[gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

[João Henriques]

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.abraham at gmail.com>wrote:

> On Wed, Jun 5, 2013 at 2:53 PM, João Henriques <
> joao.henriques.32353 at 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
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-- 
João Henriques