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There are two problems with running MPI jobs under SGE which are relatively frequent:
To run OpenMPI job under SGE you need to meet at least the following pre-conditions:
--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
configurecommand invocation. In simplest case this can be the only parameter. For example:
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 "
line switch to the Open MPI
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"
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..
A typical submit script would look like this:
#!/bin/bash # #$ -cwd ##$ -j y #$ -S /bin/bash #$ -M YYYYYY@seas.harvard.edu #$ -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
Here's description of the options embedded in the script header:
|-cwd||Run in the current working directory|
||Stdout and stderr in same output file|
|-S /bin/bash||Use the bash shell|
|-M username@...||Mail notifications to this email address|
|-pe orte 8||Use parallel environment named "orte" for 8 MPI processes|
|-o filename||Output file for stdout|
|-e filename||File for stderr|
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 submittedand immediately can see that the job has been queued. ?
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"?
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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 $PBS_O_WORKDIR module load openmpi/gnu mpirun ./hellompiMore information on the module command and PBS can be found in their respective User Guides.
Open MPI is a Message Passing Interface (MPI) library project combining technologies and resources from several other projects (FT-MPI, LA-MPI, LAM/MPI, and PACX-MPI). It is used by many TOP500 supercomputers including Roadrunner, which was the world's fastest supercomputer from June 2008 to November 2009, and K computer, the fastest supercomputer since June 2011. The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
Project website: http://www.open-mpi.org/
Load SGE module
The following Modules files should be loaded for this package:
For GNU:module load openmpi/openmpi-gnu
For Intel:module load openmpi/openmpi-intel
Use the openmpi parallel environment in your job script (example for a 4 slot job)#$ -pe openmpi 4
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 USERID@uab.edu #$ -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 $NSLOTS hello_world_gnu_openmpi
I've installed openmpi , not in
/usr/...but in a
/commun/data/packages/openmpi/, it was compiled with
I've added a new PE in SGE as descibed in http://docs.oracle.com/cd/E19080-01/n1.grid.eng6/817-5677/6ml49n2c0/index.html
# /commun/data/packages/openmpi/bin/ompi_info | grep gridengine MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.3) # qconf -sq all.q | grep pe_ pe_list make orte
Without SGE, the program runs without any problem, using several processors.
/commun/data/packages/openmpi/bin/orterun -np 20 ./a.out args
Now I want to submit my program to SGE
In the Open MPI FAQ, I read:
# Allocate a SGE interactive job with 4 slots # from a parallel environment (PE) named 'orte' shell$ 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
mpiruncommand 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.phpmpi openmpi sungridengine
=== answer ===
May 31 at 19:30
PierreIn my case setting "job_is_first_task FALSE" and "control_slaves TRUE" solved the problem.
1 Answer 1
# 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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