1. Introduction

2. MPI, or Distributed Parallel Jobs with Explicit Message Passing

   1. ORTE or OpenMPI

   2. MPICH or MVAPICH

3. Multi-threaded, or OpenMP, Parallel Jobs

   1. Multi-threaded job

   2. OpenMP job

4. Examples

1. Introduction

• A parallel job is a job that uses more than one CPU.

• Since the cluster is a shared resource, it is the GE that allocates CPUs, known as slots in GE jargon, to jobs, hence a parallel job must request a set of slots when it is submitted.

• A parallel job must request a parallel environment and a number of slots using the -pe <name> N specification to qsub, where

  • <name> is either mpich, orte or mthread (see below);

  • the value of N is the number of requested slots and can be specified a N-M, where N is the minimum and M the maximum number of slots requested;

  • that option can be an embedded directive.

  • The job script access the nnmber of allocated slots via an environment variable (NSLOTS) and,

  • for MPI jobs, gets the list of computed nodes via a so-called machines file.

• There are two types of parallel jobs:

1. 1. MPI or distributed jobs: the CPUs can be distributed over multiple compute nodes.

      PROs	There is conceptually no limit on how many CPUs can be used, the cumulative amount of CPUs and memory a job can use can get quite large. The GE can find (a lot of) unused CPUs on a busy machine by finding them on different nodes
      CONs	Each CPU should assume to be on a separate compute node and thus must communicate with the other CPUs to exchange information (aka message passing). Programming can get more complicated and the inter-process communication can become a bottleneck.

   2. Multi-threaded jobs: all the CPUs must be on the same compute node.

      PROs	All CPUs can share a common memory space, inter-process communication can be very efficient (being local) and programming can be simpler;
      CONs	Can only use as many CPUs as there is on the largest compute node, and can get them only if they are not in use by someone else.

• How do I know which type of parallel job to submit to?
  The author of the software will in most cases specify if the application can be parallelized and how
  • Some analysis are parallelized by submitting a slew of independent serial jobs,
    
    • in which case using a job array may be the best approach;
  • some analysis use explicit message passing (MPI); while
  • some analysis use a programming model that can use multiple threads.  

• We currently do not support hybrid parallel jobs: jobs that would use both multi-threaded and distributed models.

2. MPI, or Distributed Parallel Jobs with Explicit Message Passing

• A MPI job runs code that uses an explicit message passing programming scheme known as MPI.
• There are two distinct implementations of the MPI protocol:
  
  • MPICH and
  • ORTE;
• OpenMPI is an ORTE implementation of MPI;
• MVAPICH is a MPICH implementation, using explicitly the InfiniBand as transport fabric (faster message passing).
• OpenMPI is not OpenMP
  • OpenMPI is the ORTE implementation of MPI;
  • OpenMP is an API for multi-platform shared-memory parallel programming.

The following grid of modules, corresponding to a combination of compiler & implementation, is available on Hydra:

In fact, there are more version specific modules available, check with

   % ( module -t avail ) | & grep pi

for a complete list, then use

   % module whatis <module-name>

or

   % module help <module-name>

where <module-name> is one of the listed module to get more specific information.

2.a ORTE or OpenMPI

The following example shows how to write an ORTE/OpenMPI job script:

# /bin/sh
#
#$ -S /bin/sh
#$ -cwd -j y -N hello -o hello.log
#$ -pe orte 72
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS distributed over:
cat $PE_HOSTFILE
#
# load gcc's compiler and openmpi
module load gcc/4.9/openmpi-4.9.2
#
# run the program hello
mpirun -np $NSLOTS ./hello
#
echo = `date` job $JOB_NAME done

This example will

• show the content of the machine file (i.e. the distribution of compute nodes)
• load the OpenMPI module for gcc version 4.9.2, and
• run the program hello,
• requesting 72 slots (CPUs).

It assumes that the program hello was build using gcc v4.9.2

2.b MPICH or MVAPICH

The following example shows how to write a MVAPICH job script:

# /bin/csh
#
#$ -cwd -j y - N hello -o hello.log
#$ -pe mpich 72
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo using $NSLOTS slots on:
sort $TMPDIR/machines | uniq -c
#
# load PGI's mvapich
module load pgi/mvapich
#
# run the program hello
mpirun -np $NSLOTS -machinefile $TMPDIR/machines ./hello
#
echo = `date` job $JOB_NAME done

This example will

• show the content of the machine file (i.e. the distribution of compute nodes),
  •  using sort & uniq to produce a compact list, in a "hostname no_of_CPUs" format.
• load the MVAPICH module for the PGI compiler, and
• run the program hello,
• requesting 72 slots (CPUs).

It assumes that the program hello was build using the PGI compiler and the MVAPICH library/module to enable the IB as the transport fabric.

You could replace MVAPICH by MVPICH if you do not want to use the IB.

2.c Notes

• The command mpirun is aliased by the module file to use the full path of the correct version for each case.
• Do not use a full path specification to a version of mpirun, using a wrong version of mpirun will result in unpredictable results.
  You can check which version correspond to a module with either
     % module show <module-name>
  or, if you use the C-shell,
     % alias mpirun 
  of, is your use the Bourne shell
     % declare -f mpirun
  
  

• The following is  a simple trick to get the MPI code full path and use it on the mpirun line:

  Bourne shell syntax	C-Shell syntax
  # load the module module load tools/mpidemo # get the full path bin=`which demo_mpi` # show what will be executed declare -f mpirun echo mpirun -np $NSLOTS $bin # run it mpirun -np $NSLOTS $bin	# load the module module load tools/mpidemo # get the full path set bin = `which demo_mpi` # show what will be executed alias mpirun echo mpirun -np $NSLOTS $bin # run it mpirun -np $NSLOTS $bin

  This example assumes that the module tools/mpidemo set things up to run the MPI code mpidemo, and

  show how to prevent having to use anywhere a full path. While mpirun search your PATH to find the executable,

  the mpirun started on other compute nodes may not have the same PATH since the associated module is likely to not have been loaded.
  
  

• The error message:

  [proxy:0:0@compute-N-M.local] HYDU_create_process

  (./utils/launch/launch.c:75): execvp error on file <code> (No such file or directory)

  means the mpirun could not find the executable <code>.

   

• In most cases use mvapich and not mpich, as to use the IB fabric.
  
  

• One can query the technical implementation details of MPI for each module,

  since each MPI-enabling module implement a slightly different version of MPI.

  • You query the precise details of each implementation as follow:

    Command	to
    % module show <module-file>	Show how the module changes your Un*x environment. All the modules set the same env variables: MPILIB MPIINC MPIBIN plus either OPENMPI, MPICH, or MVAPICH, and set the alias mpirun to use the corresponding full path.
    % module help <module-file>	Show details on the module, and how to retrieve the details of the specific build.
    	Depending on the MPI implementation (ORTE or MPICH)
    % module load <module-file> % ompi_info [-all]	Show precise details of an ORTE implementation (as shown by module help <module-file>)
    or
    % module load <module-file> % mpirun -info	Show precise details of an MPICH/MVAPICH implementation (as shown by module help <module-file>)

    
    
    

3. Multi-threaded, or OpenMP, Parallel Jobs

A multi-threaded job is a job that will make use of more than one CPU but needs all the CPUs to be on the same compute node.

3.a Multi-threaded job

The following example shows how to write a multi-threaded script:

# /bin/sh
#
#$ -S /bin/sh
#$ -cwd -j y -N demo -o demo.log
#$ -pe mthread 32
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS
#
# load the demo (fictional) module
module load tools/demo
#
# convert the generic parameter file, gen-params, to a specific file
# where the number of thread are inserted where the string MTHREADS is found
sed "s/MTHREADS/$NSLOTS/" gen-params > all-params
#
# run the demo program specifying all-params as the parameter file
demo -p all-params
#
echo = `date` job $JOB_NAME done

This example will the tool "demo" using 32 CPUs (slots). The script

• loads the tools/demo module,
• parses the file gen-params and replace every occurrence of the string MTHREAD by the allocated number of slots (via $NSLOTS),
  
  • using the stream editor sed (man sed),
• saves the result to a file called all-params,
• runs the tool demo and with the parameter file all-params.

3.b OpenMP job

The following example shows how to write an OpenMP job script:

# /bin/csh
#
#$ -cwd -j y -N hellomp -o hellomp.log
#$ -pe mthread 32
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + NSLOTS = $NSLOTS
#
# load the pgi module
module load pgi
#
# set the variable OMP_NUM_THREADS to the content of NSLOTS
# this tell OpenMP applications how many threads/slots/CPUs to use
setenv OMP_NUM_THREADS $NSLOTS 
#
# run the hellomp OpenMP program, build w/ PGI
./hellomp
#
echo = `date` job $JOB_NAME done

This example will run the program hellomp, that was compiled with the PGI compiler, using 32 threads (CPUs/slots). The script

• loads the pgi  module,
• sets OMP_NUM_THREADS to the content of NSLOTS to specify the number of threads
• runs the program hellomp.

4. Examples

You can find examples of simple/trivial test cases with source code, Makefile, job file and log file under /home/hpc/examples

(list of examples still missing)

Last Updated 19 Jan 2016 SGK.