Re: [gmx-users] Reducing Standard Error output
Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the lincs warnings will exist and be reported in at least the .log file regardless of the verbosity. Initialy we had this minimized using these parameters define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes (I borrowed it from acpypi tutorial) Apparently this does not minimize the system quite enough. So I am now reducing emtol to 10 and nsteps to 10,000. I will see if I get convergence. Are there other recomendations regarding minimization? Should we consider constraining the molecule? One idea is 1st minimization with constraints 2nd minimization without constraints 3rd md with constraints 4th md without constraints -- 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] Reducing Standard Error output
Jack Shultz wrote: Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the lincs warnings will exist and be reported in at least the .log file regardless of the verbosity. Initialy we had this minimized using these parameters define = -DFLEXIBLE integrator = cg ; steep nsteps = 200 constraints = none emtol = 1000 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 coulombtype = PME ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes (I borrowed it from acpypi tutorial) Apparently this does not minimize the system quite enough. So I am now reducing emtol to 10 and nsteps to 10,000. I will see if I get convergence. Are there other recomendations regarding minimization? Should we consider constraining the molecule? One idea is 1st minimization with constraints 2nd minimization without constraints 3rd md with constraints 4th md without constraints First, you need to understand that restraints and constraints are different, and the purpose for using them. See manual for that. Also see http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation 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
Re: [gmx-users] Reducing Standard Error output
Even though I can sucessfully run this when I remove the verbose flag, it causes another problem. We keep trac of the progress of indivual simulations using a code modfication in sim_util.c 124: f = fopen(progress.txt, w); 125- if (!f) return; 126- fprintf(f, %g, (step - ir-init_step) / (float) ir-nsteps); 127- fclose(f); Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings 2) modify the code so it reports progress regardless of verbose flag On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- 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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Reducing Standard Error output
Jack Shultz wrote: Even though I can sucessfully run this when I remove the verbose flag, it causes another problem. We keep trac of the progress of indivual simulations using a code modfication in sim_util.c 124: f = fopen(progress.txt, w); 125- if (!f) return; 126- fprintf(f, %g, (step - ir-init_step) / (float) ir-nsteps); 127- fclose(f); Apparently this code is only used if the app is in verbose mode. So I guess we have two choices: 1) either find the cause of the lincs warnings That is always necessary if you don't want an expensive random number generator. Your simulation system is ill conditioned, and the lincs warnings will exist and be reported in at least the .log file regardless of the verbosity. 2) modify the code so it reports progress regardless of verbose flag Sure, but that's independent of the former. You should consider other modifications too - opening and closing a file every integration step might be prohibitively expensive. Since from previous threads you're monitoring this progress file with some other process to report to the user, you should consider more efficient means of such communication, such as an inter-process socket. Mark On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. 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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Reducing Standard Error output
Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime:95 s Fraction complete: 0.2 step 200, remaining runtime:70 s Fraction complete: 0.4 step 300, remaining runtime:46 s Fraction complete: 0.6 step 400, remaining runtime:23 s Fraction complete: 0.8 Writing final coordinates. step 500, remaining runtime: 0 s Fraction complete: 1 Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:119.000119.000100.0 1:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 55.372 3.138 0.728 32.990 gcq#0: Thanx for Using GROMACS - Have a Nice Day For our project's workflow we are extending the simulations using these arguments, -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md but I notice there is much more standard error output than I was expecting, in addition to a LINCS WARNING. Should I be worried about that warning? Is there a way we can turn off these error reports for each timestep? Step 785, time 1.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051275, max 3.234419 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 103.70.0973 0.4065 0.0960 Step 786, time 1.572 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.31, max 0.001926 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 69.50.4065 0.0962 0.0960 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Reducing Standard Error output
Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. Jack On Thu, Dec 3, 2009 at 10:36 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jack, The option -v is for verbose output. The LINCS warnings may indicate an issue regarding the stability of your system. They usually precede crashes. Maybe you need to equilibrate a bit further. Hope it helps, Tsjerk On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz j...@drugdiscoveryathome.com wrote: Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime: 95 s Fraction complete: 0.2 step 200, remaining runtime: 70 s Fraction complete: 0.4 step 300, remaining runtime: 46 s Fraction complete: 0.6 step 400, remaining runtime: 23 s Fraction complete: 0.8 Writing final coordinates. step 500, remaining runtime: 0 s Fraction complete: 1 Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 119.000 119.000 100.0 1:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 55.372 3.138 0.728 32.990 gcq#0: Thanx for Using GROMACS - Have a Nice Day For our project's workflow we are extending the simulations using these arguments, -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md but I notice there is much more standard error output than I was expecting, in addition to a LINCS WARNING. Should I be worried about that warning? Is there a way we can turn off these error reports for each timestep? Step 785, time 1.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051275, max 3.234419 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 103.7 0.0973 0.4065 0.0960 Step 786, time 1.572 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.31, max 0.001926 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 69.5 0.4065 0.0962 0.0960 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Reducing Standard Error output
Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. 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
Re: [gmx-users] Reducing Standard Error output
yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham mark.abra...@anu.edu.au wrote: Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- 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 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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
