Run MPI On Grid'5000

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See also: HPC and HTC tutorial | Run MPI On Grid'5000 | Accelerators on Grid5000
Note.png Note

This tutorial is actively maintained by the Grid'5000 team. If you encounter problems, please report them (see the Support page). Additionally, as it is a wiki page, you are free to make minor corrections yourself if needed. If you would like to suggest a more fundamental change, please contact the Grid'5000 team.

Introduction

MPI is a programming interface that enables the communication between processes of a distributed memory system. This tutorial focuses on setting up MPI environments on Grid'5000 and only requires a basic understanding of MPI concepts. For instance, you should know that standard MPI processes live in their own memory space and communicate with other processes by calling library routines to send and receive messages. For a comprehensive tutorials on MPI, see the IDRIS course on MPI. There are several freely-available implementations of MPI, including Open MPI, MPICH2, MPICH, LAM, etc. In this practical session, we focus on the Open MPI implementation.

Before following this tutorial you should already have some basic knowledge of OAR (see the Getting Started tutorial) . For the second part of this tutorial, you should also know the basics about OARGRID (see the Advanced OAR tutorial).

Running MPI on Grid'5000

When attempting to run MPI on Grid'5000 you will face a number of challenges, ranging from classical setup problems for MPI software to problems specific to Grid'5000. This practical session aims at driving you through the most common use cases, which are:

  • Setting up and starting Open MPI on a default environment using oarsh.
  • Setting up and starting Open MPI on a default environment using the allow_classic_ssh option.
  • Setting up and starting Open MPI to use high performance interconnect.
  • Setting up and starting latest Open MPI library version.
  • Setting up and starting Open MPI to run on several sites using oargridsub.


Using Open MPI on a default environment

The default Grid'5000 environment provides Open MPI 2.0.2 (see ompi_info).

Creating a sample MPI program

For the purposes of this tutorial, we create a simple MPI program where the MPI process of rank 0 broadcasts an integer (42) to all the other processes. Then, each process prints its rank, the total number of processes and the value he received from the process 0.

In your home directory, create a file ~/mpi/tp.c and copy the source code:

Terminal.png frontend:
mkdir ~/mpi
Terminal.png frontend:
vi ~/mpi/tp.c
#include <stdio.h>
#include <mpi.h>
#include <unistd.h>
#include <time.h> /* for the work function only */
#include <unistd.h>

int main (int argc, char *argv []) {
       char hostname[257];
       int size, rank;
       int i, pid;
       int bcast_value = 1;

       gethostname(hostname, sizeof hostname);
       MPI_Init(&argc, &argv);
       MPI_Comm_rank(MPI_COMM_WORLD, &rank);
       MPI_Comm_size(MPI_COMM_WORLD, &size);
       if (!rank) {
            bcast_value = 42;
       }
       MPI_Bcast(&bcast_value,1 ,MPI_INT, 0, MPI_COMM_WORLD );
       printf("%s\t- %d - %d - %d\n", hostname, rank, size, bcast_value);
       fflush(stdout);

       MPI_Barrier(MPI_COMM_WORLD);
       MPI_Finalize();
       return 0;
}

You can then compile your code:

Terminal.png frontend:
mpicc ~/mpi/tp.c -o ~/mpi/tp

Setting up and starting Open MPI on a default environment using oarsh

Submit a job:

Terminal.png frontend:
oarsub -I -l nodes=3

oarsh is the remote shell connector of the OAR batch scheduler. It is a wrapper around the ssh command that handles the configuration of the SSH environment. You can connect to the reserved nodes using oarsh from the submission frontal of the cluster or from any node. As Open MPI defaults to using ssh for remote startup of processes, you need to add the option --mca orte_rsh_agent "oarsh" to your mpirun command line. Open MPI will then use oarsh in place of ssh.

Terminal.png node:
mpirun --mca orte_rsh_agent "oarsh" -machinefile $OAR_NODEFILE ~/mpi/tp

You can also set an environment variable (usually in your .bashrc):

Terminal.png bashrc:
export OMPI_MCA_orte_rsh_agent=oarsh
Terminal.png node:
mpirun -machinefile $OAR_NODEFILE ~/mpi/tp

Open MPI also provides a configuration file for --mca parameters. In your home directory, create a file as ~/.openmpi/mca-params.conf

orte_rsh_agent=oarsh
filem_rsh_agent=oarcp

You should have something like:

helios-52       - 4 - 12 - 42
helios-51       - 0 - 12 - 42
helios-52       - 5 - 12 - 42
helios-51       - 2 - 12 - 42
helios-52       - 6 - 12 - 42
helios-51       - 1 - 12 - 42
helios-51       - 3 - 12 - 42
helios-52       - 7 - 12 - 42
helios-53       - 8 - 12 - 42
helios-53       - 9 - 12 - 42
helios-53       - 10 - 12 - 42
helios-53       - 11 - 12 - 42

You may have (lot's of) warning messages if Open MPI cannot take advantage of any high performance hardware. At this point of the tutorial, this is not important as we will learn how to select clusters with high performance interconnect in greater details below. Error messages might look like this:

[[2616,1],2]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:

Module: OpenFabrics (openib)
  Host: helios-8.sophia.grid5000.fr

Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
warning:regcache incompatible with malloc
warning:regcache incompatible with malloc
warning:regcache incompatible with malloc

or like this:

[griffon-80.nancy.grid5000.fr:04866] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_mtl_mx: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[griffon-80.nancy.grid5000.fr:04866] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_btl_mx: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[griffon-80.nancy.grid5000.fr:04865] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_mtl_mx: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
[griffon-80.nancy.grid5000.fr:04867] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_mtl_mx: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)
...

You could use FAQ#How_to_use_MPI_in_Grid5000.3F to avoid this warnings.

Setting up and starting Open MPI on a default environment using allow_classic_ssh

If you prefer using ssh as a connector instead of oarsh, submit a job with the allow_classic_ssh type:

Terminal.png frontend:
oarsub -I -t allow_classic_ssh -l nodes=3

Launch your parallel job:

Terminal.png node:
mpirun -machinefile $OAR_NODEFILE ~/mpi/tp
Note.png Note

Using allow_classic_ssh option avoids OAR resources confinement mechanism with cpuset to restrict the jobs on assigned resources. Therefore, allow_classic_ssh cannot be used with jobs sharing nodes between users (i.e. for reservations at the core level).

Setting up and starting Open MPI to use high performance interconnect

By default, Open MPI tries to use any high performance interconnect (e.g. Infiniband, Omni-Path) it can find. Options are available to either select or disable an interconnect:

MCA parameters (--mca) can be used to select the drivers that are used at run-time by Open MPI. To learn more about the MCA parameters, see also:

To learn more about specific Omni-Path tools, refer to this page.

If you want to disable native support for high performance networks, use --mca btl self,sm,tcp --mca mtl ^psm2,ofi. The first part disables the openib backend, and the second part disables the psm2 backend (used by Omni-Path). This will switch to TCP backend of Open MPI.

Nodes with Infiniband or Omni-Path interfaces also provide an IP over Infiniband interface (these interfaces are named ibX), and can still be used by the TCP backend. To also disable their use, use --mca btl_tcp_if_exclude ib0,lo or select a specific interface with --mca btl_tcp_if_include eno2. You will ensure that 'regular' Ethernet interface is used.

We will be using OSU micro benchmark to check the performances of high performance interconnects.

To download, extract and compile our benchmark, do:

Terminal.png frontend:
cd ~/mpi
Terminal.png frontend:
tar -xf osu-micro-benchmarks-5.6.1.tar.gz

{{Term|location=frontend|cmd=cd osu-micro-benchmarks-5.6.1/}

Terminal.png frontend:
make CC=$(which mpicc) CXX=$(which mpicxx)

As we will benchmark two MPI processes, reserve only one core in two distinct nodes. If your reservation includes more resources, you will have to create a MPI machinefile file with only two entries, such as follow:

Terminal.png frontend:
oarsub -I -l nodes=2
Terminal.png node:
uniq $OAR_NODEFILE | head -n 2 > /tmp/machinefile

Infiniband hardware is available on several sites. For example, you will find clusters with Infiniband interconnect in Rennes (20G), Nancy (20G) and Grenoble (20G & 40G).

To reserve one core of two distinct nodes with:

  • a 20G InfiniBand interconnect (DDR, Double Data Rate):
Terminal.png frontend:
oarsub -I -l /nodes=2/core=1 -p "ib='DDR'"
  • a 40G InfiniBand interconnect (QDR, Quad Data Rate):
Terminal.png frontend:
oarsub -I -l /nodes=2/core=1 -p "ib='QDR'"

To check if the support for InfiniBand is available in Open MPI, run:

Terminal.png node:
ompi_info | grep openib

you should see something like this:

                MCA btl: openib (MCA v2.1.0, API v3.0.0, Component v3.1.3)

To start the network benchmark, use:

Terminal.png node:
cd osu-micro-benchmarks-5.6.1/
Terminal.png node:
mpirun --mca orte_rsh_agent "oarsh" -machinefile /tmp/machinefile ./mpi/pt2pt/osu_latency

Specificity of uva and uvb cluster on Sophia

uva and uvb are connected to a 40G QDR Infiniband network. But this network uses a partition key : PKEY

As a result, if you want to use mpi with the infiniband network, you have to specify the partition key (which is 8100) with the following option --mca btl_openib_pkey "0x8100"

Use a newer Open MPI version using modules

If you need latest Open MPI version you should use the module command.

Terminal.png frontend:
module av
----------------------- /grid5000/spack/share/spack/modules/linux-debian9-x86_64 -----------------------
[...]
openmpi/3.1.3_gcc-6.4.0
openmpi/4.0.1_gcc-6.4.0
[...]
Terminal.png frontend:
module load openmpi/4.0.1_gcc-6.4.0
Terminal.png frontend:
mpirun --version

You must recompile simple MPI example on the frontend with this new version.

Terminal.png frontend:
mpicc ~/mpi/tp.c -o ~/mpi/tp

After you must submit a job and use the same Open MPI library version on the node.

Terminal.png frontend:
oarsub -I -l nodes=3
Terminal.png node:
module load openmpi/4.0.1_gcc-6.4.0

The last step is tu run simple example. As the module environment through a ssh connection is lost we use $(which mpirun) command.

Terminal.png node:
$(which mpirun) --mca orte_rsh_agent "oarsh" -machinefile $OAR_NODEFILE ~/mpi/tp

More advanced use cases

Running MPI on several sites at once

In this section, we are going to execute a MPI process over several Grid'5000 sites. In this example we will use the following sites: Rennes, Sophia and Grenoble, using oargrid for making the reservation (see the Advanced OAR tutorial for more information).

Warning.png Warning

Open MPI tries to figure out the best network interface to use at run time. However, selected networks are not always "production" Grid'5000 network which is routed between sites. In addition, only TCP implementation will work between sites, as high performance networks are only available from the inside of a site. To ensure correct network is selected, add the option --mca opal_net_private_ipv4 "192.168.0.0/16" --mca btl_tcp_if_exclude ib0,lo --mca btl self,sm,tcp to mpirun

Warning.png Warning

By default, Open MPI may use only the short name of the nodes specified into the nodesfile; but to join grid5000 nodes that are located on different sites, we must use the FQDN names. For Open Mpi to correctly use FQDN names of the nodes, you must add the following option to mpirun: --mca orte_keep_fqdn_hostnames t

The MPI program must be available on each site you want to use. From the frontend of one site, copy the mpi/ directory to the two other sites. You can do that with rsync. Suppose that you are connected in Sophia and that you want to copy Sophia's mpi/ directoy to Grenoble and Rennes.

Terminal.png fsophia:
rsync -avz ~/mpi/ nancy.grid5000.fr:mpi/
Terminal.png fsophia:
rsync -avz ~/mpi/ grenoble.grid5000.fr:mpi/

(you can also add the --delete option to remove extraneous files from the mpi directory of Nancy and Grenoble).

Reserve nodes in each site from any frontend with oargridsub (you can also add options to reserve nodes from specific clusters if you want to):

Terminal.png frontend:
oargridsub -w 02:00:00 nancy:rdef="nodes=2",grenoble:rdef="nodes=2",sophia:rdef="nodes=2" > oargrid.out

Get the oargrid Id and Job key from the output of oargridsub:

Terminal.png frontend:
export OAR_JOB_KEY_FILE=$(grep "SSH KEY" oargrid.out | cut -f2 -d: | tr -d " ")
Terminal.png frontend:
export OARGRID_JOB_ID=$(grep "Grid reservation id" oargrid.out | cut -f2 -d=)

Get the node list using oargridstat and copy the list to the first node:

Terminal.png frontend:
oargridstat -w -l $OARGRID_JOB_ID | grep -v ^$ > ~/gridnodes
Terminal.png frontend:
oarcp ~/gridnodes $(head -1 ~/gridnodes):

Connect to the first node:

Terminal.png frontend:
oarsh $(head -1 ~/gridnodes)

And run your MPI application:

Terminal.png node:
cd ~/mpi/
Terminal.png node:
mpirun -machinefile ~/gridnodes --mca orte_rsh_agent "oarsh" --mca opal_net_private_ipv4 "192.168.0.0/16" --mca btl_tcp_if_exclude ib0,lo --mca btl self,sm,tcp --mca orte_keep_fqdn_hostnames t tp



See also: HPC and HTC tutorial | Run MPI On Grid'5000 | Accelerators on Grid5000