Page History

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• rhel5 - Red Hat Enterprise Linux 5.8 or CentOS 5.8.
• rhel6 - Red Hat Enterprise Linux 6.3 or CentOS 6.3.
• ubu12rhel7 - Ubuntu 12.04 LTSRed Hat Enterprise Linux 7.2 or CentOS 7.2.

Different minor versions of the same platform may also work, for example one could try to install ubu12 software on Ubuntu 12.10. This might work but not work but not be officially supported.

Prerequisites

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• System packages for rhel5
• System packages for rhel6
• System packages for ubu12

Site setup

Once all prerequisites are fulfilled one can move to the next step - setting up software distribution on your site/machine. For that one has to download a script from SLAC and run it, this has to be done from the user account that manages software and has write access to root directory created in previous step.

# for RHEL5/6
curl -o site-setup.sh http://pswww.slac.stanford.edu/psdm-repo/dist_scripts/site-setup.sh
# for RHEL7
curl -o site-setup.sh http://pswww.slac.stanford.edu/psdm-repo/dist_scripts/site-setup-rh7.sh
# for both
chmod 755 site-setup.sh

The script takes one argument which is a location of the root directory:

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apt-get update
apt-get install psdm-release-ana-latest-rhel5

For Ubuntu 12.04:

apt-get update
apt-get install psdm-release-ana-latest-ubu12

More than one platform can be installed at once, e.g.:

apt-get update
apt-get install psdm-release-ana-latest-ubu12rhel5 psdm-release-ana-latest-rhel6

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and you are ready. (You should probably do this from some other account).

Installation Customization

If you have installed a release in a non-standard locations (rather than at /reg/g/psdm) at your site/computer then the MPI application won't be able to find certain files. That's because the installation path for the library is hard-wired into OpenMPI binaries and libraries at a time when the library is being built. This problem is explained in this OpenMPI FAQ. A solution to this problem is to find a location where the library is installed within your release and set an environment variable OPAL_PREFIX overriding the base path. Here is how this variable could be set at SLAC for RHEL5 if you're using TCSH.

setenv OPAL_PREFIX /reg/g/psdm/sw/external/openmpi/1.8.1/x86_64-rhel5-gcc41-opt/

Also, starting with release ana-0.14.1 you can specify the location of your data directory (the equivalent of "/reg/d/psdm" at SLAC) with the environment variable SIT_PSDM_DATA.  You can also do this when you specify the DataSource with an option similar to "dir=/reg/d/ffb/amo/amoi0114/xtc", but the environment variable provides a clean method to do so "globally".

MPI

Starting with ana-0.18.0, the openmpi package is built to dynamically load lsf components. Offsite users will typically not have lsf. sit_setup will, by default, set the following environment variables

OMPI_MCA_ess  ^lsf
OMPI_MCA_ras   ^lsf
OMPI_MCA_plm  ^lsf

Advanced users may want to control these environment variables themselves. If so, set

SIT_NO_MODIFY_OMPI_ENV=1

If your offsite has a lsf installation you want to try, set LSF_PACKAGE_LIB appropriately. sit_setup will use this directory instead.

Release upgrade

When you want to upgrade to the new version of the analysis release run this from the same account that was used to install everything:

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These commands will find out what is the most recent release available at SLAC, download it with all dependencies and install. If you installed release for multiple architectures (rhel5/rhel6/ubu12) then they all will be upgraded.

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