9.10. Launching with Grid Engine

9.10.1. Verify Grid Engine support

Important

To build Grid Engine support in PRRTE, you will need to explicitly request the SGE support with the --with-sge command line switch to PRRTE’s configure script.

To verify if support for Grid Engine is configured into your PRRTE installation, run prte_info as shown below and look for gridengine.

shell$ prte_info | grep gridengine
              MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.3)

9.10.2. Launching

When Grid Engine support is included, PRRTE will automatically detect when it is running inside SGE and will just “do the Right Thing.”

Specifically, if you execute an prterun command in a Grid Engine job, it will automatically use the Grid Engine mechanisms to launch and kill processes. There is no need to specify what nodes to run on — PRRTE will obtain this information directly from Grid Engine and default to a number of processes equal to the slot count specified. For example, this will run 4 application processes on the nodes that were allocated by Grid Engine:

# Get the environment variables for Grid Engine

# (Assuming Grid Engine is installed at /opt/sge and $Grid
# Engine_CELL is 'default' in your environment)
shell$ . /opt/sge/default/common/settings.sh

# Allocate an Grid Engine interactive job with 4 slots from a
# parallel environment (PE) named 'foo' and run a 4-process job
shell$ qrsh -pe foo 4 -b y prterun -n 4 mpi-hello-world

There are also other ways to submit jobs under Grid Engine:

# Submit a batch job with the 'prterun' command embedded in a script
shell$ qsub -pe foo 4 my_prterun_job.csh

# Submit a Grid Engine and application job and prterun in one line
shell$ qrsh -V -pe foo 4 prterun hostname

# Use qstat(1) to show the status of Grid Engine jobs and queues
shell$ qstat -f

In reference to the setup, be sure you have a Parallel Environment (PE) defined for submitting parallel jobs. You don’t have to name your PE “foo”. The following example shows a PE named “foo” that would look like:

shell$ qconf -sp foo
   pe_name            foo
   slots              99999
   user_lists         NONE
   xuser_lists        NONE
   start_proc_args    NONE
   stop_proc_args     NONE
   allocation_rule    $fill_up
   control_slaves     TRUE
   job_is_first_task  FALSE
   urgency_slots      min
   accounting_summary FALSE
   qsort_args         NONE

Note

qsort_args is necessary with the Son of Grid Engine distribution, version 8.1.1 and later, and probably only applicable to it.

Note

For very old versions of Sun Grid Engine, omit accounting_summary too.

Note

For Open Cluster Scheduler / Gridware Cluster Scheduler it is necessary to set ign_sreq_on_mhost (ignoring slave resource requests on the master node) to FALSE.

You may want to alter other parameters, but the important one is control_slaves, specifying that the environment has “tight integration”. Note also the lack of a start or stop procedure. The tight integration means that mpirun automatically picks up the slot count to use as a default in place of the -n argument, picks up a host file, spawns remote processes via qrsh so that Grid Engine can control and monitor them, and creates and destroys a per-job temporary directory ($TMPDIR), in which PRTE’s directory will be created (by default).

Be sure the queue will make use of the PE that you specified:

shell$ qconf -sq all.q
[...snipped...]
pe_list               make cre foo
[...snipped...]

To determine whether the Grid Engine parallel job is successfully launched to the remote nodes, you can pass in the MCA parameter --prtemca plm_base_verbose 1 to prterun.

This will add in a -verbose flag to the qrsh -inherit command that is used to send parallel tasks to the remote Grid Engine execution hosts. It will show whether the connections to the remote hosts are established successfully or not.

Various Grid Engine documentation with pointers to more used to be available at the Son of GridEngine site, and configuration instructions were found at the Son of GridEngine configuration how-to site. This may no longer be true.

An actively developed (2024, 2025) open source successor of Sun Grid Engine is Open Cluster Scheduler. It maintains backward compatibility with SGE and provides many new features. An MPI parallel environment setup for OpenMPI is available in the Open Cluster Scheduler GitHub repository.

9.10.3. Grid Engine tight integration support of the `qsub -notify` flag

If you are running SGE 6.2 Update 3 or later, then the -notify flag is supported. If you are running earlier versions, then the -notify flag will not work and using it will cause the job to be killed.

To use -notify, one has to be careful. First, let us review what -notify does. Here is an excerpt from the qsub man page for the -notify flag.

The -notify flag, when set causes Sun Grid Engine to send warning signals to a running job prior to sending the signals themselves. If a SIGSTOP is pending, the job will receive a SIGUSR1 several seconds before the SIGSTOP. If a SIGKILL is pending, the job will receive a SIGUSR2 several seconds before the SIGKILL. The amount of time delay is controlled by the notify parameter in each queue configuration.

Let us assume the reason you want to use the -notify flag is to get the SIGUSR1 signal prior to getting the SIGTSTP signal. PRRTE forwards some signals by default, but others need to be specifically requested. The following MCA param controls this behavior:

prte_ess_base_forward_signals: Comma-delimited list of additional signals (names or integers) to forward to
application processes [\"none\" => forward nothing]. Signals provided by
default include SIGTSTP, SIGUSR1, SIGUSR2, SIGABRT, SIGALRM, and SIGCONT

Within that constraint, something like this batch script can be used:

#! /bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -N Job1
#$ -pe foo 16
#$ -j y
#$ -l h_rt=00:20:00
prterun -n 16 mpi-hello-world

However, one has to make one of two changes to this script for things to work properly. By default, a SIGUSR1 signal will kill a shell script. So we have to make sure that does not happen. Here is one way to handle it:

#! /bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -N Job1
#$ -pe ompi 16
#$ -j y
#$ -l h_rt=00:20:00
exec prterun -n 16 mpi-hello-world

Alternatively, one can catch the signals in the script instead of doing an exec on the mpirun:

#! /bin/bash
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -N Job1
#$ -pe ompi 16
#$ -j y
#$ -l h_rt=00:20:00

function sigusr1handler()
{
    echo "SIGUSR1 caught by shell script" 1>&2
}

function sigusr2handler()
{
    echo "SIGUSR2 caught by shell script" 1>&2
}

trap sigusr1handler SIGUSR1
trap sigusr2handler SIGUSR2

prterun -n 16 mpi-hello-world

9.10.4. Grid Engine job suspend / resume support

To suspend the job, you send a SIGTSTP (not SIGSTOP) signal to prterun. prterun will catch this signal and forward it to the mpi-hello-world as a SIGSTOP signal. To resume the job, you send a SIGCONT signal to prterun which will be caught and forwarded to the mpi-hello-world.

Here is an example on Solaris:

shell$ prterun -n 2 mpi-hello-world

In another window, we suspend and continue the job:

shell$ prstat -p 15301,15303,15305
   PID USERNAME  SIZE   RSS STATE  PRI NICE      TIME  CPU PROCESS/NLWP
 15305 rolfv     158M   22M cpu1     0    0   0:00:21 5.9% mpi-hello-world/1
 15303 rolfv     158M   22M cpu2     0    0   0:00:21 5.9% mpi-hello-world/1
 15301 rolfv    8128K 5144K sleep   59    0   0:00:00 0.0% mpirun/1

shell$ kill -TSTP 15301
shell$ prstat -p 15301,15303,15305
   PID USERNAME  SIZE   RSS STATE  PRI NICE      TIME  CPU PROCESS/NLWP
 15303 rolfv     158M   22M stop    30    0   0:01:44  21% mpi-hello-world/1
 15305 rolfv     158M   22M stop    20    0   0:01:44  21% mpi-hello-world/1
 15301 rolfv    8128K 5144K sleep   59    0   0:00:00 0.0% mpirun/1

shell$ kill -CONT 15301
shell$ prstat -p 15301,15303,15305
   PID USERNAME  SIZE   RSS STATE  PRI NICE      TIME  CPU PROCESS/NLWP
 15305 rolfv     158M   22M cpu1     0    0   0:02:06  17% mpi-hello-world/1
 15303 rolfv     158M   22M cpu3     0    0   0:02:06  17% mpi-hello-world/1
 15301 rolfv    8128K 5144K sleep   59    0   0:00:00 0.0% mpirun/1

Note that all this does is stop the mpi-hello-world processes. It does not, for example, free any pinned memory when the job is in the suspended state.

To get this to work under the Grid Engine environment, you have to change the suspend_method entry in the queue. It has to be set to SIGTSTP. Here is an example of what a queue should look like.

shell$ qconf -sq all.q
qname                 all.q
[...snipped...]
starter_method        NONE
suspend_method        SIGTSTP
resume_method         NONE

Note that if you need to suspend other types of jobs with SIGSTOP (instead of SIGTSTP) in this queue then you need to provide a script that can implement the correct signals for each job type.

9.10. Launching with Grid Engine

9.10.1. Verify Grid Engine support

9.10.2. Launching

9.10.3. Grid Engine tight integration support of the qsub -notify flag

9.10.4. Grid Engine job suspend / resume support

9.10.3. Grid Engine tight integration support of the `qsub -notify` flag