Submitting a vina (autodock) job

Vina understands multithreading, and will automatically spawn four threads on a four-core machine. This means that you are better-off asking directly for -N1 (ie. one node) and avoid complications. To submit a job

  • Collect all your files in a directory. For example :
-rw------- 1 glykos glykos 253037 Mar  8 11:26 4HD5.pdbqt
-rw------- 1 glykos glykos   1474 Mar  8 11:26 GlcNAc.pdbqt
-rw------- 1 glykos glykos    152 Mar  8 11:26 example.cfg
  • Prepare a submission script, let's say script.sh containing the following:
#!/bin/tcsh 
 
vina --config example.cfg
 
exit
  • Submit it to the non-cuda partition of the cluster :
sbatch -p noncuda -n4 -N1 script.sh

Results will appear in the current directory, the output will be contained in the file slurm-*.out, and the directory will look something like this after job completion :

-rw------- 1 glykos glykos 253037 Mar  8 11:26 4HD5.pdbqt
-rw------- 1 glykos glykos   1474 Mar  8 11:26 GlcNAc.pdbqt
-rw------- 1 glykos glykos    152 Mar  8 11:26 example.cfg
-rw-r--r-- 1 glykos glykos  13869 Mar  8 11:40 out.pdbqt
-rw-r--r-- 1 glykos glykos     46 Mar  8 11:33 script.sh
-rw-r--r-- 1 glykos glykos   1792 Mar  8 11:40 slurm-3040.out


research/howto/submitting_a_vina_autodock_job.txt · Last modified: 2014/03/20 16:43 by glykos