cheatsheet.txt

# sinfo, squeue, sacct etc.
sinfo -p general

# Example: Performance
cd Examples/Performance
sbatch -c 1 bwa.sh # runs out of RAM (default 5GB/core)
sbatch -c 10 --mem=5g bwa.sh # also runs out
sbatch -c 10 # runs ok.  Show htop, scontrol, sacct, 
Htop: H combines threads.  F5 shows tree
sacct -j jobid
control show job jobid

# Example: Performance
$ module load Globus-CLI
$ globus login
(you'll get a url.  Open that in a browser, authenticate, and copy the code.  Enter the code on command line.)
$ globus endpoint search RobsGlobus
$ globus endpoint search yale#grace
(set env vars to R and G)
$ globus ls -l $R:/
$ globus transfer -r -s size $R:data $G:tmp/data
(returns taskid)
$ globus task show taskid

# Example Profiling python with cProfile and kernprof
#
cd Examples/Profiling
module load Python
(get compute node with srun, module load Python)
python -m cProfile -o bad.prof bad.py
(takes a minute or two)

(in python)
import pstats
p=pstats.Stats('prof.out')
p.sort_stats('time').print_stats()

or
kernprof for line-by-line
module load Python
(decorate functions with @profile)
kernprof -l bad2.py
python -m line_profiler  bad2.py.lprof

kernprof -l good.py > /dev/null
python -m line_profiler good.py.lprof

# Example: GenomePL using dSQ
cd Examples/GenomePL
module load dSQ
dSQ --jobfile tasks.sh > run.sh
sbatch run.sh #fails
sacct -j jobid
sbatch --mem=10g run.sh

# Example: R-Bootstrap
cd R-Bootstrap
sbatch parboot.sh

# Example: Namd, parallel C
cd Example/stmv
sbatch multi.sh
sbatch gpu.sh

# Example mclapply in R: R-Kmeans
cd R-Kmeans
sbatch parkmeans.sh

# Example: parallel map in Python, travelling salesman
cd Example/TSP
srun --pty -p interactive -c 10 bash
import Python
python seq.py
python map.py
python parmap.py

# Parallel C: OpenMP
make
./mm