Deprecated: please see new documentation site.


Queen Bee will be available as of Tuesday, February 23, 2010 after an upgrade to the system. In addition to finishing the file system recovery, the kernel, InfiniBand software, and Lustre were also upgraded to new versions to help eliminate problems we have been experiencing with the kernel and the Lustre file system. We have also deployed new versions of the core software stack. This page explains changes that users will notice after Queen Bee's recent upgrade.

Software

All software packages are now listed under /usr/local/packages/<package_name>/<package_version>/<compiler-compiler_version>.

Users can find a listing of all software available on Queen Bee here (QB Tab). If there is software that you used to use before the upgrade that is no longer available, please first check if we've provided a newer version and be sure to update your ~/.soft file with the appropriate keys (listed on the software page). Please note that the names of many softenv keys changed after the upgrade. If the software is not listed, please send a email to sys-help@loni.org with your software request, as well as a description of why you need the software, and if it will be used only by yourself, or multiple users.

Recompiling User Codes

We have upgraded the Intel and GNU compilers as well as the mvapich packages. As such, if you are running MPI jobs, you will need to recompile your code. The default mvapich-compiler package is now mvapich-1.1-intel-11.1. Please send email to sys-help@loni.org if you have problems recompiling your codes.

Many libraries have also been recompiled and the location of the libraries have changed as notited above. Please be sure to update your paths to point to the appropriate location of the necessary libraries.

OpenMPI issues

OpenMPI has been upgraded to version 1.3.4. A very important difference between this version and the old 1.2.x versions is that, in the new version, the "-machinefile $PBS_NODEFILE" option MUST be used with the mpirun command, otherwise all processes will be started on the master node only rather than spreading across all nodes.

TeraGrid Packages

TeraGrid packages are available as before and should work without any issues. The packages are currently in the same location as before the upgrade but will be moved shortly to /usr/local/packages/teragrid.

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