Usage on TSUBAME2.5 at Tokyo Institute of Technology

TSUBAME2.5 has 12 CPU cores and 3 GPU cards in each node. The followings are recommended installation scheme, example of the batch script file for hybrid MPI/OpenMP calculation using 24 nodes (144 MPI processors and 2 OpenMP threads with GPGPU calculation), and a command to submit a job.

Installation

$ cd /home/user/genesis/src
$ . /usr/apps.sp3/env/set_cuda-6.5.sh
$ . /usr/apps.sp3/env/set_ompi-1.8.2_i2013.1.046_cuda6.5.sh
$ ./configure --enable-gpu --enable-single --with-cuda='/usr/apps.sp3/cuda/6.5'
$ make 
$ make install


Batch script

Number of OpenMP threads and number of GPU cards are specified in run.sh and wrap.sh, respectively.

Notice: GENESIS 1.1.2 or later may not require wrap.sh. You can omit that script from the following sample.

run.sh:

#!/bin/sh

CUDADIR="/usr/apps.sp3/cuda/6.5"
OMPIDIR="/usr/apps.sp3/mpi/openmpi/1.8.2/i2013.1.046_cuda6.5"
BINDIR="/home/user/genesis/bin"

export PATH="${OMPIDIR}/bin:${CUDADIR}/bin:${PATH}"
export LD_LIBRARY_PATH="${CUDADIR}/lib64:${OMPIDIR}/lib:${LD_LIBRARY_PATH}"
export OMP_NUM_THREADS=2
cd ${PBS_O_WORKDIR}
MPIPROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

mpirun -n $MPIPROCS -hostfile $PBS_NODEFILE -x OMP_NUM_THREADS=$OMP_NUM_THREADS -x PATH=$PATH -x LD_LIBRARY_PATH=$LD_LIBRARY_PATH ./wrap.sh $BINDIR/spdyn INP > log

wrap.sh:

#!/bin/bash
lr=${OMPI_COMM_WORLD_LOCAL_RANK:-0}
gpuid=`expr ${lr} \% 3`
export CUDA_VISIBLE_DEVICES=${gpuid}
$@


Usage

# All scripts should be executable
$ chmod u+x run1.sh run2.sh
$ chmod u+x wrap.sh

# Execute run1.sh and run2.sh sequentially
$ t2sub -et 1 -q S -l select=24:mpiprocs=6:ncpus=12:gpus=3:mem=40gb -l walltime=24:00:00 -W group_list=t2g-hpxxxxxx run1.sh

$ t2sub -et 1 -q S -l select=24:mpiprocs=6:ncpus=12:gpus=3:mem=40gb -l walltime=24:00:00 -W group_list=t2g-hpxxxxxx -W depend=afterany:xxxxxxx.t2zpbsXX run2.sh

# Check running jobs
$ t2stat

# Delete a job 
$ t2del JOB_ID

# Check available CPU time
$ t2group

In the t2sub command (select=AAA:mpiprocs=BBB:ncpus=CCC:gpus=DDD:mem=EEE),

AAA: Number of nodes
BBB: Number of MPI processors in one node (should be 12/OMP_NUM_THREADS)
CCC: Number of CPU cores in one node (should be always 12)
DDD: Number of GPU cards in one node (should be always 3)
EEE: Memory size

CCC/BBB should be OMP_NUM_THREADS, group_list is the group ID you have, and depend=afterany: is the previous job ID. For details, please see the user guide of TSUBAME2.5.