Dear Openmpi Users,
I am reserving several processors with SGE upon which I want to run a number of
openmpi jobs, all of which individually (and combined) use
less than the reserved number of processors. The code I am using uses
BLACS, and when blacs_pinfo is called I get a seg fault. If the code doesn't
call blacs_pinfo it runs fine being submitted in this manner. blacs_pinfo
simply returns the number of available processors, so I suspect this is an
issue with SGE and openmpi and the requested node number being different to
that given to mpirun.
Can anyone explain why this would happen with openmpi jobs using BLACS on the
SGE? And suggest maybe a way around it?
Many thanks
Conn
example submission script:
#!/bin/bash -f -l
#$ -V
#$ -N test
#$ -S /bin/bash
#$ -cwd
#$ -l vf=1800M
#$ -pe ib-ompi 12
#$ -q infiniband.q
BIN=~/bin/program
fori inXPOL,YPOL,ZPOL;do
mkdir ${TMPDIR}/4ZP;
mkdir ${TMPDIR}/4ZP/$i;
cp ./4ZP/$i/*${TMPDIR}/4ZP/$i;
done
cd ${TMPDIR}/4ZP/XPOL;
mpirun -np 4-machinefile ${TMPDIR}/machines $BIN >output &
cd ${TMPDIR}/4ZP/YPOL;
mpirun -np 4-machinefile ${TMPDIR}/machines $BIN >output &
cd ${TMPDIR}/4ZP/ZPOL;
mpirun -np 4-machinefile ${TMPDIR}/machines $BIN >output ;
fori in XPOL YPOL ZPOL ;do
cp ${TMPDIR}/4ZP/$i/*${HOME}/4ZP/$i;
done
blacs_pinfo.c:
#include "Bdef.h"
#if (INTFACE == C_CALL)
void Cblacs_pinfo(int *mypnum,int *nprocs)
#else
F_VOID_FUNC blacs_pinfo_(int *mypnum,int *nprocs)
#endif
{
int ierr;
extern int BI_Iam,BI_Np;
/*
*Ifthis is our first call,will need to setup some stuff
*/
if(BI_F77_MPI_COMM_WORLD ==NULL)
{
/*
* TheBLACS always call f77's mpi_init. If the user is using C, he should
* explicitly call MPI_Init . . .
*/
MPI_Initialized(nprocs);
#ifdef MainInF77
if (!(*nprocs)) bi_f77_init_();
#else
if (!(*nprocs))
BI_BlacsErr(-1, -1, __FILE__,
"Users with C main programs must explicitly call MPI_Init");
#endif
BI_F77_MPI_COMM_WORLD = (int *) malloc(sizeof(int));
#ifdef UseF77Mpi
BI_F77_MPI_CONSTANTS = (int *) malloc(23*sizeof(int));
ierr = 1;
bi_f77_get_constants_(BI_F77_MPI_COMM_WORLD, &ierr, BI_F77_MPI_CONSTANTS);
#else
ierr = 0;
bi_f77_get_constants_(BI_F77_MPI_COMM_WORLD, &ierr, nprocs);
#endif
BI_MPI_Comm_size(BI_MPI_COMM_WORLD, &BI_Np, ierr);
BI_MPI_Comm_rank(BI_MPI_COMM_WORLD, &BI_Iam, ierr);
}
*mypnum = BI_Iam;
*nprocs = BI_Np;
}
