RE: [gmx-users] SMP/Parallel mdrun
> Date: Thu, 27 Nov 2008 02:49:10 + > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] SMP/Parallel mdrun > > Hi Mark, > > Mark Abraham wrote: > > Terminology - GROMACS is not threaded, but uses MPI processes for > > parallelism. > > Yes, I gathered that. > >> I have an MPI-compiled version of gromacs v4.0 and am attempting to > >> get parallel execution on a 2x2 core AMD Opteron system via: > >> > >> $ lamboot > >> $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 > > > > -N does nothing, and -np is no longer accepted - as you'd know from > > reading mdrun -h, right? > That is a bit of a condecending way of putting it. If I knew -N did > nothing and -np was no longer accepted, then of course I would not have > used them. In fact, I was reading the documentation from a file called > "manual-4.0.pdf" which stated: > > " > If you have a single machine with multiple processors you don’t have to > use the mpirun com- > mand, but you can do with an extra option to mdrun: > % mdrun -np 8 -s topol -v -N 8 > " > > so that is where I took the example from. I think this PDF was linked > from the gromacs "documentation" section of the website. > Ah, I was not aware of this small section in the manual. This information was already outdated about a decade ago. I will remove it. Note that mdrun also does not have the option -N. (for some reason, which I still do not know, mdrun does not check it command line options, unlike all other Gromacs programs) Berk > > Like most MPI parallel codes, you need to use mpirun. If your lam > > environment is correctly configured, then I think you will not need > > -np 4 as an argument to mpirun. > > > > Also, probably you are actually running a non-MPI gromacs, since by > > default, using --enable-mpi will suffix mdrun to be mdrun_mpi. > Doesn't look like it: > > $ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi > $ make > $ make install > $ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun > mdrun > > Anyway, thanks for your suggestions because I now have it working via: > > $ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4 > > and I see 4 processes running at 100% and an estimated run time 25% of > the serial version. > > Ian. > > -- > Ian Stokes-Rees, Research Associate > SBGrid, Harvard Medical School > http://sbgrid.org > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] SMP/Parallel mdrun
Ian Stokes-Rees wrote: Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? That is a bit of a condecending way of putting it. If I knew -N did nothing and -np was no longer accepted, then of course I would not have used them. In fact, I was reading the documentation from a file called "manual-4.0.pdf" which stated: " If you have a single machine with multiple processors you don’t have to use the mpirun com- mand, but you can do with an extra option to mdrun: % mdrun -np 8 -s topol -v -N 8 " so that is where I took the example from. I think this PDF was linked from the gromacs "documentation" section of the website. Hmmm that's been in the documentation since v3.3 and I've never seen code that might make it work. That looks like a documentation error. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] SMP/Parallel mdrun
Hi Mark, Mark Abraham wrote: Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. Yes, I gathered that. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? That is a bit of a condecending way of putting it. If I knew -N did nothing and -np was no longer accepted, then of course I would not have used them. In fact, I was reading the documentation from a file called "manual-4.0.pdf" which stated: " If you have a single machine with multiple processors you don’t have to use the mpirun com- mand, but you can do with an extra option to mdrun: % mdrun -np 8 -s topol -v -N 8 " so that is where I took the example from. I think this PDF was linked from the gromacs "documentation" section of the website. Like most MPI parallel codes, you need to use mpirun. If your lam environment is correctly configured, then I think you will not need -np 4 as an argument to mpirun. Also, probably you are actually running a non-MPI gromacs, since by default, using --enable-mpi will suffix mdrun to be mdrun_mpi. Doesn't look like it: $ ./configure --prefix=/opt/osg-shared/se/app/site --with-pic --enable-mpi $ make $ make install $ ls /opt/osg-shared/se/app/site/bin/ | grep mdrun mdrun Anyway, thanks for your suggestions because I now have it working via: $ mpirun -np 4 /opt/osg-shared/se/app/site/bin/mdrun -s ../1WOM.tpr -v -N 4 and I see 4 processes running at 100% and an estimated run time 25% of the serial version. Ian. -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] SMP/Parallel mdrun
Ian Stokes-Rees wrote: I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. Terminology - GROMACS is not threaded, but uses MPI processes for parallelism. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 -N does nothing, and -np is no longer accepted - as you'd know from reading mdrun -h, right? Like most MPI parallel codes, you need to use mpirun. If your lam environment is correctly configured, then I think you will not need -np 4 as an argument to mpirun. Also, probably you are actually running a non-MPI gromacs, since by default, using --enable-mpi will suffix mdrun to be mdrun_mpi. however there is then only a single thread executing. Do I need to preprocess the topology file? Not with gromacs 4. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] SMP/Parallel mdrun
I am a computational scientist working with a physical chemist to try to parallelize her use of gromacs -- today is my first day using the application and I am not succeeding in getting multiple threads. I have an MPI-compiled version of gromacs v4.0 and am attempting to get parallel execution on a 2x2 core AMD Opteron system via: $ lamboot $ mdrun -np 4 -s ../1WOM.tpr -v -N 4 however there is then only a single thread executing. Do I need to preprocess the topology file? In the first instance, getting mdrun going in parallel on an SMP machine is the higher priority. Next I will look at running it on a cluster. TIA. Ian -- Ian Stokes-Rees, Research Associate SBGrid, Harvard Medical School http://sbgrid.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
