This page may be updated with more detailed information as the time for the upgrade approaches.

After a few years of service, the ecgate Linux cluster will go through a software update on the 15th of February 2017 which involves both the operating system and the default software stack for additional libraries and utilities.

Any existing executables and libraries should be compatible with the new system and should still work. No recompilation is needed but it is advisable to make sure everything works with the new set of compiler and libraries.

Highlights

  • Operating system update: from Red Hat Enterprise Linux (RHEL) 6.4 to 6.8.
  • Compiler: from GCC 4.4.7 to 5.3
  • Updated defaults for a number of additional libraries and tools. This bulk update includes utilities like python or R, as well as libraries such as netcdf 4. The old defaults are still available tagged as "old" in modules. See below for details.

How to test the new configuration

A new partition of the cluster has been created with the new setup for this occasion. The nodes on that partition are RHEL 6.8 and any fresh login on those loads the new default environment.

The jobs on the test partition can be submitted replacing the usual sbatch command with sbatch_test.

Note that using this command, the environment from the submitting session WILL NOT be propagated to the job in the test partition. A fresh environment with the new defaults will be loaded instead for the job.

SLURM is not affected by this upgrade, so the rest of batch commands such as squeue, scancel, sqos, etc. will remain unchanged.

Once the upgrade is completed, the test partition will disappear along with the sbatch_test command.

To test interactive applications such as sms/xcdp, ecflow, or prepIFS you can log in to ecgb18 doing 'ssh ecgb18'

List of changes in software defaults:

The defaults for ECMWF packages such as grib_api, eccodes, magics or metview are not affected.

SOFTWAREOLD DEFAULTNEW DEFAULTNotes
GCC4.4.75.3https://gcc.gnu.org/gcc-5/
python2.7.32.7.12
  • Updated all extra python modules
  • MKL used for linear algebra in numpy

https://hg.python.org/cpython/raw-file/v2.7.12/Misc/NEWS

R2.15.23.3.1
  • Updated all extra R packages
  • MKL used for all linear algebra operations

https://cran.r-project.org/doc/manuals/r-release/NEWS.html

hdf4.2.104.2.12https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.12/src/hdf-4.2.12-RELEASE.txt
hdf51.8.10p11.8.17https://support.hdfgroup.org/ftp/HDF5/releases/ReleaseFiles/hdf5-1.8.17-RELEASE.txt
netcdf44.3.24.4.1
  • Built with hdf5 1.8.17

http://www.unidata.ucar.edu/blogs/news/entry/netcdf-4-4-1

cdo1.6.11.7.2
  • With Grib, netcdf 4, hdf5 and Magics support

https://code.zmaw.de/news/349

nco4.0.84.6.1http://nco.sourceforge.net/ANNOUNCE
gdal1.9.22.1.1https://trac.osgeo.org/gdal/wiki/Release/2.1.1-News
geos3.4.23.5.0https://trac.osgeo.org/geos/browser/tags/3.6.0/NEWS
proj44.8.04.9.2https://github.com/OSGeo/proj.4/blob/4.9.2/ChangeLog
gsl1.152.2.1http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS
boost1.50.01.61.0http://www.boost.org/users/history/version_1_61_0.html

Regrettably, we are no longer able to provide access to the IDL and PV-WAVE software packages on ecgate.  Anyone using IDL might like to try instead the open source GNU data language package (GDL).  GDL provides full syntax compatibility with IDL up to version 7.1 and some features of IDL version 8.  GDL can be accessed with:

module load gdl
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