title          :: Use multiple CPUs, set OMP_NUM_THREADS
presentation   :: 
scripts        ::
date           :: 2020-03
speaker        :: Taylor
outline        :: 
Many programs in AFNI can use multiple CPUs/threads
+ More than 30 programs have been compiled with OpenMP
+ Ex: 3dQwarp, 3dAllineate, 3dClustSim, 3dUnifize, 3dFWHMx, ...
Find out how many CPUs you have on your system
+ easiest way: "afni_system_check.py -check_all | grep CPU"
Find out how many CPUs the parallelized progs are using
+ easiest way: "3dQwarp -hview", and see terminal for thread count
+ NB: thread count in opened help file might not be correct (could be old)
Can change/specify with OMP_NUM_THREADS environment variable
+ find out your shell with "echo $0"
+ if it is bash, then open ~/.bashrc
  - can add line (change '6' as appropriate):  "export OMP_NUM_THREADS=6"
  - then save+close file
  - in terminal "source ~/.bashrc" or open new terminal
  - check, e.g., with "3dQwarp -hview"
+ if it is tcsh, then open ~/.cshrc
  - can add line (change '6' as appropriate):  "setenv OMP_NUM_THREADS 6"
  - then save+close file
  - in terminal "source ~/.cshrc" or open new terminal
  - check, e.g., with "3dQwarp -hview"
Examples are given of setting same variable in bash or tcsh scripts
+ similar syntax as in setting ~/.bashrc or ~/.cshrc
+ can make sure variable is passed along to sub-shells
+ special example if using a cluster (such as NIH's biowulf)
  - can set the OMP_NUM_THREADS to get set to automatically be
    the same number of CPUs as the submitted batch/slurm command,
    which is controlled by $SLURM_CPUS_PER_TASK variable (on Biowulf)
  - other clusters may have different variable names for submitted 
    CPU usage, but same idea applies