Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
On Tue, Aug 5, 2014 at 9:24 PM, Theodore Si sjyz...@gmail.com wrote: Please compare the file 8.log https://onedrive.live.com/ redir?resid=990FCE59E48164A4%212481authkey=%21AI9ThbRY_ 7ZgAg8ithint=file%2clog and 512.log https://onedrive.live.com/ redir?resid=990FCE59E48164A4%212482authkey=% 21APLkizOBzXtPHxsithint=file%2clog. These runs report the use of 8 MPI ranks with 2 OpenMP threads per rank, and 512 MPI ranks with 1 OpenMP thread per rank. GROMACS (like a lot of codes) use hybrid MPI/OpenMP parallelism, and when describing a run it is normally incorrect to mention only one aspect. Their M E G A - F L O P S A C C O U N T I N part are different as 8.log has no standalone NxN VdW [F] and NxN VdW [VF]. 512.log has the following lines. NxN VdW [F] 17.077648 563.562 0.0 NxN VdW [VF]0.002592 0.111 0.0 Why the difference? They report on calls to different kernels. Only the forces are required for MD. Energies (ie. V) are extra work, so they're only done when necessary. This was a key optimization in 4.6. In your run, they were not often required. And the both have NxN Ewald Elec. + VdW [F] NxN Ewald Elec. + VdW [VF] Does NxN Ewald Elec. + VdW [F] mean NxN Ewald Elec. and NxN VdW [F]? If it is the case, why 512.log has both NxN Ewald Elec. + VdW [F] and NxN VdW [F]? They report on the calls to different kernels. If you have a chunk of atoms that don't have charges, you'd be pretty happy to call a kernel that didn't waste time doing that. Likewise if you don't need the energy, mdrun doesn't compute it. This is discovered at run time, so if you distribute the work to different numbers of compute units, then one of them might end up with some clusters that only have atoms that lack charge. The clustering is opportunistic, so differences are expected. In your next runs, you might observe the opposite behaviour. That said, the flops output is scarcely meaningful (even if the reporting is accurate). Performance is dominated by considerations of load balance, and the subsequent information deals with that. Mark On 8/5/2014 10:11 PM, Mark Abraham wrote: On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Why is there a NxN VdW [F] on a separate line?
This is extracted from a log file of a mdrun of 512 openMP threads without GPU acceleration. Since the first line and third line both have N*N Vdw [F], does the former include the latter? As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Why is there a NxN VdW [F] on a separate line?
Please compare the file 8.log https://onedrive.live.com/redir?resid=990FCE59E48164A4%212481authkey=%21AI9ThbRY_7ZgAg8ithint=file%2clog and 512.log https://onedrive.live.com/redir?resid=990FCE59E48164A4%212482authkey=%21APLkizOBzXtPHxsithint=file%2clog.Their M E G A - F L O P S A C C O U N T I N part are different as 8.log has no standalone NxN VdW [F] and NxN VdW [VF]. 512.log has the following lines. NxN VdW [F] 17.077648 563.562 0.0 NxN VdW [VF]0.002592 0.111 0.0 Why the difference? And the both have NxN Ewald Elec. + VdW [F] NxN Ewald Elec. + VdW [VF] Does NxN Ewald Elec. + VdW [F] mean NxN Ewald Elec. and NxN VdW [F]? If it is the case, why 512.log has both NxN Ewald Elec. + VdW [F] and NxN VdW [F]? On 8/5/2014 10:11 PM, Mark Abraham wrote: On Tue, Aug 5, 2014 at 4:00 AM, Theodore Si sjyz...@gmail.com wrote: This is extracted from a log file There's no data. The list cannot accept attachments, so you need to copy-paste a relevant chunk, or upload a log file to a file-sharing service. of a mdrun of 512 openMP threads without GPU acceleration. mdrun will refuse to run with 512 OpenMP threads - please report your mdrun command line rather than your mental model of it. Since the first line and third line both have N*N Vdw [F], does the former include the latter? No, but there is no line with N*N Vdw [F]. Please be precise if you are asking for detailed information. As we can see, in the log file of a mdrun of 8 openMP threads without GPU acceleration, there is no standalone N*N Vdw [F], why the difference? Can't tell, don't know what is different between the two runs. My guess is that the former run is actually running on 64 MPI ranks, each of 8 OpenMP threads, in which case you have domain decomposition per MPI rank, and in that case there are separate calls to kernels that are aimed at computing the interactions associated with atoms whose home is in different domains. You should see the ratio vary as the number of ranks varies. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
