Testing openMPI environment on SGE

There are two problems with running MPI jobs under SGE which are relatively frequent:

• ulimit problem with infiniband in SGE
• MPI startup(): RLIMIT_MEMLOCK too small problem with SGE and Infiniband

To run OpenMPI job under SGE you need to meet at least the following pre-conditions:

1. SGE Parallel Environment should be correct. For MPI you should set "job_is_first_task FALSE" and "control_slaves TRUE".
2. All nodes should be assessable via ssh with passwordless login from the head node.
3. OpenMPI should be compiled with the "--with-sge" command line switch. In case you forget to do this errors thqat you will get will have no point to this fact. MPI often complains about inability to start daemon on the slave.  SGE support is not enabled by default: you need to explicitly request the SGE support during compilation using the "--with-sge" command line switch in configure command invocation. In simplest case this can be the only parameter. For example:

   ./configure --with-sge

4. Intel compiler libraries and OpenMPI libraries should be made available on all computational nodes.
5. Environment should be correct and identical for all computational nodes, including such variables as PATH and  LD_LIBRARY_PATH (this can be achieved by modifying .bashrc file for the particular application account, for example vasp). Forgetting providing nessesary values can lead to the errors in loading requred libraries but often the error message has no relation to the root couse so you should check this pre-requisite especially attentively. 
6. You should create correct SGE submit script. Please node that submit script does not create the environment on other computation nodes except that first on which it runs.
   • Environment specified in submit script and environment specified in .bash rc script should be identical. SGE launch the script on a single node. Launching slave process is done by mpirun.
   • Machines file should be either generated in policy startup script or directly in submit script. You should not assume that it will be provided automatically by SGE.
7. ulimit - locked memory limit should be set correctly on all the computational nodes.

Example of the setup a parallel environment (pe) under SGE (often called "orte"), which tells SGE how to run MPI codes using Open-MPI libraries is provided in SGE Parallel Environment

SGE support is not enabled by default. For Open MPI v1.3 and later, you need to explicitly request the SGE support during compilation with the "--with-sge" command line switch to the Open MPI configure script.

For example:

./configure --with-sge

SGE will wrap your job and start the child processes for you; you just need to build your code and create a submit  script that embeds SGE queue options as well and shell commands for setting up the environment and invoking mpirun.

Regarding basics of MPI parallel programming, please check out online tutorials such as one from LLNL National Labs.

To determine whether the SGE parallel job is successfully launched to the remote nodes, you can pass in the MCA parameter "--mca plm_base_verbose 1" to mpirun.

Various SGE documentation with pointers to more is available at the Son of GridEngine site, and configuration instructions can be found at the Son of GridEngine configuration how-to site..

Submit Script

A typical submit script would look like this:

#!/bin/bash
#
#$ -cwd
##$ -j y
#$ -S /bin/bash
#$ -M [email protected]
#$ -pe orte 8
#$ -o output/hello.out
#$ -e output/hello.err
#
# Use modules to setup the runtime environment
#
. /etc/profile
module load compilers/intel/11.1
module load mpi/openmpi/1.4.2/intel 
#
# Execute the run
#
mpirun -np $NSLOTS ./hello

Note that this will need to be modified to match your environment and the cluster. In particular, check the

• Your email address after the -M option
• Name of the "pe" parallel environment .. this is "orte" on the hpc cluster
• appropriate module names
• path to your executable
• path to your output and stderr files (the run will fail, for example, if the ./output directory in the example weren't present)

SGE Options

Here's description of the options embedded in the script header:

• The next stanza is specific to SEAS's use of modules, and sets up modules and then load the desired modules for this binary.

• The last is the invocation of mpirun itself (which mpirun to use is determined by the modules loaded.)

Submitting

To submit the job to SGE, we use the "qsub" command:

parrott@hpc mpi> qsub sge-mpi.sh
Your job 6 ("sge-mpi.sh") has been submitted

Once queued, it will start running, and its state change from "qw" to "r"

And when complete, will leave the queue. The output file should appear in the current directory, in this case names ".o6" and ".po6", since the job ID was "6".

You can see the status of available compute nodes using "qhost"

NEWS CONTENTS

• 200102 : OpenMPI Usage Instructions ( OpenMPI Usage Instructions, )
• 200102 : OpenMPI - UABgrid Documentation ( OpenMPI - UABgrid Documentation, )
• 200102 : Load SGE module ( )
• 200102 : Parallel Environment ( )
• 200102 : Submit Script ( )
• 200102 : openmpi - Submitting Open MPI jobs to SGE - Stack Overflow ( openmpi - Submitting Open MPI jobs to SGE - Stack Overflow, )

Old News ;-)

OpenMPI Usage Instructions -- Penn state

Running OpenMPI Executables Through PBS

MPI executables need to be launched with the commmand mpirun. The mpirun command takes care of starting up all of the parallel processes in the MPI job. The following is an example PBS script for running an OpenMPI job across four processors. Note that the proper OpenMPI version needs to be loaded before running the job.

#PBS -l nodes=4:ppn=1
#PBS -l walltime=2:00:00
#PBS -j oe

cd $PBS_O_WORKDIR

module load openmpi/gnu
mpirun ./hellompi

More information on the module command and PBS can be found in their respective User Guides.

OpenMPI - UABgrid Documentation

Open MPI is a Message Passing Interface (MPI) library project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI). It is used by many TOP500 supercomputers including Roadrunner, which was the world's fastest supercomputer from June 2008 to November 2009, and K computer, the fastest supercomputer since June 2011. The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.

Project website: http://www.open-mpi.org/

Load SGE module

The following Modules files should be loaded for this package:

For GNU:

module load openmpi/openmpi-gnu

For Intel:

module load openmpi/openmpi-intel

Parallel Environment

Use the openmpi parallel environment in your job script (example for a 4 slot job)

#$ -pe openmpi 4

Submit Script

To enable verbose Grid Engine logging for OpenMPI, add the following the mpirun command in the job script --mca pls_gridengine_verbose 1, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -N j_openmpi_hello
#$ -pe openmpi 4
#$ -l h_rt=00:20:00,s_rt=0:18:00
#$ -j y
#
#$ -M [email protected]
#$ -m eas
#
# Load the appropriate module files
. /etc/profile.d/modules.sh
module load openmpi/openmpi-gnu

#$ -V

mpirun --mca pls_gridengine_verbose 1 -np $NSLOTS hello_world_gnu_openmpi

openmpi - Submitting Open MPI jobs to SGE - Stack Overflow

I've installed openmpi , not in /usr/... but in a /commun/data/packages/openmpi/ , it was compiled with --with-sge.

I've added a new PE in SGE as descibed in http://docs.oracle.com/cd/E19080-01/n1.grid.eng6/817-5677/6ml49n2c0/index.html

# /commun/data/packages/openmpi/bin/ompi_info | grep gridengine
MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.3)

# qconf -sq all.q | grep pe_
pe_list               make orte

Without SGE, the program runs without any problem, using several processors.

/commun/data/packages/openmpi/bin/orterun -np 20 ./a.out args

Now I want to submit my program to SGE

In the Open MPI FAQ, I read:

# Allocate a SGE interactive job with 4 slots
# from a parallel environment (PE) named 'orte'
shell$ qsh -pe orte 4

but my output is:

qsh -pe orte 4
Your job 84550 ("INTERACTIVE") has been submitted
waiting for interactive job to be scheduled ...
Could not start interactive job.

I've also tried the mpirun command embedded in a script:

$ cat ompi.sh
#!/bin/sh
/commun/data/packages/openmpi/bin/mpirun  \
    /path/to/a.out args

but it fails

$ cat ompi.sh.e84552
error: executing task of job 84552 failed: execution daemon on host "node02" didn't accept task
--------------------------------------------------------------------------
A daemon (pid 18327) died unexpectedly with status 1 while attempting
to launch so we are aborting.

There may be more information reported by the environment (see above).

This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
error: executing task of job 84552 failed: execution daemon on host "node01" didn't accept task
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.

How can I fix this?

---

answer in the openmpi mailing list: http://www.open-mpi.org/community/lists/users/2013/02/21360.php

mpi openmpi sungridengine

=== answer ===

May 31 at 19:30

Pierre
1 Answer 1

In my case setting "job_is_first_task FALSE" and "control_slaves TRUE" solved the problem.

# qconf -mp mpi1 

pe_name            mpi1
slots              9
user_lists         NONE
xuser_lists        NONE
start_proc_args    /bin/true
stop_proc_args     /bin/true
allocation_rule    $fill_up
control_slaves     TRUE
job_is_first_task  FALSE
urgency_slots      min
accounting_summary FALSE

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Last modified: March, 12, 2019