This is not official documentation for the Vienna Scientific Cluster. For this check the VSC Wiki. Instead, this is my personal cheat sheet of things that are not well documented elsewhere. Also while the content is focused on the VSC, most of the things mentioned here also apply to similar setups that use Slurm at other universities.
Always request an interactive session when running anything using a non-trivial amount of CPU power!
# Quick interactive session
➜ salloc --ntasks=2 --mem=2G --time=01:00:00
Don’t forget to then connect to the node you get assigned:
➜ ssh n1234-567
$HOME is limited to 100 GB and storing/compiling code. Anything else should be stored at
The file size and number of files is limited by group. The current status can be read using
➜ mmlsquota --block-size auto -j data_fs00000 data
for $DATA and
➜ mmlsquota --block-size auto -j home_fs00000 home
for $HOME where
00000 is the ID of the own project (accessible using
# Job scripts
# Basic Template
Your job script is a regular bash script (
.sh file). In addition, you can specify options to
sbatch in the beginning of your file:
#!/bin/bash #SBATCH --job-name=somename #SBATCH --mail-type=ALL #SBATCH --firstname.lastname@example.org
--job-name: A short name for this job. It is often displayed truncated after a few characters.
--mail-type=ALL: notify on all events per E-Mail
In these cases
--long-option value are equivalent.
# Single Core job
--ntask=1 and the amount of memory you need.
#SBATCH --ntasks=1 # (also -n 1) #SBATCH --mem 2G
All options can be found in the slurm documentation. A few useful ones are:
-N: request X nodes
--time: limit the run time, e.g.
10:00for 10 hours
--mem: memory limit, e.g.
-o: where to store the output of the executed script
--dependency=afterany:1234: only run job after job with ID 1234 has terminated
# Useful Environment Variables
Especially the latter can be used e.g. for running MPI programs with the requested number of CPU cores:
➜ mpiexec -np $SLURM_NPROCS ./program
# Submitting Jobs
A job script can be submitted using
➜ sbatch jobfile.sh # you can also add sbatch options here
Just like in regular shell scripts, you can pass arguments to
jobfile.sh like this
➜ sbatch jobfile.sh somevalue
and then access
$1 in your script. This way multiple similar jobs can be submitted without needing to edit the jobscript.
The current status of jobs in the Queue can be seen using
➜ squeue -u username
Especially useful is the estimated start time of a scheduled job:
➜ squeue -u username --start
A lot more information about scheduling including the calculated priority of jobs can be found using
➜ sprio -u username
This will also show the reason why the job is still queued for which an explanation can be found in the slurm documentation or the VSC wiki.
Details about past Jobs (like maximum memory usage), can be found using
sacct. You can manually specify the needed columns or display most of them using
➜ sacct -j 2052157 --long
# SSH login via login.univie.ac.at
official docs (but we are using the more modern ProxyJump instead of Agent forwarding as this way we don’t have to trust the intermediate server with our private key)
Access to VSC is only possible from IP addresses of the partner universities. If you are from the University of Vienna and don’t want to use the VPN, an SSH tunnel via
login.univie.ac.at is an alternative.
To connect to the login server, the easiest thing is to put the config for the host in your
~/.ssh/config (create it, if it doesn’t yet exist).
Host loginUnivie HostName login.univie.ac.at User testuser12 # replace with your username # the following are needed if you are using OpenSSH 8.8 or newer # and the login server isn't yet updated to a never version HostkeyAlgorithms +ssh-rsa PubkeyAcceptedAlgorithms +ssh-rsa
This way you should now be able to test connecting to the login server using
➜ ssh loginUnivie
Then you can add another entry to
~/.ssh/config on your computer for VSC that uses
ProxyJump to connect via the
loginUnivie entry we just created.
Host vsc5 Hostname vsc5.vsc.ac.at User vscuser ProxyJump loginUnivie # Port 27 # (only use if you are using ssh keys)
➜ ssh vsc5
# Spack Modules
(official docs, that this guide builds on. More useful tips can be found in the spack documentation)
Software that is needed can be loaded via modules. The easiest way to find the right module for the current processor architecture, is directly querying
spack, which is used to provide all compiled libraries and applications. There should never be a need to run
module directly and doing so might accidentally pick libraries that are not intended for the current processor architecture.
# Finding the right module
The easiest way is using
➜ spack find cmake
If you get a long output, you can ignore everything above the
==> N installed package(s) line as it is unrelated to your current query. In case this only returns one module that fits your requirements, you can directly replace
spack find with
spack load to load this module.
But most of the time, you will find multiple modules which differ in their properties (and
spack load will fail if the query resolves to more than one package):
➜ spack find cmake ==> 4 installed packages -- linux-almalinux8-zen / email@example.com ----------------------------- firstname.lastname@example.org -- linux-almalinux8-zen2 / email@example.com ----------------------- firstname.lastname@example.org -- linux-almalinux8-zen3 / email@example.com --------------------------- firstname.lastname@example.org -- linux-almalinux8-zen3 / email@example.com --------------------------- firstname.lastname@example.org
The most important property is the version and it is denoted with an
@ sign. Another property is the compiler the program or library was compiled with and it can be separated with a
So if you want to load e.g.
cmake version 3.x.x compiled with
gcc version 11, you could directly search for it and subsequently load it.
➜ spack find cmake@3%gcc@11 ➜ spack load cmake@3%gcc@11
This way if another minor update of cmake is released, your command will load it. If you don’t like this, check the next section.
Sometimes there are also multiple variants of the same module.
spack info modulename can give you an overview over all of them, but that doesn’t mean that all combinations of variants/compilers/versions are offered at VSC. If you are for example interested in the
hdf5 library with MPI support, you can search for the following (
-v gives you the exact properties of each module):
➜ spack find -v hdf5 +mpi
# “Locking” modules
If you dislike the fact that
spack load queries don’t resolve to specific packages, but just filters that describe the properties you want or prefer exactly specifying the version of a package for reproducibility, you can find the hash of package using
spack find -l and can then use
/hash to always refer to this exact package:
➜ spack find -l gsl ==> 1 installed package -- linux-almalinux8-zen3 / email@example.com --------------------------- 4rhrhm3 firstname.lastname@example.org $ spack load /4rhrhm3
# Find currently loaded modules
# List all currently loaded packages ➜ spack find --loaded # Unload all currently loaded packages ➜ spack unload --all
# Avoiding broken programs due to loaded dependencies
Loading a spack module not just loads the specified module, but also all dependencies of this module. With some modules like
openmpi that dependency tree can be quite large.
➜ spack find -d openmpi%gcc -- linux-almalinux8-zen3 / email@example.com --------------------------- firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com slurm@22-05-2-1 firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org email@example.com firstname.lastname@example.org
And loading module like
ncurses from spack means that programs that depend on those libraries, but the versions provided by the base operating system, will crash.
➜ spack load openmpi%gcc ➜ nano somefile.txt Segmentation fault (core dumped) ➜ htop Segmentation fault (core dumped)
One can avoid this by unloading the affected modules afterwards.
➜ spack unload ncurses ➜ spack unload openssl
But in many cases one doesn’t need all dependency modules and is really just interested in e.g.
openmpi itself. Therefore, one can ignore the dependencies with
# doesn't affect non-openmpi programs ➜ spack load --only package openmpi%gcc
# Comparing modules
Sometimes two packages look exactly the same:
➜ spack find -vl fftw -- linux-almalinux8-zen2 / email@example.com ----------------------- mmgor5w firstname.lastname@example.org+mpi+openmp~pfft_patches precision=double,float cy5tkce email@example.com+mpi+openmp~pfft_patches precision=double,float
Then you can use
spack diff to
➜ spack diff /mmgor5w /cy5tkce
--- firstname.lastname@example.org/mmgor5w3daiwtsdbyl4dfhjsueaciry2 +++ email@example.com/cy5tkcetpgx35rok2lqfi3d66rjptkva @@ depends_on @@ - fftw intel-oneapi-mpi build + fftw openmpi build [...]
Therefore, we know that in this example the first package depends on intel-oneapi-mpi and the second one on
# Debugging modules
Sometimes one needs to know what
spack load somepackage does exactly (e.g. because a library is still not found even though you loaded the module). Adding
spack load prints out all commands that would be executed during the
module load allowing you to understand what is going on.
➜ spack load --sh cmake%gcc@8 export ACLOCAL_PATH=[...]; export CMAKE_PREFIX_PATH=[...]; export CPATH=[...]; export LD_LIBRARY_PATH=[...]; export LIBRARY_PATH=[...]; export MANPATH=[...]; export PATH=[...]; export PKG_CONFIG_PATH=[...]; export SPACK_LOADED_HASHES=[...];
# Commonly used modules
This is a list of modules I commonly use. While it might not be directly usable for other people and will go out of date quickly, it might still serve as a good starting point.
spack load --only package openmpi@firstname.lastname@example.org/rpec5sw spack load --only package email@example.com spack load --only package firstname.lastname@example.org # GNU Autotools spack load --only package email@example.com/uglkavv # firstname.lastname@example.org +mpi spack load --only package email@example.com spack load --only package firstname.lastname@example.org spack load --only package email@example.com spack load --only package firstname.lastname@example.org spack load --only package email@example.com # spack load --only package firstname.lastname@example.org module load gcc/11.2.0-gcc-11.2.0-5i4t2bo spack load --only package email@example.com%gcc@11