Ok, thanks once again. I will do my best to overcome this issue. Best regards, João Henriques
On Wed, Jun 5, 2013 at 3:33 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 > -- João Henriques -- 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