This page is for anyone who has recently upgraded (or is otherwise in the process of upgrading) their managed Linux workstation from bionic to focal.
Please note that there are some differences between the software packages available for focal compared to those that are or were available for bionic. We have highlighted some of the differences that are most likely to be of interest to our users.
Please read this page in conjunction with the list of supported software on our focal image.
Default Modules
On bionic and earlier, we provided a module called standard-apps which automatically loaded a number of standard applications. In practice we have found that this has become less and less useful over time, and as of bionic the applications automatically loaded by standard-apps were as follows:
- foxit : no longer available in focal
- vmd : you should manually run module load vmd if necessary
- matlab : available on the path by default; you only need to load a module if you need the non-default version
- uscfchimera : you should manually run module load uscfchimera if necessary
We still provide the standard-apps module to avoid errors for users who have a .bashrc which loads it, but as of focal the module does nothing and should not be used.
The module free-compilers previously automatically loaded solarisstudio but that is a very old compiler and as is more likely to be hurtful than helpful to have it loaded, so it is no longer loaded automatically. You can still load it yourself should you so wish.
Available Modules
Of the modules that the Computer Officers have packaged for focal, the following are available (as of 2022-03-22):
$ module av -------------- /usr/local/share/modules/modulefiles --------------- ambertools/21 moe/2020.0901 anaconda/python3/5.2.0 moe/current anaconda/python3/5.3.1 mpi/intel/2021/2/0 anaconda/python3/2021.11 mpi/mpich/gnu/4.0.1 aten/2.1.9 mpi/openmpi/64/gnu/4.1.2 cmake/3.19.1 nag/64/5.2/721 compilers nag/64/5.3.1/907 free-compilers/64 nag/64/5.3/854 gaussian/03-E01 nag/64/6.0/1037 gaussian09/09-E01/amd64 nag/64/6.1/6116 gaussian09/09-E01/amd64_sse4 nag/64/6.2/6214 gaussian16/16-B01/x86_64 nag/64/7.0/7005 gaussian16/16-B01/x86_64_avx nag/64/7.1/7101 gaussian16/16-B01/x86_64_avx2 netcdf/gnu/4.8.1 gaussian16/16-B01/x86_64_sse4 netcdf/intel/4.8.1 grads/2.2.1 netcdff/gnu/4.5.4 hdf5/gnu/serial/1.12.1 netcdff/intel/4.5.4 hdf5/intel/serial/1.12.1 nvhpc-cuda/22.2 icc/64/2020/4/304 nvhpc/22.2 icc/64/2021/3/0 nwchem/7.0.2 icc/64/2022/0/1 oneapi-compiler-rt/64/2021/3/0 idb/2021.5.0 oneapi-compiler-rt/64/2022/0/1 idb/latest orca/5.0.3 ifort/64/2020/4/304 schrodinger/2019-1 ifort/64/2021/3/0 schrodinger/2021-4 ifort/64/2022/0/1 schrodinger/2022-1 intelpython/python3/2020/4/100 schrodinger/current jmol/14.2.15 solarisstudio/12.3 julia/1.6.6 standard-apps julia/1.7.2 tbb/64/2021/2/0 knime/4.0.2 tbb/64/2021/3/0 mathematica/12.2.0 tbb/64/2022/0/1 mathematica/current theory-compilers/64 matlab/current ucc-apps matlab/R2021a ucsfchimera/1.16 matlab/R2022a vmd/64/1.9.2 mkl/64/2020/0/4 vmd/64/1.9.3 mkl/64/2021/0/3 xmakemol/5.16GL mkl/64/2022/0/0 xtb/6.3.2 moe/2020.09
If there was a module that you used as part of your workflow on bionic, please check that either the same module is available on focal, or a suitable alternative. You may need to upgrade to newer versions.
Please note in particular that Python 2 is not installed by default and no anaconda module is provided for Python 2. If you have any scripts that refer to /usr/bin/python then you will either need to install a package that provides that binary or (preferably) update your scripts to use /usr/bin/python3 instead.
The hdf5 modules may not support binding with Fortran 2003.
System packages
The following system packages are not available at all on focal:
- banshee
- eclipse
- libgrib-api0: Please migrate to libeccodes instead. See https://confluence.ecmwf.int/display/ECC
- octave-odepkg
- python-cf: The upstream package claims to have Python 3 support; please try using through anaconda.
- python3-subversion
- xpdf
- xxdiff
The following system packages used to be pre-installed on our bionic image but are not pre-installed on focal:
- mercurial (depends on Python 2).
Other
Ubuntu handles printing slightly differently in focal than it did previously. As a result, some printers may not work (either without re-configuration or possibly even at all). If you are worried about upgrading because you need to use a particular printer/printer model, let us know and we will do our best to advise.
Questions
If you have any questions about the managed Ubuntu 20.04 focal offering, please contact the Computer Officers.
