Difference between revisions of "Using Wynton"

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   perl step1-reformat-split_database_index-version2.pl database_index
 
   perl step1-reformat-split_database_index-version2.pl database_index
 
   check the new database_index file
 
   check the new database_index file
 
+
  cat database_index.new | awk '{ print "if test -e " $1 "; then echo " $1"; fi"}'>run.sh
 
+
  bash run.sh >>database_index.new.csh
 
+
  step3
 +
  change the dock3.7 submit files
 +
  cp -r /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/ ./
 +
  then change the position of kingbo to username
 +
  get_dock_files.csh: cp -v /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/dock/* .
 +
  rundock.csh:/wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/get_dock_files.csh
 +
  subdock.csh:qsub -t 1-$dirnum /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/rundock.csh "$dock"
 +
  submit.csh:/wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/subdock.csh /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/dock.csh
 +
  step4
 +
  submit the job
 +
  python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py ./ leads $database $num count
 +
  csh /wynton/home/shoichetlab/username/scripts/step2-submit-jobs/submit.csh
 +
  Notes:
 +
  you can change the runing time of job in file rundock.csh #$ -l h_rt=24:00:00 
 +
  You disk space is only 1TB, check it!!!!!!
 
[[Category:Internal]]
 
[[Category:Internal]]

Revision as of 11:54, 26 July 2019

Here is how to use Wynton with DOCK/ZINC

https://ucsf-hpc.github.io/wynton/status/index.html

$ ssh <username>@wynlog1.compbio.ucsf.edu
   OR
$ $ ssh <username>@log2.wynton.ucsf.edu
  • 3 here are the disks:
[benwong@wynlog1 ~]$ ls -lh /bks 
total 93K
drwxr-xr-x.  8 root  root    8 Oct  7  2018 ex1
drwxr-xr-x. 10 root  root   10 Oct  7  2018 ex2
drwxr-xr-x. 19 root  root   19 Oct  7  2018 ex3
drwxr-xr-x.  9 root  root    9 Oct  7  2018 ex4
drwxr-xr-x. 14 root  root   14 Oct  7  2018 ex5
drwxr-xr-x.  9 root  root    9 Oct  7  2018 ex6
drwxr-xr-x.  8 root  root    8 Jul 17  2018 ex7
drwxr-xr-x.  8 root  root    8 May  3  2018 ex8
drwxr-xr-x. 10 root  root   10 Jun 11 16:15 ex9
drwxrwxr-x. 67 42024 1010 4.0K Mar 15 15:18 soft
drwxr-xr-x. 46 root  root 4.0K Sep 17  2018 work

NOTE: wynton uses automount. /bks will appear empty until you specifically ls the disk you want. ls /bks may appear blank but if you do ls /bks/soft or /bks/ex9, the disk should automatically mount when you list it. If it's not working, then something's wrong.

  • 4 here is the script
 updated by xiaobo wan (2019/7/26)
 step1 
 login wynton (ssh <username>@wynlog1.compbio.ucsf.edu)
 step2 
 reformat the database_index
 cp -r /wynton/home/shoichetlab/kingbo/scripts/step1-reformat-split_database_index/step1-reformat-split_database_index-version2.pl ./
 cp -r /wynton/home/shoichetlab/kingbo/scripts/step1-reformat-split_database_index/check-split.list.new ./
 perl step1-reformat-split_database_index-version2.pl database_index
 check the new database_index file
 cat database_index.new | awk '{ print "if test -e " $1 "; then echo " $1"; fi"}'>run.sh
 bash run.sh >>database_index.new.csh
 step3
 change the dock3.7 submit files 
 cp -r /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/ ./
 then change the position of kingbo to username
  get_dock_files.csh: cp -v /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/dock/* .
  rundock.csh:/wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/get_dock_files.csh
  subdock.csh:qsub -t 1-$dirnum /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/rundock.csh "$dock"
  submit.csh:/wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/subdock.csh /wynton/home/shoichetlab/kingbo/scripts/step2-submit-jobs/dock.csh
 step4
  submit the job 
  python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py ./ leads $database $num count
  csh /wynton/home/shoichetlab/username/scripts/step2-submit-jobs/submit.csh
 Notes: 
 you can change the runing time of job in file rundock.csh #$ -l h_rt=24:00:00  
 You disk space is only 1TB, check it!!!!!!