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Subject: [OMPI users] Openmpi SGE and BLACS
From: Conn ORourke (conn.orourke_at_[hidden])
Date: 2012-01-13 08:12:01


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; }