Marshall server

This site contains information about the Bristol Econometrics server: Marshall

server address: marshall.efm.bris.ac.uk

Current users

1. we23202        Lars Nesheim
2.                Stefan Hubner

Unix tips

set unlimited stack size

ulimit -s unlimited

build openmpi

wget xf https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.bz2
tar xf openmpi-5.0.5.tar.bz2
cd openmpi-5.0.5
./configure \
    CC=${ONEAPI_ROOT}/compiler/2024.2/bin/icx \
    CXX=${ONEAPI_ROOT}/compiler/2024.2/bin/icpx \
    FC=${ONEAPI_ROOT}/compiler/2024.2/bin/ifx \
    F77=${ONEAPI_ROOT}/compiler/2024.2/bin/ifx \
    OMPI_CC=${ONEAPI_ROOT}/compiler/2024.2/bin/icx \
    OMPI_CXX=${ONEAPI_ROOT}/compiler/2024.2/bin/icpx \
    OMPI_FC=${ONEAPI_ROOT}/compiler/2024.2/bin/ifx \
    OMPI_F77=${ONEAPI_ROOT}/compiler/2024.2/bin/ifx \
    --prefix=/opt/openmpi-5.0.5
sudo make install -j 32 
export PATH=/opt/openmpi-5.0.5/bin:$PATH
export LD_LIBRARY_PATH=/opt/optenmpi-5.0.5/lib:$LD_LIBRARY_PATH

disks:

  # df -h / /opt /home/
  Filesystem                    Size  Used Avail Use% Mounted on
  /dev/mapper/rl_marshall-root  120G   21G  100G  18% /
  /dev/mapper/rl_marshall-opt   200G   67G  134G  34% /opt
  /dev/mapper/data-home         2.2T  1.7T  568G  75% /home
  /dev/mapper/rl_marshall-tmp   100G  838M  100G   1% /tmp
  /dev/mapper/ssd-data          477G  3.4G  474G   1% /ssd
  /home = bulk data space

  /opt = software

  130GB unallocated. Options:
    50GB allocated to swap
    80GB unallocated

Questions

2. "soft" disk quota limits for /home for now at 1000GB

Software

1. CUDA => 12.6 installed along with GPU drivers for this. nvidia-smi displays correct info for card and driver. No further testing done.

2. gcc and gfortran -> Default system versions installed (8.4) => gcc 14.2.0 installed from local repo, available via module commands

3. R => R 4.4.1 installed already by "Compute" role

4. Julia => 1.10.4 installed from local repo, available via module

5. Matlab R2024 => Installed from local repo, available via module

6. Rstudio (for EL8) -> tar.gz for latest version from : https://download1.rstudio.org/electron/rhel8/x86_64/rstudio-2024.09.0-375-x86_64-fedora.tar.gz => Installed into /opt/ with a module but not yet tested in a GUI => Available via module

7. Python -> 3.6.8 provided by system packages as python3 -> python3.11 already installed as well -> Note that the 3.6.8 version is the one with most of the packages, such as numpy and scipy. If a newer version is required we can always add something as a module, via Anaconda or something other route.

8. VSCode => Available as code; no module load required

9. Intel oneapi base toolkit => Manually installed but with module files created into /opt/modulefiles/intel (via /opt/intel/oneapi/modulefiles-setup.sh --output-dir=/opt/modulefiles/intel) => Lots of installed modules now shown by module avail

10. Intel HPC toolkit => Manually installed but with module files created into /opt/modulefiles/intel

11. Nag Fortran libraries (for both Intel Fortran and GNU Fortran)

From https://support.nag.com/content/downloads-nag-library these versions apply:

• GNU gcc/gfortran version 8.1 or compatible -> https://support.nag.com/content/downloads-nag-library-nll6i27dgl (NLL6I27DG licence)

• Fortran Compiler: Intel Classic Fortran version 2021.4.0 and compatible C Compiler: Intel Classic C/C++ version 2021.4.0 and compatible GNU C version 7.3 and compatible -> https://support.nag.com/content/downloads-nag-library-nll6i302nl (NLL6I30XN licence)

• Fortran Compiler: Intel Classic Fortran version 2021.4.0 and compatible Intel Classic Fortran version 19.0.5.281 and compatible C Compiler: Intel Classic C/C++ version 2021.4.0 and compatible Intel Classic C/C++ version 19.0.5.281 and compatible GNU C version 10.3 and compatible GNU C version 11.2 and compatible -> https://support.nag.com/content/downloads-nag-library-nll6i302bl (NLL6I30XB licence)

=> Modules shown by module avail, but you'll need to load the appropriate Intel compiler/library modules as well. Note that icc is called icx now, so the examples compile but only when this is changed. Perhaps an alias will fix this?

12. Graphical interface Thinlinc

You should also be able to use `x2go' to connect to the host, which makes the connection over ssh but allows the use of a GUI remotely. If you are on a managed host then hopefully this is available in the Software Centre, but if not then it can be installed for various platforms from https://wiki.x2go.org/doku.php/download%3Astart

I've ensured that the KDE desktop is available for use from x2go, but we can add others as required. (Note that GNOME will not work with x2go because of some extensions it uses which are not supported by x2go)