1. Update siman to the last version
2. In the description of clusters in simanrc, add 'scratch' variable and provide path to your scratch folder, which should start with /scr followed by you personal folder: On razor128 could be any name On Magnus (do not use, because we have old ssd disks on magnus ) should be different from your home folder name.
CLUSTERS['raz128'] = { 'address':'aksenov@10.30.98.103', 'vasp_com':'srun vasp_std', 'homepath':'/home/aksenov/', 'schedule':'SLURM', 'corenum':16, 'scratch':'/scr/aksenov/', # this is new variable, which turns on calculation on scratch 'modules':'source /etc/profile.d/modules.sh; module load devtools/mpi/mpich/4.2.1/gcc/11.2; module load devtools/math/mkl/2024.1.0.695; module load q-ch/vasp/5.4.4_mpich_mkl;' }
To check the calculation progress you can add the following alias to your .bashrc:
alias qs="squeue -o '%o' | awk -F / '{\$(NF--)} {gsub(\" \",FS)}; {gsub(\"home\", \"scr\")} \$0=\"cd \"\$0 '"
But be aware that before switching to calculation folder on scratch you should ssh to the corresponding node:
squeue # check number node of your calculation, e.g. node02 ssh n2 qs # shows paths to scratch cd path # choose required job from the output of qs
Below is example of script which will be created: You can see that your calculation folder is copied to scratch, the calculation is executed in scratch and then the results and moved back to you home folder
#!/bin/bash #SBATCH -J Fe26Al.ifn5.s4eqd1d20.0A22nclsons110 #SBATCH -N 1 #SBATCH -n 16 #SBATCH -o /home/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110/sbatch.out #SBATCH -e /home/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110/sbatch.err #SBATCH -p zen4 #create folder in scratch, copy files, and switch to scratch folder mkdir -pv /scr/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110 cp /home/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110/* /scr/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110 cd /scr/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110 source /etc/profile.d/modules.sh; module load zen4/vasp/5.4.4_openmpi_gcc_aocl export PATH=$PATH:/home/aksenov//tools/ #Basic run: python /home/aksenov//tools/siman/cluster_runners/shiftk.py > shiftk.log #Footer section, copy files back and remove folder from scratch mv /scr/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110/* /home/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110 rm -r /scr/aksenov/Fe/MAE/Fe26Al.ifn5.s4eqd1d20.0A22nclsons110