MPICH2 with Sun Grid Engine

http://idolinux.blogspot.com/2010/04/mpich2-with-sun-grid-engine.html

MPICH2 with Sun Grid Engine

A prerequisite to this install log is a configured and validated Sun Grid Engine (SGE) 6.2 installation. Read more about that at Deploying Sun Grid Engine on a Cluster.

MPICH2 is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2). The goals of MPICH2 are: (1) to provide an MPI implementation that efficiently supports different computation and communication platforms including commodity clusters (desktop systems, shared-memory systems, multicore architectures), high-speed networks (10 Gigabit Ethernet, InfiniBand, Myrinet, Quadrics) and proprietary high-end computing systems (Blue Gene, Cray, SiCortex) and (2) to enable cutting-edge research in MPI through an easy-to-extend modular framework for other derived implementations. -www.mcs.anl.gov

There are multiple ways to integrate MPICH2 and SGE:

• Tight Integration of the mpd startup method
• Tight Integration of the daemonless smpd startup method
• Tight Integration of the daemon-based smpd startup method
• Tight Integration of the gforker startup method

This build log will cover the first method with mpd. Download, build an install MPICH2.

# cd /usr/global/src/
# wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.2.1p1/mpich2-1.2.1p1.tar.gz
# tar xzvf mpich2-1.2.1p1.tar.gz
# cd mpich2-1.2.1p1
# ./configure --prefix=/usr/global/mpich2-1.2.1p1 2>&1 |tee config.log
# make 2>&1 |tee build.log
# make install 2>&1 |tee install.log
# ln -s /usr/global/mpich2-1.2.1p1 /usr/global/mpich2
# export PATH=/usr/global/mpich2/bin:$PATH
# export LD_LIBRARY_PATH=/usr/global/mpich2/lib:$LD_LIBRARY_PATH
# which mpicc
/usr/global/mpich2/bin/mpicc

Configure the queue shell.

# qconf -mq all.q
shell                 /bin/bash
shell_start_mode      unix_behavior

Download and install integration scripts.

# cd /usr/global/src/
# wget http://gridengine.sunsource.net/howto/mpich2-integration/mpich2-62.tgz
# cd /usr/global/sge/
# tar xzvf /usr/global/src/mpich2-62.tgz
# cd mpich2_mpd/src
# ./aimk
# ./install.sh

Create the parallel execution environment template file by pasting the following into a mpich2_mpd.template file:

pe_name            mpich2_mpd
slots              64
user_lists         NONE
xuser_lists        NONE
start_proc_args    /usr/global/sge/mpich2_mpd/startmpich2.sh -catch_rsh $pe_hostfile \
                   /usr/global/mpich2
stop_proc_args     /usr/global/sge/mpich2_mpd/stopmpich2.sh -catch_rsh \
                   /usr/global/mpich2
allocation_rule    $round_robin
control_slaves     TRUE
job_is_first_task  FALSE
urgency_slots      min
accounting_summary FALSE

Import the pe config.

# qconf -Ap mpich2_mpd.template

Add the pe to the allowed list in your queue.

# qconf -mq all.q
pe_list               make mpich2_mpd

Enable killing of the processes at the end of a job.

# qconf -mconf
execd_params                 ENABLE_ADDGRP_KILL=TRUE

As a normal user, submit a test job.

$ mkdir ~/test
$ cd ~/test
$ echo 'export PATH=/usr/global/mpich2/bin:$PATH' >>~/.bashrc
$ echo 'export LD_LIBRARY_PATH=/usr/global/mpich2/lib:$LD_LIBRARY_PATH' >>~/.bashrc
$ . ~/.bashrc 
$ which mpicc
/usr/global/mpich2/bin/mpicc
$ echo 'MPD_SECRETWORD=mr45-j9z' >~/.mpd.conf
$ chmod 600 ~/.mpd.conf
$ mpicc -o mpihello mpihello.c
$ qsub mpich2_mpd.sh

mpich2_mpd.sh

#!/bin/bash
# Export all environment variables
#$ -V
# Your job name
#$ -N test
# Use current working directory
#$ -cwd
# Join stdout and stderr
#$ -j y
# PARALLEL ENVIRONMENT:
#$ -pe mpich2_mpd 4
export MPICH2_ROOT=/usr/global/mpich2
export PATH=$MPICH2_ROOT/bin:$PATH
export MPD_CON_EXT="sge_$JOB_ID.$SGE_TASK_ID"
echo "Got $NSLOTS slots."
# The order of arguments is important. Forst global, then local options.
mpiexec -machinefile $TMPDIR/machines -n $NSLOTS ~/test/mpihello
exit 0

mpihello.c

// a simple mpi test
// compile with:
// $ mpicc -o ~/mpi_hello mpi_hello.c
#include <stdio.h>
#include <mpi.h>
int main (argc, argv)
     int argc;
     char *argv[];
{
  int rank,size;
  MPI_Init(&argc,&argv); /* starts MPI */
  MPI_Comm_rank(MPI_COMM_WORLD,&rank); /* get current process id */
  MPI_Comm_size(MPI_COMM_WORLD,&size); /* get number of processes */
  printf("Hello world from process %d of %d\n",rank,size);
  MPI_Finalize();
  return 0;
}

Check output.

$ cat test.po4479 
-catch_rsh /var/spool/sge/node06/active_jobs/4479.1/pe_hostfile /usr/global/mpich2
node06:1
node11:1
node10:1
node08:1
startmpich2.sh: check for local mpd daemon (1 of 10)
/usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node06 /usr/global/mpich2/bin/mpd
startmpich2.sh: check for local mpd daemon (2 of 10)
startmpich2.sh: check for mpd daemons (1 of 10)
/usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node11 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -n
/usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node10 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -n
/usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node08 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -n
startmpich2.sh: check for mpd daemons (2 of 10)
startmpich2.sh: got all 4 of 4 nodes

$ cat test.o4479 
Got 4 slots.
Hello World from Node 0.
Hello World from Node 2.
Hello World from Node 3.
Hello World from Node 1.

$ ssh node06 ps -e f -o pid,ppid,pgrp,command --cols=120 |less
...
 3538     1  3538 /usr/global/sge/bin/lx24-amd64/sge_execd
24471  3538 24471  \_ sge_shepherd-4479 -bg
24568 24471 24568  |   \_ /bin/bash /var/spool/sge/node06/job_scripts/4479
24569 24568 24568  |       \_ python2.4 /usr/global/mpich2/bin/mpiexec -machinefile /tmp/4479.1.all.q/machines -n 4 /hom
24517  3538 24517  \_ sge_shepherd-4479 -bg
24518 24517 24518      \_ /usr/global/sge/utilbin/lx24-amd64/qrsh_starter /var/spool/sge/node06/active_jobs/4479.1/1.nod
24528 24518 24528          \_ python2.4 /usr/global/mpich2/bin/mpd
24570 24528 24570              \_ python2.4 /usr/global/mpich2/bin/mpd
24571 24570 24571                  \_ /home/myuser/test/mpihello
...
24509     1 24472 /usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node06 /usr/global/mpich2/bin/mpd
24532     1 24472 /usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node11 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -
24534     1 24472 /usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node10 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -
24537     1 24472 /usr/global/sge/bin/lx24-amd64/qrsh -inherit -V node08 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -
...

$ ssh node11 ps -e f -o pid,ppid,pgrp,command --cols=120 |less
...
 3681     1  3681 /usr/global/sge/bin/lx24-amd64/sge_execd
20881  3681 20881  \_ sge_shepherd-4479 -bg
20882 20881 20882      \_ /usr/global/sge/utilbin/lx24-amd64/qrsh_starter /var/spool/sge/node11/active_jobs/4479.1/1.nod
20889 20882 20889          \_ python2.4 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -n
20890 20889 20890              \_ python2.4 /usr/global/mpich2/bin/mpd -h node06 -p 51413 -n
20891 20890 20891                  \_ /home/myuser/test/mpihello
...

Test MPICH2 without SGE.

$ ssh node01
$ /usr/global/mpich2/bin/mpdboot -f /etc/machine.list -n 4
$ /usr/global/mpich2/bin/mpdtrace
$ /usr/global/mpich2/bin/mpdringtest
$ /usr/global/mpich2/bin/mpiexec -n 4 hostname
$ /usr/global/mpich2/bin/mpiexec -n 4 /bin/sh -c "hostname; ping -c1 node01; whoami"
$ /usr/global/mpich2/bin/mpiexec -n 4 ~/test/mpihello
$ /usr/global/mpich2/bin/mpdallexit

References:

• Tight Integration of the MPICH2 library into SGE
• MPICH2 DOCS