Run MPI On Grid'5000
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Note |
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This page 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) and Kadeploy (see the Getting Started 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_sshoption. - Setting up and starting Open MPI to use high performance interconnect.
- Setting up and starting Open MPI to run on several sites using
oargridsub. - Setting up and starting your own Open MPI library inside a Kadeploy image.
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:
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frontend:
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mkdir ~/mpi |
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frontend:
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vi ~/mpi/tp.c |
#include <stdio.h>
#include <mpi.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:
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frontend:
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mpicc ~/mpi/tp.c -o ~/mpi/tp |
Setting up and starting Open MPI on a default environment using oarsh
Submit a job:
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frontend:
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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.
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node:
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mpirun --mca orte_rsh_agent "oarsh" -machinefile $OAR_NODEFILE ~/mpi/tp |
You can also set an environment variable (usually in your .bashrc):
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bashrc:
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export OMPI_MCA_orte_rsh_agent=oarsh |
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node:
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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:
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frontend:
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oarsub -I -t allow_classic_ssh -l nodes=3 |
Launch your parallel job:
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node:
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mpirun -machinefile $OAR_NODEFILE ~/mpi/tp |
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Note |
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Using | |
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:
- The Open MPI FAQ about tuning parameters
- How do I tell Open MPI which IP interfaces / networks to use?
- The Open MPI documentation about OpenFabrics (ie: Infiniband)
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. 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 eth1. You will ensure that 'regular' Ethernet interface is used.
We will be using NetPIPE to check the performances of high performance interconnects.
To download, extract and compile NetPIPE, do:
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frontend:
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cd ~/mpi |
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frontend:
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frontend:
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tar -xf NetPIPE-3.7.1.tar.gz |
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frontend:
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cd NetPIPE-3.7.1 |
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frontend:
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make mpi |
As NetPipe only works between 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:
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frontend:
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oarsub -I -l nodes=2 |
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node:
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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):
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frontend:
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oarsub -I -l /nodes=2/core=1 -p "ib='DDR'" |
- a 40G InfiniBand interconnect (QDR, Quad Data Rate):
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frontend:
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oarsub -I -l /nodes=2/core=1 -p "ib='QDR'" |
To check if the support for InfiniBand is available in Open MPI, run:
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node:
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ompi_info | grep openib |
you should see something like this:
MCA btl: openib (MCA v2.1.0, API v3.0.0, Component v2.0.2)
To start the network benchmark, use:
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node:
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cd ~/mpi/NetPIPE-3.7.1 |
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node:
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mpirun --mca orte_rsh_agent "oarsh" -machinefile /tmp/machinefile NPmpi |
Without high performance interconnect, results looks like this:
0: 1 bytes 4080 times --> 0.31 Mbps in 24.40 usec
1: 2 bytes 4097 times --> 0.63 Mbps in 24.36 usec
...
122: 8388608 bytes 3 times --> 896.14 Mbps in 71417.13 usec
123: 8388611 bytes 3 times --> 896.17 Mbps in 71414.83 usec
The latency is given by the last column for a 1 byte message; the maximum throughput is given by the last line (896.17 Mbps in that case).
With Infiniband 40G (QDR), you should have much better performance that using Ethernet:
0: 1 bytes 30716 times --> 4.53 Mbps in 1.68 usec 1: 2 bytes 59389 times --> 9.10 Mbps in 1.68 usec ... 121: 8388605 bytes 17 times --> 25829.13 Mbps in 2477.82 usec 122: 8388608 bytes 20 times --> 25841.35 Mbps in 2476.65 usec 123: 8388611 bytes 20 times --> 25823.40 Mbps in 2478.37 usec
Less than 2 ms of latency and almost 26 Gbit/s of bandwitdh !
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"
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).
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Warning |
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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 | |
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Warning |
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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.
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fsophia:
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rsync -avz ~/mpi/ nancy.grid5000.fr:mpi/ |
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fsophia:
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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):
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frontend:
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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:
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frontend:
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export OAR_JOB_KEY_FILE=$(grep "SSH KEY" oargrid.out | cut -f2 -d: | tr -d " ") |
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frontend:
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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:
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frontend:
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oargridstat -w -l $OARGRID_JOB_ID | grep -v ^$ > ~/gridnodes |
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frontend:
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oarcp ~/gridnodes $(head -1 ~/gridnodes): |
Connect to the first node:
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frontend:
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oarsh $(head -1 ~/gridnodes) |
And run your MPI application:
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node:
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cd ~/mpi/ |
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node:
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mpirun -machinefile ~/gridnodes --mca orte_rsh_agent "oarsh" --mca opal_net_private_ipv4 "192.168.0.0/16" --mca btl_tcp_if_exclude ib0,lo --mca btl self,sm,tcp --mca orte_keep_fqdn_hostnames t tp |
Make your own Kadeploy image with latest Open MPI version
Build a Kadeploy image
If you need latest Open MPI version, or use Open MPI with specific compilation options, you must recompile Open MPI from sources. In this section we are going to build an image that includes latest version of Open MPI built from sources. Note that you could also build and install this custom Open MPI in your home directory, without requiring deploying (i.e., using ./configure --prefix=$HOME/openmpi/).
This image will be based on jessie-x64-base. Let's deploy it:
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frontend:
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oarsub -I -t deploy -l nodes=1,walltime=2 |
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frontend:
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kadeploy3 -f $OAR_NODEFILE -e jessie-x64-base -k |
Connect to reserved node as root:
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frontend:
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ssh root@$(head -1 $OAR_NODEFILE) |
Download Open MPI sources from official website:
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node:
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cd /tmp/ |
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node:
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tar -xf openmpi-1.10.2.tar.bz2
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node:
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cd openmpi-1.10.2
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Install build dependencies:
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node:
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apt-get update |
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node:
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apt-get -y install g++ make gfortran f2c libblas-dev |
Configure, compile and install:
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node:
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./configure --libdir=/usr/local/lib64 --with-memory-manager=none
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node:
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make -j8
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node:
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make install
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To run our MPI applications, we create a dedicated user named mpi. We add it to the rdma group to allow access to Infiniband hardware. Also, we copy the ~root/authorized_keys files so that we can login as user mpi from the frontend. We also create an SSH key for identifying the mpi user (needed by Open MPI).
groupadd rdma useradd -m -g rdma mpi -d /var/mpi -s /bin/bash echo "* hard memlock unlimited" >> /etc/security/limits.conf echo "* soft memlock unlimited" >> /etc/security/limits.conf mkdir ~mpi/.ssh cp ~root/.ssh/authorized_keys ~mpi/.ssh chown -R mpi ~mpi/.ssh su - mpi ssh-keygen -N "" -P "" -f /var/mpi/.ssh/id_rsa cat .ssh/id_rsa.pub >> ~/.ssh/authorized_keys echo " StrictHostKeyChecking no" >> ~/.ssh/config exit # exit session as MPI user exit # exit the root connection to the node # You can then copy your file from the frontend to the mpi home directory: rsync -avz ~/mpi/ mpi@$(head -1 $OAR_NODEFILE):mpi/ # copy the tutorial
Save the newly created image by using tgz-g5k:
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frontend:
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ssh root@$(head -1 $OAR_NODEFILE)
tgz-g5k > $HOME/public/jessie-openmpi.tgz |
Copy the description file of jessie-x64-base:
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frontend:
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kaenv3 -p jessie-x64-base | grep -v visibility > $HOME/public/jessie-openmpi.dsc
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Change the image name in the description file; we will use an http URL for multi-site deployment:
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frontend:
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sed -i "s,server://.*images/jessie-x64-base.*,http://public.$(hostname -f| cut -d. -f2).grid5000.fr/~$USER/jessie-openmpi.tgz," $HOME/public/jessie-openmpi.dsc
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Release your job:
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frontend:
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oardel $OAR_JOB_ID |
Use your Kadeploy image
Single site
Reserve some nodes and deploy them:
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frontend:
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oarsub -I -t deploy -l /nodes=3
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frontend:
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kadeploy3 -a $HOME/public/jessie-openmpi.dsc -f $OAR_NODEFILE -k
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Copy machines file and connect to first node:
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frontend:
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scp $OAR_NODEFILE mpi@$(head -1 $OAR_NODEFILE):nodes |
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frontend:
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ssh mpi@$(head -1 $OAR_NODEFILE) |
Copy your MPI application to other nodes and run it:
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node:
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cd ~/mpi/ |
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node:
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/usr/local/bin/mpicc tp.c -o tp |
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node:
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for node in $(uniq ~/nodes | grep -v $(hostname)); do scp ~/mpi/tp $node:~/mpi/tp; done
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node:
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/usr/local/bin/mpirun -machinefile ~/nodes ./tp |
Multiple sites
Choose three clusters from 3 different sites.
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frontend:
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oargridsub -t deploy -w 02:00:00 cluster1:rdef="nodes=2",cluster2:rdef="nodes=2",cluster3:rdef="nodes=2" > oargrid.out |
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frontend:
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export OARGRID_JOB_ID=$(grep "Grid reservation id" oargrid.out | cut -f2 -d=) |
Get the node list using oargridstat:
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frontend:
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oargridstat -w -l $OARGRID_JOB_ID | grep grid > ~/gridnodes |
Deploy on all sites using the --multi-server option :
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frontend:
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kadeploy3 -f gridnodes -a $HOME/public/jessie-openmpi.dsc -k --multi-server |
Copy machines file and connect to first node:
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frontend:
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scp ~/gridnodes mpi@$(head -1 ~/gridnodes): |
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frontend:
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ssh mpi@$(head -1 ~/gridnodes) |
Copy your MPI application to other nodes and run it:
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node:
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cd ~/mpi/ |
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node:
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/usr/local/bin/mpicc tp.c -o tp |
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node:
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for node in $(uniq ~/gridnodes | grep -v $(hostname)); do scp ~/mpi/tp $node:~/mpi/tp; done
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node:
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/usr/local/bin/mpirun -machinefile ~/gridnodes --mca btl self,sm,tcp --mca opal_net_private_ipv4 "192.168.0.0/16" --mca btl_tcp_if_exclude ib0,lo --mca orte_keep_fqdn_hostnames 1 tp |