diff options
Diffstat (limited to 'topics')
| -rw-r--r-- | topics/hpc/guix/R.gmi | 21 | ||||
| -rw-r--r-- | topics/hpc/octopus/slurm-user-guide.gmi | 44 |
2 files changed, 58 insertions, 7 deletions
diff --git a/topics/hpc/guix/R.gmi b/topics/hpc/guix/R.gmi index 193379f..ab85af7 100644 --- a/topics/hpc/guix/R.gmi +++ b/topics/hpc/guix/R.gmi @@ -51,26 +51,29 @@ Error in dyn.load(libLFile) : /gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libstdc++.so.6: version 'GLIBCXX_3.4.29' not found (required by /tmp/RtmpKqzbYg/file3245e787c.so) ``` -as describes in, for example +as described in, for example => https://issues.guix.gnu.org/60200 The reason is that the gfortran-toolchain is actually built with the older gcc (even though gfortran itself is at 11.0). That is why we drop the overall toolchain to gcc-toolchain@10. -Once that works, to run the tool we can use a non-container shell +Note that issues.guix.gnu.org is worth searching when encountering problems. + +Once that build works inside a container, to run the tool we can move out and use a non-container shell ``` mkdir -p $HOME/.Rlibs && guix shell --share=$HOME/.Rlibs libpng pkg-config openblas gsl grep bzip2 libxml2 xz gfortran-toolchain r-curl zlib gcc-toolchain@10 sed gawk make r r-preprocesscore curl r-tidyverse openssl nss-certs linux-libre-headers bash which coreutils -- env R_LIBS_SITE=$HOME/.Rlibs:$R_LIBS_SITE R_LIBS_USER=$HOME/.Rlibs R ``` -Fully functional. But this is not what we want to poor our users down the throat. One option is to use `guix shell` with a manifest file that loads above dependencies. But, now it works, why not create a profile with +Now R is fully functional. But this is not what we want our users to type. +One option is to use `guix shell` with a manifest file that loads above dependencies. But, now it works, why not create a profile with ``` mkdir -p $HOME/opt guix install libpng pkg-config openblas gsl grep bzip2 libxml2 xz gfortran-toolchain r-curl zlib gcc-toolchain@10 sed gawk make r r-preprocesscore curl r-tidyverse openssl nss-certs linux-libre-headers bash which coreutils -p $HOME/opt/R ``` -Now we can do, after setting the environment (note there are a lot of parameters in that profile file which should be visible to R) +Now we can do, after setting the environment (note there are a lot of parameters in that profile file `$HOME/opt/R/etc/profile' which should be visible to R) ``` . $HOME/opt/R/etc/profile @@ -97,8 +100,12 @@ or some other package, such as install.packages("qtl") ``` -And in the final step make sure this loads in the user's shell environment and also works on cluster nodes. So all the user has to do is type 'R'. Try to submit a slurm job: +And in the final step make sure this loads in the user's shell environment and also works on cluster nodes. So all the user has to do is type 'R'. Try to get a shell on a node with + +``` +srun -N 1 --mem=32G --pty /bin/bash +``` -TBD +In the shell you can run R and check all environment settings. As I added them to the '~/.bashrc' file, they should work in bash. -As a final note - I tested all of this on my workstation first. Because Guix is reproducible, once it works, it is easy to repeat on a remote server. +As a final note - apart from SLURM - I tested all of this on my workstation first. Because Guix is reproducible, once it works, it is easy to repeat on a remote server. diff --git a/topics/hpc/octopus/slurm-user-guide.gmi b/topics/hpc/octopus/slurm-user-guide.gmi new file mode 100644 index 0000000..d00987a --- /dev/null +++ b/topics/hpc/octopus/slurm-user-guide.gmi @@ -0,0 +1,44 @@ +# Slurm User Guide on Ocotopus HPC + +The Octopus HPC uses slurm. There are many online resources for using slurm on HPC, including + +=> https://servicedesk.surf.nl/wiki/display/WIKI/SLURM+batch+system +=> https://www.carc.usc.edu/user-information/user-guides/hpc-basics/slurm-cheatsheet/ + +In this document we discuss where differences may occur. For one, Octopus is one of the busiest HPCs in the world, no kidding, because of the large scale pangenome effort at UTHSC. +As a user you will likely notice that. When you plan to fire up large jobs please discuss this on our matrix channel, otherwise jobs may get banned. Also Octopus is run by its users, pretty much in the form of a do-ocracy. Please respect our efforts. + +Important warning: Octopus is non-HIPAA. Octopus is not designed to handle sensitive data. Running clinical data without the right permissions is punishable by law. Use designated HIPAA systems for that type of data and analysis. + +# Useful commands + +sinfo tells you about the slurm nodes: + +``` +sinfo -i +``` + +sbatch allows you to submit a batch job + +``` +sbatch +``` + +To get a shell prompt on one of the nodes + +``` +srun -N 1 --mem=32G --pty /bin/bash +``` + + +# Differences + +## Guix (look ma, no modules) + +No modules: Octopus does not use the venerable module system to support deployment. In contrast it uses the modern Guix packaging system. In the future we may add Nix support too. + +An example of using R with guix is described here: + +=> ../../guix/R + +If you choose, you can still use conda, brew, spack, Python virtualenv, and what not. Userland tools will work, even Docker or singularity may work. |