-hoover nsttcouple = 1 tc-grps = protein non-protein tau_t= 0.1 0.1 ref_t= 310 310 Pcoupl = no gen_vel = yes gen_temp = 310 gen_seed = 173529 constraints = all-bonds Error: Getting Loaded... Reading file full031K_mdrun_ions.tpr, VERSION 4.5.3 (single precision) Loaded with Money NOTE: The load imbalance in PME FFT and solve is 48%. For optimal PME load balancing PME grid_x (144) and grid_y (144) should be divisible by #PME_nodes_x (128) and PME grid_y (144) and grid_z (144) should be divisible by #PME_nodes_y (1) Step 0, time 0 (ps) PSIlogger: Child with rank 82 exited on signal 11: Segmentation fault PSIlogger: Child with rank 79 exited on signal 11: Segmentation fault PSIlogger: Child with rank 2 exited on signal 11: Segmentation fault PSIlogger: Child with rank 1 exited on signal 11: Segmentation fault PSIlogger: Child with rank 100 exited on signal 11: Segmentation fault PSIlogger: Child with rank 97 exited on signal 11: Segmentation fault PSIlogger: Child with rank 98 exited on signal 11: Segmentation fault PSIlogger: Child with rank 96 exited on signal 6: Aborted ... Ps, for now I don't care about the imbalanced PME load unless it's independent from my problem. Cheers André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] pdb2gmx -merge non interactive
Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] pdb2gmx -merge non interactive
Hi, thanks for your answer! I think this only refers to the -ff force field selection. I tried several scripting solutions to pass y to the pdb2gmx questions whether to do the merging or not. Maybe my wires are just crossed but i did not find any hint to get rid of this questions. Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all the chains are included into the .top-file. It is then not possible for me (in an easy way) to include my restraints into the same .top file because that would lead to a wrong order. To cut a long story short... I need -merge in a script and there i don't need interactivity at all ;) Thx for your time André Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] pdb2gmx -merge non interactive
Hmm... although it is necessary to run it through on the command line once to see what the order of arguments should be ...exactly is the main problem as I don't know all the time how many chains are in the files I'm processing. Pdb2gmx asks for every chain included in your files. Though I can assume 8 chains in 99% of the files, I wanted to know if there may be a switch included in pdb2gmx like -ff. Maybe I prescan my files to get the amount of chains and then pass that value to my pdb2gmx script. Anyway, thanks for your answer, I appreciate it! What exactly did you try? Something like this? pdb2gmx -f a.gro EOF 5 y EOF I have not done -merge myself, but I often pass in multiple 'command-line' arguments in a scripts, although it is necessary to run it through on the command line once to see what the order of arguments should be. I could be the one whose wrong as I have never done -merge, but then again I have never had a problem automating any of the gromacs tools and I don't see why this one should be any different. -- original message -- Hi, thanks for your answer! I think this only refers to the -ff force field selection. I tried several scripting solutions to pass y to the pdb2gmx questions whether to do the merging or not. Maybe my wires are just crossed but i did not find any hint to get rid of this questions. Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- -- 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 Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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
