mpi-start for site administrators
Contents
Installation
Binary Distribution
Binary packages for mpi-start are generated in EMI using ETICS. Check EMI repositories for the correct package for your distribution. Once you have the repositories configured you only need to install the package using your favorite package manager.
For RedHat based distributions:
yum install mpi-start
Debian based:
apt-get install mpi-start
If you are running a gLite site, you may prefer to install the glite-mpi or emi-mpi (for EMI-2 and onwards) meta-package that includes the yaim plugin for configuraton. Information about this package is available at MPI-Utils.
For RedHat based distributions:
yum install emi-mpi
Debian based:
apt-get install emi-mpi
The nodes where the user applications will be executed (Worker Nodes) also require a working MPI implementation, Open MPI and MPICH-2 are recommended. The devel packages should also be installed in order to allow user to compile their applications. Refer to your OS repositories for the exact packages. In the case of SL5, Open MPI (including devel packages) can be installed with the following command line:
yum install openmpi openmpi-devel
devel packages and compilers
Some devel packages of the MPI packages do not include the compiler as (e.g. gcc, gcc-gfortran, gcc-g++) dependency! They should be installed also if you want to support the compilation of MPI applications.
Upgrading from EMI-1 to EMI-2
There are no major changes in functionality between EMI-1 and EMI-2 releases, but the metapackage has changed the name from glite-mpi to emi-mpi. If you configure the EMI-2 repos in a EMI-1 installation, the metapackage will be upgraded without the need to specify anything.
$ yum upgrade ... LOG HERE ....
Source Distribution
Source can be retrieved from the mercurial repository.
Installation is as easy as "make install". The default installation prefix is /usr. If a non default installation wants to be done, use the PREFIX variable in make install
$ make install PREFIX=/opt/mpi-start
In this case, is recommendable setting the installation the environment variable I2G_MPI_START to point to mpi-start script (although this is not mandatory anymore).
$ export I2G_MPI_START=/opt/mpi-start/bin/mpi-start
mpi-start Configuration
yaim Configuration
There is a yaim plugin available for configuring gLite sites, check the documentation at MPI-Utils page.
Manual Configuration
mpi-start is designed to auto detect most of the site configurations without any administrator intervention. The default installation will automatically detect:
- the batch scheduler at the site: currently PBS/Torque, SGE, LSF, Condor and Slurm are supported.
- existence of shared file system in the job running directory
mpi-start uses a set of files to configure its behavior. There are several paths where the files can be located. All of them will be checked when looking for hooks, execution environments or scheduler plugins. These are the paths (and the order) used by default in mpi-start:
Any path pointed by environment variable MPI_START_ETC.
A .mpi-start directory at current user's home.
The etc/mpi-start under mpi-start installation path. On default installations
that would be /.
The first file that mpi-start checks is the mpi-config.local file. This should contain the appropriate location of your local MPI installations and any other modifications you want to introduce in the default behavior. mpi-start includes such file with the default configuration for your system in RHEL/SL 5, RHEL/SL 6 and Ubuntu.
Typical variables that the administrator can set in this file are:
Variable |
Meaning |
MPI_DEFAULT_FLAVOUR |
name of the default flavour for jobs running at the site |
MPI_<flavour>_PATH |
Path of the bin and lib directories for the MPI flavour |
MPI_<flavour>_MODULE |
Name of the module that loads the MPI flavour environment. When defined, the MPI_<flavour>_PATH will not be used. |
MPI_<flavour>_VERSION |
preferred version of the MPI flavour |
MPI_<flavour>_MPIEXEC |
Path of the MPIEXEC binary for the specific flavour |
MPI_<flavour>_MPIEXEC_PARAMS |
Parameters for the MPIEXEC of the flavour |
MPI_<flavour>_MPIRUN |
Path of the MPIRUN binary for the specific flavour |
MPI_<flavour>_MPIRUN_PARAMS |
Parameters for the MPIRUN of the flavour |
I2G_<flavour>_PREFIX |
Path of the MPI installation for the MPI flavour |
MPI_<flavour>_MPI<compiler> |
Location of the compiler for the flavour. Compiler may be one of CC, F90, F77 or CXX |
A known issue with the setting of the I2G_<flavour>_PREFIX variable makes them useless, please use the MPI_<flavour>_PATH variable instead!
If MPI_<flavour>_MPIEXEC or MPI_<flavour>_MPIRUN are not defined, mpi-start will try to use the mpiexec or mpirun that are found in the current PATH.
Hooks
Hooks may change the behavior of mpi-start and provide additional features such as file distribution and configuration of compiler flags. Site admins can add their own hooks via the local hook mechanism.
mpi-start includes hooks for distributing the files needed for the execution of an application. By default it tries to find the most suitable method for copying the files, using shared filesystems whenever they are found. However, the filesystem detection may not work for all sites, or the shared filesystem may be in a different location to the execution path making it impossible for mpi-start to detect its availability. Check Hooks Framework for more information.