diff options
| -rw-r--r-- | topics/hpc/guix/R.gmi | 25 | ||||
| -rw-r--r-- | topics/hpc/octopus/slurm-user-guide.gmi | 5 |
2 files changed, 28 insertions, 2 deletions
diff --git a/topics/hpc/guix/R.gmi b/topics/hpc/guix/R.gmi index ab85af7..6d300a0 100644 --- a/topics/hpc/guix/R.gmi +++ b/topics/hpc/guix/R.gmi @@ -10,6 +10,8 @@ The R language, for all its complexity and thousands of packages, is relatively For our purposes we had to support a package that is not in CRAN, but in one of the derived packaging systems for R. The MEDIPS package is part of the BiocManager installer and pulls in dependencies and builds them from source. +## Test with guix container + The first step was to build the package in a Guix container (guix shell -C) because that prevents from underlying dependencies getting linked from the HPC linux distro (in our case Debian Linux). For fixing the build and finding dependencies start from: ``` @@ -59,6 +61,9 @@ The reason is that the gfortran-toolchain is actually built with the older gcc ( Note that issues.guix.gnu.org is worth searching when encountering problems. +## Run without Guix container + + Once that build works inside a container, to run the tool we can move out and use a non-container shell ``` @@ -100,6 +105,8 @@ or some other package, such as install.packages("qtl") ``` +## Run on PBS + 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 ``` @@ -108,4 +115,22 @@ srun -N 1 --mem=32G --pty /bin/bash 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. +Finally set up a slurm script + +``` +#!/bin/bash +#SBATCH -t 1:30:00 +#SBATCH -N 1 +#SBATCH --mem=32G + +# --- Display environment +env +set +R -e 'library("MEDIPS")' +``` + 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. + +For more information see + +=> ../octopus/slurm-user-guide diff --git a/topics/hpc/octopus/slurm-user-guide.gmi b/topics/hpc/octopus/slurm-user-guide.gmi index feda19f..f7ea6d4 100644 --- a/topics/hpc/octopus/slurm-user-guide.gmi +++ b/topics/hpc/octopus/slurm-user-guide.gmi @@ -16,6 +16,7 @@ sinfo tells you about the slurm nodes: ``` sinfo -i +sinfo -R # show node state ``` squeue gives info about the job queue @@ -30,7 +31,7 @@ sbatch allows you to submit a batch job sbatch ``` -To get a shell prompt on one of the nodes +To get a shell prompt on one of the nodes (useful for testing your environment) ``` srun -N 1 --mem=32G --pty /bin/bash @@ -47,4 +48,4 @@ An example of using R with guix is described here: => ../../hpc/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. +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 as they work from Guix. |