Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU
Hi, On 11/24/10 2:59 AM, lin hen wrote: hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1 steps, 20.0 ps. Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.2# Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 90.796 90.796100.0 1:30 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.060 19.034 1.261* gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes) The CPU version running results shows as following: ./mdrun Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.3# Average load imbalance: 4.7 % Part of the total run time spent waiting due to load imbalance: 2.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Parallel run - timing based on wallclock. * NODE (s) Real (s) (%) Time: 86.176 86.176100.0 1:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:741.634 35.849 20.054 1.197* gcq#0: Thanx for Using GROMACS - Have a Nice Day The gpu version looks *slower *than cpu version, does it make sense? Is there anyway I could optimize? In the default build, the CPU version will use all available cores on the machine and it's faster. 2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : ./mdrun Back Off! I just backed up md.log to ./#md.log.9# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Starting 16 threads --- Program mdrun, VERSION 4.5.2 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day Where could I modify this nodes#? Give the option -nt to mdrun to specify the number of threads you want to launch, e.g. $ mdrun -nt 8 3. for CPU benchmark dhfr-impl-inf.bench I modified cpu-imp-RF-inf.mdp: nsteps 1 grompp -f cpu-imp-RF-inf.mdp -o topol.tpr it will show: NOTE 1 [file cpu-imp-RF-inf.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... NOTE 2 [file topol.top, line 23568]: System has non-zero total charge: -1.10e+01 GB parameter(s) missing or negative for atom type 'H0' --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Everybody's Good Enough For Some Change" (LIVE) and when I run ./mdrun the steps still -1, infinite time How could I genete the right topol.tpr? Did you search the mailing lists? Copy and paste the error message in http://www.gromacs.org/Support/Mailing_Lists/Search and you will get a top hit http://lists.gromacs.org/pipermail/gmx-users/2010-September/053764.html You are using grompp 4.5.1 and mdrun 4.5.2 !? Remove all gromacs installs that you have, make a clean 4.5.3 install and try again. Rossen Thanks a lot. YY -- 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] 3 questions of gromacs 4.5.2 for both CPU and GPU
Hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1 steps, 20.0 ps. Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.2# Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. NODE (s) Real (s) (%) Time: 90.796 90.796100.0 1:30 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.060 19.034 1.261 gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes) The CPU version running results shows as following: ./mdrun Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.3# Average load imbalance: 4.7 % Part of the total run time spent waiting due to load imbalance: 2.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 86.176 86.176100.0 1:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:741.634 35.849 20.054 1.197 gcq#0: Thanx for Using GROMACS - Have a Nice Day The gpu version looks slower than cpu version, does it make sense? Is there anyway I could optimize? 2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : ./mdrun Back Off! I just backed up md.log to ./#md.log.9# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Starting 16 threads --- Program mdrun, VERSION 4.5.2 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day Where could I modify this nodes#? 3. for CPU benchmark dhfr-impl-inf.bench I modified cpu-imp-RF-inf.mdp: nsteps 1 grompp -f cpu-imp-RF-inf.mdp -o topol.tpr it will show: NOTE 1 [file cpu-imp-RF-inf.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... NOTE 2 [file topol.top, line 23568]: System has non-zero total charge: -1.10e+01 GB parameter(s) missing or negative for atom type 'H0' --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Everybody's Good Enough For Some Change" (LIVE) and when I run ./mdrun the steps still -1, infinite time How could I genete the right topol.tpr? Thanks a lot. YY -- 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] 3 questions of gromacs 4.5.2 for both CPU and GPU
hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s memtest in progress...done, no errors detected starting mdrun 'Protein in water' 1 steps, 20.0 ps. Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.2# Post-simulation ~15s memtest in progress...done, no errors detected OpenMM run - timing based on wallclock. NODE (s) Real (s) (%) Time: 90.796 90.796100.0 1:30 (Mnbf/s) (MFlops) (ns/day) (hour/ns) Performance: 0.000 0.060 19.034 1.261 gcq#100: "Jesus Can't Save You, Though It's Nice to Think He Tried" (Black Crowes) The CPU version running results shows as following: ./mdrun Writing final coordinates. Back Off! I just backed up confout.gro to ./#confout.gro.3# Average load imbalance: 4.7 % Part of the total run time spent waiting due to load imbalance: 2.7 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 86.176 86.176100.0 1:26 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:741.634 35.849 20.054 1.197 gcq#0: Thanx for Using GROMACS - Have a Nice Day The gpu version looks slower than cpu version, does it make sense? Is there anyway I could optimize? 2. For the CPU benchmark dhfr-impl-1nm.bench, when I run : ./mdrun Back Off! I just backed up md.log to ./#md.log.9# Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) Starting 16 threads --- Program mdrun, VERSION 4.5.2 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 1.02425 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanx for Using GROMACS - Have a Nice Day Where could I modify this nodes#? 3. for CPU benchmark dhfr-impl-inf.bench I modified cpu-imp-RF-inf.mdp: nsteps 1 grompp -f cpu-imp-RF-inf.mdp -o topol.tpr it will show: NOTE 1 [file cpu-imp-RF-inf.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... NOTE 2 [file topol.top, line 23568]: System has non-zero total charge: -1.10e+01 GB parameter(s) missing or negative for atom type 'H0' --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 870 Fatal error: Can't do GB electrostatics; the forcefield is missing 1 values for atomtype radii, or they might be negative . For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Everybody's Good Enough For Some Change" (LIVE) and when I run ./mdrun the steps still -1, infinite time How could I genete the right topol.tpr? Thanks a lot. YY-- 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
