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| {{{#!wiki caution '''Batch system and MPI''' The batch system may need extra configuration for the submission of MPI jobs. In PBS, you may use the automatic creation of the submit filter with the `MPI_SUBMIT_FILTER` variable. In the case of SGE you need to configure a parallel environment. Check the documentation of your batch system for any further details. }}} |
Contents
Functional Description
MPI-Utils is a meta package that provide mpi-start and a yaim mpi module in order to ease the installation of MPI support in the nodes.
Installation
MPI-Utils is a meta package that depends on MPI-Start and the yaim mpi module for configuration of the MPI support in the CE and WN. Administrators must install a MPI implementation and configure it at the site. Most Linux distributions provide ready to use packages for Open MPI and MPICH implmentations.
MPI-Utils can be installed from the EMI repositories, and should be as easy as:
yum install glite-mpi
In the WN, a MPI implementation must be installed also. Open MPI is recommended (the devel package allows users to compile their applications):
yum install openmpi openmpi-devel
devel packages and compilers
The devel packages of the MPI packages do not include the compiler as dependency! You should install it also if you want to support the compilation of MPI applications (e.g. gcc, gcc-gfortran, gcc-g++)
Configuration
Configuration is necessary on both the CE and WNs in order to support and advertise MPI correctly (see Site Configuration for details). This is performed by the yaim MPI module which should be run on both types of nodes.
Configure MPI in site-info.def
Individual "flavours" of MPI are enabled by setting the associated variable to "yes". For example, to enable Open MPI, add the following:
1 MPI_OPENMPI_ENABLE="yes"
The version of the MPI implementation must also be specified for the CE configuration with the variable MPI_<FLAVOUR>_VERSION, for Open MPI version 1.3:
1 MPI_OPENMPI_VERSION="1.3"
You may also set the path to non default locations for a flavour of MPI with the variable MPI_<FLAVOUR>_PATH, but should not be used unless necessary:
1 MPI_OPENMPI_PATH="/opt/openmpi-1.3/"
Possible flavours are:
- OPENMPI, for Open MPI
- MPICH for MPICH-1
- MPICH2 for MPICH-2
- LAM for LAM-MPI
The variables are:
Variable |
Mandatory |
Value |
MPI_<FLAVOUR>_ENABLE |
YES |
set to "yes" if you want to enable the <flavour> |
MPI_<FLAVOUR>_VERSION |
YES |
set to the supported version of the <flavour> |
MPI_<FLAVOUR>_PATH |
NO |
set to the path of supported version of the <flavour>, usually is automatically detected by the yaim WN plugin |
MPI_SHARED_HOME |
NO |
set this to "yes" if you have a shared home area between WNs. |
MPI_SSH_HOST_BASED_AUTH |
NO |
set it to "yes" if you have SSH based authentication between WNs |
MPI_<FLAVOUR>_MPIEXEC |
NO |
If you are using OSC mpiexec (only in PBS/Torque sites), set this to the location of the mpiexec program, e.g. "/usr/bin/mpiexec" |
MPI_MPI_START |
NO |
Location of mpi-start if not installed in standard location /opt/mpi-start/bin/mpi-start |
MPI_DEFAULT_FLAVOUR |
NO |
Set it to the default flavour for your site, if undefined, the first defined flavour will be used |
MPI_SUBMIT_FILTER |
NO |
Set this to "yes" to configure the submit filter for torque batch system that enables the submission of parallel jobs |
Here is an example configuration:
1 #----------------------------------
2 # MPI-related configuration:
3 #----------------------------------
4 # Several MPI implementations (or "flavours") are available.
5 # If you do NOT want a flavour to be installed/configured, set its variable
6 # to "no". Else, set it to "yes" (default). If you want to use an
7 # already installed version of an implementation, set its "_PATH" and
8 # "_VERSION" variables to match your setup (examples below).
9 #
10 # NOTE 1: the CE_RUNTIMEENV will be automatically updated in the file
11 # functions/config_mpi, so that the CE advertises the MPI implementations
12 # you choose here - you do NOT have to change it manually in this file.
13 # It will become something like this:
14 #
15 # CE_RUNTIMEENV="$CE_RUNTIMEENV
16 # MPI_MPICH
17 # MPI_MPICH2
18 # MPI_OPENMPI
19 # MPI_LAM"
20 #
21 # NOTE 2: it is currently NOT possible to configure multiple concurrent
22 # versions of the same implementations (e.g. MPICH-1.2.3 and MPICH-1.2.7)
23 # using YAIM. Customize "/opt/glite/yaim/functions/config_mpi" file
24 # to do so.
25
26 MPI_MPICH_ENABLE="yes"
27 MPI_MPICH_VERSION="1.2.7p1"
28
29 MPI_MPICH2_ENABLE="yes"
30 MPI_MPICH2_VERSION="1.0.4"
31
32 MPI_OPENMPI_ENABLE="yes"
33 MPI_OPENMPI_VERSION="1.1"
34
35 MPI_LAM_ENABLE="yes"
36 MPI_LAM_VERSION="7.1.2"
37
38 # set Open MPI as default flavour
39 MPI_DEFAULT_FLAVOUR=OPENMPI
40
41 # Enable the configuration of parallel jobs in torque
42 MPI_SUBMIT_FILTER="yes"
43
44
45 #---
46 # Example for using an already installed version of MPI.
47 # Setting "_PATH" and "_VERSION" variables will prevent YAIM
48 # from downloading and installing the gLite-provided packages.
49 # Just fill in the path to its current installation (e.g. "/usr")
50 # and which version it is (e.g. "6.5.9").
51 #---
52 MPI_MPICH_PATH="/opt/mpich-1.2.7p1/"
53 MPI_MPICH2_PATH="/opt/mpich2-1.0.4/"
54
55 # If you do NOT provide a shared home, set $MPI_SHARED_HOME to "no" (default).
56 #
57 MPI_SHARED_HOME="yes"
58
59 #
60 # If you do NOT have SSH Hostbased Authentication between your WNs, set the below
61 # variable to "no" (default). Else, set it to "yes".
62 #
63 MPI_SSH_HOST_BASED_AUTH="no"
64
65 #
66 # If you provide an 'mpiexec' for MPICH or MPICH2, please state the full path to
67 # that file here (http://www.osc.edu/~pw/mpiexec/index.php). Else, leave empty.
68 #
69 #MPI_MPICH_MPIEXEC="/usr/bin/mpiexec"
70 MPI_MPICH_MPIEXEC="/usr/bin/mpiexec"
Configure CE
The profile for configuring the CE is MPI_CE.
/opt/glite/yaim/bin/yaim -c -s site-info.def -n MPI_CE -n <other_ce_profiles>
Batch system and MPI
The batch system may need extra configuration for the submission of MPI jobs. In PBS, you may use the automatic creation of the submit filter with the MPI_SUBMIT_FILTER variable. In the case of SGE you need to configure a parallel environment. Check the documentation of your batch system for any further details.
Configure WN
For a worker node:
/opt/glite/yaim/bin/yaim -c -s site-info.def -n MPI_WN -n <other_WN_profiles>
Testing
You can do some basic tests by logging in on a WN as a pool user and running the following:
[dte056@cagnode48 dte056]$ env|grep MPI_
You should see something like this:
MPI_MPICC_OPTS=-m32 MPI_SSH_HOST_BASED_AUTH=yes MPI_OPENMPI_PATH=/opt/openmpi/1.1 MPI_LAM_VERSION=7.1.2 MPI_MPICXX_OPTS=-m32 MPI_LAM_PATH=/usr MPI_OPENMPI_VERSION=1.1 MPI_MPIF77_OPTS=-m32 MPI_MPICH_VERSION=1.2.7 MPI_MPIEXEC_PATH=/opt/mpiexec-0.80 MPI_MPICH2_PATH=/opt/mpich2-1.0.4 MPI_MPICH2_VERSION=1.0.4 I2G_MPI_START=/opt/mpi-start/bin/mpi-start MPI_MPICH_PATH=/opt/mpich-1.2.7p1
You can also try submitting a job to your site, please read MPI-Start user documentation