On Wed, Jun 5, 2013 at 2:53 PM, João Henriques < joao.henriques.32...@gmail.com> wrote:
> Sorry to keep bugging you guys, but even after considering all you > suggested and reading the bugzilla thread Mark pointed out, I'm still > unable to make the simulation run over multiple nodes. > *Here is a template of a simple submission over 2 nodes:* > > --- START --- > #!/bin/sh > # > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # > # Job name > #SBATCH -J md > # > # No. of nodes and no. of processors per node > #SBATCH -N 2 > #SBATCH --exclusive > # > # Time needed to complete the job > #SBATCH -t 48:00:00 > # > # Add modules > module load gcc/4.6.3 > module load openmpi/1.6.3/gcc/4.6.3 > module load cuda/5.0 > module load gromacs/4.6 > # > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > # > grompp -f md.mdp -c npt.gro -t npt.cpt -p topol -o md.tpr > mpirun -np 4 mdrun_mpi -gpu_id 01 -deffnm md -v > # > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > --- END --- > > *Here is an extract of the md.log:* > > --- START --- > Using 4 MPI processes > Using 4 OpenMP threads per MPI process > > Detecting CPU-specific acceleration. > Present hardware specification: > Vendor: GenuineIntel > Brand: Intel(R) Xeon(R) CPU E5-2650 0 @ 2.00GHz > Family: 6 Model: 45 Stepping: 7 > Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc > pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 > tdt x2apic > Acceleration most likely to fit this hardware: AVX_256 > Acceleration selected at GROMACS compile time: AVX_256 > > > 2 GPUs detected on host en001: > #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible > #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible > > > ------------------------------------------------------- > Program mdrun_mpi, VERSION 4.6 > Source code file: > /lunarc/sw/erik/src/gromacs/gromacs-4.6/src/gmxlib/gmx_detect_hardware.c, > line: 322 > > Fatal error: > Incorrect launch configuration: mismatching number of PP MPI processes and > GPUs per node. > "per node" is critical here. > mdrun_mpi was started with 4 PP MPI processes per node, but you provided 2 > GPUs. > ...and here. As far as mdrun_mpi knows from the MPI system there's only MPI ranks on this one node. For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > --- END --- > > As you can see, gmx is having trouble understanding that there's a second > node available. Note that since I did not specify -ntomp, it assigned 4 > threads to each of the 4 mpi processes (filling the entire avail. 16 CPUs > *on > one node*). > For the same exact submission, if I do set "-ntomp 8" (since I have 4 MPI > procs * 8 OpenMP threads = 32 CPUs total on the 2 nodes) I get a warning > telling me that I'm hyperthreading, which can only mean that *gmx is > assigning all processes to the first node once again.* > Am I doing something wrong or is there some problem with gmx-4.6? I guess > it can only be my fault, since I've never seen anyone else complaining > about the same issue here. > Assigning MPI processes to nodes is a matter configuring your MPI. GROMACS just follows the MPI system information it gets from MPI - hence the oversubscription. If you assign two MPI processes to each node, then things should work. Mark -- 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
