NICS staff discovered issues during the maintenance that have caused us to delay the OS upgrade to CLE 3.1. The system has been returned to service running CLE 2.2, the version in production prior to the maintenance. We will announce a new date for the CLE upgrade soon.
CLE 2.2 to CLE 3.1 upgrade
The information on this page will be updated as necessary. Please check back periodically.What: Kraken's operating system is scheduled to be upgraded to Cray Linux Environment (CLE) 3.1. Users should relink their codes after the upgrade, although a full recompile may be necessary. Users should also re-submit their jobs to the queue after this maintenance as all jobs will be deleted from the queue during the upgrade. The Lustre file system on Kraken will also be upgraded from version 1.6 to 1.8. Because Lustre is a scratch filesystem, users are highly encouraged to archive their files to HPSS or otherwise safeguard their data.
When: The CLE 3.1 upgrade has been postponed until further notice.
How users will be affected
- All software compiled by the user should be relinked, although a full recompile is generally recommended due to changes in the default software versions
- We are changing the default versions and removing some versions of both Cray and 3rd party software. This will probably affect the users the most. A list of the Cray and 3rd party software as well as version cutoffs and defaults are listed at the bottom of the webpage. Users are encouraged to submit software requests for additional 3rd party software.
- Pathscale will no longer be supported - that is, no Cray or third party libraries support
- If you are doing performance tuning on an application using hardware counters through CrayPat, or if you are using the Performance API (PAPI) directly, you must load the performance tools package (perftools) 5.1 or later and recompile.
- NICS still does not support shared libraries because Cray Dynamic Shared Libraries (DSL) will not initially be supported.
- Most Cray-specific software applications have moved to /opt/cray and associated Cray-specific configuration files have moved to /etc/opt/cray. The user should not notice this change because the modules will use the correct paths. The user should continue to use modules whenever applicable.
- Cray documentation can be found at docs.cray.com
- SLES documentation can be found at www.novell.com/linux
- The Linux documentation Project can be found at www.tldp.org
Version information for Cray software
Some Cray applications will have more than one version available. Default and oldest versions available in CLE 3.1 are listed below.
| Software | Default | Oldest Version |
|---|---|---|
| acml | 4.4.0 | --- |
| apprentice2 | 5.1.3 | --- |
| atp | 1.4.1 | --- |
| cce | 7.4.4 | 7.3.4 |
| chapel | 1.4.0 | 1.3.0 |
| fftw | 3.3.0.0 | 3.2.2.1 |
| gcc | 4.6.2 | 4.4.4 |
| gdb | 7.2 | --- |
| hdf5 | 1.8.6 | 1.8.5 |
| hdf5-parallel | 1.8.6 | 1.8.5 |
| intel | 12.1.2.273 | 11.1.038 |
| iobuf | 2.0.2 | --- |
| java | jdk1.6.0_24 | --- |
| libfast | 1.0.9 | --- |
| mazama | 5.1.0 | --- |
| netcdf | 4.1.2 | 4.1.1 |
| netcdf-hdf5parallel | 4.1.2 | 4.1.1 |
| papi | 4.1.4 | 4.1 |
| perftools | 5.2.3 | 5.1.3 |
| petsc | 3.1.09 | 3.1.05 |
| petsc-complex | 3.1.09 | 3.1.05 |
| pgi | 11.9.0 | 11.4.0 |
| stat | 1.2.1.1 | --- |
| tpsl | 1.1.01 | --- |
| trilinos | 10.6.4.0 | 10.6.2.0 |
| xt-asyncpe | 5.05 | 4.9 |
| xt-atp | 1.0 | --- |
| xt-craypat | 5.1.3 | --- |
| xt-lgdb | 1.4 | --- |
| xt-libsci | 11.0.04 | 10.5.02 |
| xt-mpich2 | 5.2.3 | --- |
| xt-mpt | 5.3.5 | 5.2.3 |
| xt-papi | 4.1.0.0.2 | --- |
| xt-shmem | 5.2.3 | --- |
Version information for 3rd party software
Some applications will have more than one version available. Default and oldest versions available in CLE 3.1 are listed.
| Software | Default Version | Oldest Version |
|---|---|---|
| amber | 11 | --- |
| ambertools | 1.4 | --- |
| atlas | 3.8.3 | --- |
| cdo | 1.4.5 | --- |
| cmake | 2.8.2 | --- |
| cp2k | 2_2-branch | --- |
| desmond | 2.2.7.3_dbl | --- |
| espresso | 2.1.2j | --- |
| ferret | 6.72 | --- |
| gamess | 2010Aug10 | --- |
| glib | 2.27.0 | --- |
| global arrays | 5.0.2 | --- |
| gromacs | 4.5.3 | 4.0.7 |
| hdf4 | 4.2.6 | 4.2.5 |
| hdf5 | 1.8.6 | 1.6.10 |
| hdf5-parallel | 1.8.6 | 1.6.10 |
| hypre | 2.07b | 2.0.0 |
| lammps | 14Aug11 | 11Apr11 |
| mercurial | 1.6.4 | --- |
| ncl | 5.2.1 | 5.0.0_source |
| netcdf | 4.1.3 | 3.6.3 |
| netcdf-parallel | 4.1.3 | --- |
| numpy | 1.6.1 | --- |
| nwchem | 6 | --- |
| p-netcdf | 1.2.0 | --- |
| pango | 1.28.3 | --- |
| python | 3.1.1 | 2.7.1 |
| qbox | 1.5.0 | --- |
| qt | 4.5.2 | --- |
| scalasca | 1.3.3 | --- |
| silo | 4.8 | --- |
| subversion | 1.6.9 | --- |
| superlu | 4 | --- |
| superlu_dist | 2.4 | --- |
| tau | 2.20.3 | 2.20 |
| udunits | 2.1.13 | 1.12.9 |
| yt | 2.2 | dev |
