I'm leaning toward the possibility that it is actually only running 8 copies of the same job on different processors. My question is how does gromacs4.5 know how many processors it has available to parallelize a job? Is it specified in grompp or does it just detect it?
On Fri, Jan 28, 2011 at 1:32 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Denny Frost wrote: > >> Here's my grompp command: >> >> grompp_d -nice 0 -v -f md.mdp -c ReadyForMD.gro -o md.tpr -p top.top >> >> and my mdrun command is this: >> time mpiexec mdrun_mpi -np 8 -cpt 30000 -nice 0 -nt 1 -s >> $PBS_O_WORKDIR/md.tpr -o $PBS_O_WORKDIR/mdDone.trr -x >> $PBS_O_WORKDIR/mdDone.xtc -c $PBS_O_WORKDIR/mdDone.gro -e >> $PBS_O_WORKDIR/md.edr -g $PBS_O_WORKDIR/md.log 1> $PBS_JOBID.pgm.out 4> >> $PBS_JOBID.pgm.err >> >> > The -np option of mdrun is nonexistent, but mdrun does not check for proper > command line arguments, so you won't get an error. But then you've said > that 8 processors are active, so I still suspect that mdrun was compiled > incorrectly or in such a way that it's incompatible with your system. The > output from the .log file indicates that only one processor was used. Maybe > your admins can help you on this one, if the jobs spit out any useful > diagnostic information. > > For our cluster, we use e.g.: > > mpirun -np 8 mdrun_mpi -deffnm md > > -Justin > > I know the -cpt option is 30000 because I don't want a checkpoint file >> because every time it tries to make it, it fails due to quota issues and >> kills the job. I'm not sure why this happens, but I think it's a separate >> issue to take up with my supercomputing facility. >> >> On Fri, Jan 28, 2011 at 1:18 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Denny Frost wrote: >> >> all 8 nodes are running at full capacity, though >> >> >> What is your mdrun command line? How did you compile it? What can >> happen is something went wrong during installation, so you think you >> have an MPI-enabled binary, but it is simply executing 8 copies of >> the same job. >> >> -Justin >> >> On Fri, Jan 28, 2011 at 1:13 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Denny Frost wrote: >> >> Here's what I've got: >> >> M E G A - F L O P S A C C O U N T I N G >> >> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free >> Energy >> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or >> pairs) >> NF=No Forces >> >> Computing: M-Number >> M-Flops % Flops >> >> >> ----------------------------------------------------------------------------- >> Coul(T) + VdW(T) 1219164.751609 >> 82903203.109 80.6 >> Outer nonbonded loop 25980.879385 >> 259808.794 0.3 >> Calc Weights 37138.271040 >> 1336977.757 1.3 >> Spread Q Bspline 792283.115520 >> 1584566.231 1.5 >> Gather F Bspline 792283.115520 >> 4753698.693 4.6 >> 3D-FFT 119163.856212 >> 953310.850 0.9 >> Solve PME 2527.465668 >> 161757.803 0.2 >> NS-Pairs 47774.705001 >> 1003268.805 1.0 >> Reset In Box 371.386080 >> 1114.158 0.0 >> Shift-X 24758.847360 >> 148553.084 0.1 >> CG-CoM 1237.953600 >> 3713.861 0.0 >> Angles 18569.135520 >> 3119614.767 3.0 >> Propers 14855.308416 >> 3401865.627 3.3 >> Impropers 3094.855920 >> 643730.031 0.6 >> Virial 1242.417375 >> 22363.513 0.0 >> Stop-CM 1237.953600 >> 12379.536 0.0 >> P-Coupling 12379.423680 >> 74276.542 0.1 >> Calc-Ekin 12379.436160 >> 334244.776 0.3 >> Lincs 11760.476208 >> 705628.572 0.7 >> Lincs-Mat 245113.083072 >> 980452.332 1.0 >> Constraint-V 23520.928704 >> 188167.430 0.2 >> Constraint-Vir 11760.452496 >> 282250.860 0.3 >> >> >> ----------------------------------------------------------------------------- >> Total >> 102874947.133 100.0 >> >> >> ----------------------------------------------------------------------------- >> >> >> R E A L C Y C L E A N D T I M E A C C O U N T >> I N G >> >> Computing: Nodes Number G-Cycles >> Seconds % >> >> ----------------------------------------------------------------------- >> Neighbor search 1 99195 8779.027 3300.3 >> 3.8 >> Force 1 991941 188562.885 >> 70886.8 81.7 >> PME mesh 1 991941 18012.830 6771.6 >> 7.8 >> Write traj. 1 41 16.835 >> 6.3 >> 0.0 >> Update 1 991941 2272.379 >> 854.3 1.0 >> Constraints 1 991941 11121.146 >> 4180.8 4.8 >> Rest 1 2162.628 >> 813.0 0.9 >> >> ----------------------------------------------------------------------- >> Total 1 230927.730 >> 86813.1 100.0 >> >> ----------------------------------------------------------------------- >> >> ----------------------------------------------------------------------- >> PME spread/gather 1 1983882 17065.384 >> 6415.4 7.4 >> PME 3D-FFT 1 1983882 503.340 >> 189.2 >> 0.2 >> PME solve 1 991941 427.136 >> 160.6 0.2 >> >> ----------------------------------------------------------------------- >> >> Does that mean it's only using 1 node? That would >> explain the >> speed issues. >> >> >> That's what it looks like to me. >> >> >> -Justin >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-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 >
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