...
Finally, to plot, just use the plotting script from the tutorial as usual (no need to run this on Slurm!).
Additional Notes for Environments
I (Rachel) am using a Singularity image for non-SALT studies, made from Ines Ochoa's Docker container (here). This is a big image, and compiling it on SDF causes a crash due to insufficient tmp directory space. The solution was to specify the SINGULARITY_TMPDIR when building the image, as follows (on SDF):
| Code Block |
|---|
[rhyneman@sdf-login02 ~]$ export SINGULARITY_TMPDIR=/sdf/group/atlas/g/XbbXccTrainingData/singularity/
[rhyneman@sdf-login02 ~]$ singularity pull --dir /sdf/group/atlas/g/XbbXccTrainingData/singularity/ --disable-cache vertexing.sif docker://miaochoa/vertexing |
To use this container in an interactive SDF shell, one can just do: singularity shell /sdf/group/atlas/g/XbbXccTrainingData/singularity/vertexing.sif
One can also use this container in an SDF Jupyter notebook/shell by calling this Singularity image on creation. Just put the following commands in the "Commands to initate Jupyter" box:
| Code Block |
|---|
export SINGULARITY_IMAGE_PATH=/sdf/group/atlas/g/XbbXccTrainingData/singularity/vertexing.sif
function jupyter() { singularity exec --nv -B /sdf,/gpfs,/scratch,/lscratch ${SINGULARITY_IMAGE_PATH} jupyter $@; } |
(Not sure if the above should be exec or shell !)