[gmx-users] Question about scaling
Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC 4.7.0 MPI: Intel MPI 4.0.3.008 FFT-library: ACML 5.1.0 fma4 System: 895 spce water molecules Simulation time: 750 ps (0.002 fs timestep) Cut-off: 1.0 nm but with long-range correction ( DispCorr = EnerPres ; PME (standard settings) - but in each case no extra CPU solely for PME) V-rescale thermostat and Parrinello-Rahman barostat I get the following timings (seconds), whereas is calculated as the time which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time would be 2 * X s). These timings were taken from the *.log file, at the end of the 'real cycle and time accounting' - section. Timings: gmx-version 1cpu2cpu4cpu 4.0.7 422333843540 4.5.5 378032552878 I'm a little bit clueless about the results. I always thought, that if i have a non-interacting system and double the amount of CPUs, i would get a simulation which takes only half the time (so the times as defined above would be equal). If the system does have interactions, i would lose some performance due to communication. Due to node imbalance there could be a further loss of performance. Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu - 4cpu (2cpu a little bit faster, since going to 4cpu leads to more communication - loss of performance). All the other timings, especially that 1cpu takes in each case longer than the other cases, i do not understand. Probalby the system is too small and / or the simulation time is too short for a scaling test. But i would assume that the amount of time to setup the simulation would be equal for all three cases of one GROMACS-version. Only other explaination, which comes to my mind, would be that something went wrong during the installation of the programs... Please, can somebody enlighten me? Greetings Thomas -- 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
Re: [gmx-users] Question about scaling
Hi Thomas, On Nov 12, 2012, at 5:18 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, i did some scaling tests for a cluster and i'm a little bit clueless about the results. So first the setup: Cluster: Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR GROMACS version: 4.0.7 and 4.5.5 Compiler: GCC 4.7.0 MPI: Intel MPI 4.0.3.008 FFT-library: ACML 5.1.0 fma4 System: 895 spce water molecules this is a somewhat small system I would say. Simulation time: 750 ps (0.002 fs timestep) Cut-off: 1.0 nm but with long-range correction ( DispCorr = EnerPres ; PME (standard settings) - but in each case no extra CPU solely for PME) V-rescale thermostat and Parrinello-Rahman barostat I get the following timings (seconds), whereas is calculated as the time which would be needed for 1 CPU (so if a job on 2 CPUs took X s the time would be 2 * X s). These timings were taken from the *.log file, at the end of the 'real cycle and time accounting' - section. Timings: gmx-version 1cpu2cpu4cpu 4.0.7 422333843540 4.5.5 378032552878 Do you mean CPUs or CPU cores? Are you using the IB network or are you running single-node? I'm a little bit clueless about the results. I always thought, that if i have a non-interacting system and double the amount of CPUs, i You do use PME, which means a global interaction of all charges. would get a simulation which takes only half the time (so the times as defined above would be equal). If the system does have interactions, i would lose some performance due to communication. Due to node imbalance there could be a further loss of performance. Keeping this in mind, i can only explain the timings for version 4.0.7 2cpu - 4cpu (2cpu a little bit faster, since going to 4cpu leads to more communication - loss of performance). All the other timings, especially that 1cpu takes in each case longer than the other cases, i do not understand. Probalby the system is too small and / or the simulation time is too short for a scaling test. But i would assume that the amount of time to setup the simulation would be equal for all three cases of one GROMACS-version. Only other explaination, which comes to my mind, would be that something went wrong during the installation of the programs… You might want to take a closer look at the timings in the md.log output files, this will give you a clue where the bottleneck is, and also tell you about the communication-computation ratio. Best, Carsten Please, can somebody enlighten me? Greetings Thomas -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- 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] Question about scaling charges
Hi, all, I was talking to a friend of mine that works in an MD lab. He said that the charges from QM/MM or semiempirical need to be scaled to charges in the force field. For example, a heme will have specific charges in the force field, while hemes that represent different bound states may have a different charge distribution, depending on which method is used to calculate it. Let us say that the force field charge is +1 for simplicity and the charge is +2 by using other methods. The scaling would suggest that you would reduce the charge of the heme by one half, so that it would be compatible to the force field. However, this doesn't make sense to me, since partial charges should always be related to an electron and therefore, in principle, should never have to be scaled. I would appreciate anyone's input on it. Best wishes, Art ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
