pbdADIOS is a package to connect R with ADIOS parallel middleware for IO. Staging and in situ capability.
pbdADIOS requires:
- R version 3.1.0 or higher with pbdMPI
- ADIOS 1.7.0 library
More information about pbdADIOS can be found in the ADIOS User's Manual.
To build on sith and rhea:
module swap PE-pgi PE-gnu
module load adios/1.7.0
module load r
export ADIOS_DIR=/sw/redhat6/adios/1.7.0/rhel6_gnu4.7.1_wrappers
R CMD INSTALL pbdADIOS --configure-args="--with-adios-home=$ADIOS_DIR"
To run on sith (note: change some hard coded paths to your locations!):
qsub run_sith.sh
run_sith.sh contains:
#!/bin/sh
#PBS -N adiosis
#PBS -l nodes=1:ppn=32
#PBS -l walltime=0:30:00
#PBS -e pbs.err
#PBS -o pbs.log
source /etc/profile.d/modules.sh
module swap PE-pgi PE-gnu
module load r
module load adios/1.7.0
cd $MEMBERWORK/stf006/heat
time mpirun -np 4 --mca mpi_warn_on_fork 0 \
Rscript /ccs/home/ost/adios/pbdADIOS/tests/test_heat.r