Linux ROMIO MPI Interface

ROMIO is a particular implementation of the MPI-IO protocol, the open standard for data transfer to and from MPI.

MPI, also an open standard, was created for researchers who needed a message-passing interface optimized for high performance parallel computing.

Different working implementations for MPI, also called MPI libraries, exist. Two popular MPI libraries are MPICH from Argonne National Laboratory and Open MPI from a consortium of users including Oak Ridge National Laboratory.

Different implementations of MPI-IO also exist. The ROMIO implementation includes support for OrangeFS. Therefore, any MPI library implementation that works with ROMIO, such as MPICH and Open MPI, can also work with OrangeFS.

Setting up a ROMIO client involves one step, with options for configuring Open MPI or MPICH:

Configuring for Linux

Both MPICH and Open MPI are packaged with ROMIO. Configuring either of these MPI implementations to access OrangeFS involves two areas:

Adding OrangeFS Installation Files

To add the OrangeFS installation files to the MPI client system, Change Directory (cd) to /opt on the client and copy the /opt/orangefs directory from the build system:

scp -r hostname:/opt/orangefs /opt

where…

hostname = host name of the build system

Linking Programs to OrangeFS

When you run your Open MPI or MPICH applications, link to OrangeFS by including the -lpvfs2 option.

For example, to run a program called mytest, you would follow these steps:

  1. Compile and link the program to the pvfs2 library in your OrangeFS installation:

cc mytest.c -o mytest -L /opt/orangefs/lib -L /mpich2_install_dir/lib -I /opt/orangefs/include -I /mpich2_install_dir/include  -lpvfs2 -lmpich

where…

mpich2_install_dir = the name and path of your MPICH installation directory

Other Operating Environments

ROMIO can also run on Windows and Mac. Those platforms are less efficient for the high performance parallel computing that most ROMIO users seek in OrangeFS, so the above instructions focus on Linux client implementations only.

Install OrangeFS 2.9 with MPICH 3.0.4

Notes   You must install OrangeFS on your storage nodes and the OrangeFS system must be online prior to performing these steps. If you have not completed this step, see the Installation Guide for instructions to complete this step before proceeding.

For instructions on how to use MPICH, see MPICH User’s Guide.

Secure Shell (SSH)—without Passphrase

You must configure all clients to support secure shell connections via SSH without passing a passphrase. For more information, see Generating SSH Keys for Passwordless Login, an article from the Hortonworks Knowledgebase.

Prior to configuring MPICH, ensure that you have built shared libraries for OrangeFS:

  1. Run the same ./configure command you used when you installed OrangeFS, but add the following additional option:

–enable-shared

To configure OrangeFS to work with MPICH 3.0.4, complete the following steps:

  1. Run the following commands to remove references to methods included in MPICH that will cause errors during the ./configure stage.

Note     You will not be able to use the MPI/IO functions IReadContig and IWriteContig.

sed -i s/ADIOI_PVFS2_IReadContig/NULL/  
src/mpi/romio/adio/ad_pvfs2/ad_pvfs2.c
sed -i s/ADIOI_PVFS2_IWriteContig/NULL/
src/mpi/romio/adio/ad_pvfs2/ad_pvfs2.c

  1. Compile MPICH with –enable-shared option:

./configure –prefix=/opt/mpich-3.0.4 –enable-romio –enable-shared –with-pvfs2=/opt/orangefs –with-file-system=pvfs2

where…

/opt/orangefs = the location of your OrangeFS installation

/opt/mpich-3.0.4 = the location of your MPICH installation

Note     You can remove the –prefix command to install to/usr/local

  1. Make and install freshly compiled MPICH 3.0.4 with OrangeFS Support

·sudo make all install

  1. Set LD_LIBRARY_PATH to point to the MPICH libs

export LD_LIBRARY_PATH=/opt/mpich-3.0.4/lib:\$LD_LIBRARY_PATH

where…

opt/mpich-3.0.4 = the location of your MPICH installation

Install OrangeFS 2.9 with Open MPI 1.6.5

Notes   You must install OrangeFS on your storage nodes and the OrangeFS system must be online prior to performing these steps. If you have not completed this step, see the Installation Guide for instructions to complete this step before proceeding.

OrangeFS 2.9.0 has been successfully tested with OpenMPI 1.8.3 on CentOS 7. No patches are necessary to run OrangeFS with OpenMPI 1.8.3. If you are using this version, skip steps 1 and 2 below, and change the OpenMPI version number in step 3.

For instructions on how to use Open MPI, see Open MPI: Open Source High Performance Computing.

Secure Shell (SSH)—without Passphrase

You must configure all clients to support secure shell connections via SSH without passing a passphrase. For more information, see Generating SSH Keys for Passwordless Login, an article from the Hortonworks Knowledgebase.

Prior to configuring MPICH, ensure that you have built shared libraries for OrangeFS:

  1. Run the same ./configure command you used when you installed OrangeFS, but add the following additional option:

–enable-shared

To configure OrangeFS to work with Open MPI 1.6.5, complete the following steps.

  1. Patch the Open MPI 1.6.5 source to support OrangeFS:
    Patch the Open MPI installation using the openmpi-1.6.5-romio.patch file. This patch is available on the OrangeFS

patch -p0 < openmpi-1.6.5-romio.patch

  1. Run the following commands to remove references to methods included in Open MPI that will cause errors during the ./configure stage.

Note     You will not be able to use the MPI-IO functions IReadContig and IWriteContig.

sed -e ’s/ADIOI_PVFS2_IReadContig/NULL/’ \
-i ompi/mca/io/romio/romio/adio/ad_pvfs2/ad_pvfs2.c
sed -e ’s/ADIOI_PVFS2_IWriteContig/NULL/’ \
-i ompi/mca/io/romio/romio/adio/ad_pvfs2/ad_pvfs2.c

  1. Compile Open MPI with the –enable-shared and –with-pic options:

./configure –prefix=/opt/openmpi-1.6.5 –enable-shared –with-pic –with-io-romio-flags=“–with-pvfs2=/opt/orangefs –with-file-system=pvfs2”

where…

/opt/orangefs = the location of your OrangeFS installation

/opt/openmpi-1.6.5 = the location of your Open MPI installation

Note     You can remove the –prefix command to install to/usr/local

  1. Make and install freshly compiled Open MPI 1.6.5 with OrangeFS Support

·sudo make all install

  1. Set LD_LIBRARY_PATH to point to the Open MPI libs

export LD_LIBRARY_PATH=/opt/openmpi-1.6.5/lib:\$LD_LIBRARY_PATH

where…

/opt/orangefs = the location of your OrangeFS installation

/opt/openmpi-1.6.5 = the location of your Open MPI installation