how to compile and run MitoGen on IT4I cluster

gistfile1.txt

# once on a cluster, say after `ssh salomon`

# --------------- prepare and compile ---------------
# add necessary dev modules
. /scratch/work/project/open-19-3/simulators_libs/addModulesAtIT4I

# get sources and prepare env
git clone ...daPath...
cd $clonedFolder
mkdir BUILD
cd BUILD

# setup cmake
. /scratch/work/project/open-19-3/simulators_setupCmake.cmd

# review setup, compile
ccmake ..
make -j10

# check: should list only sys and compiler libs, no 3rd party such as lapack or TIFF
ldd ./mitogen

# test (notice it reports git commit hash)
./mitogen


# --------------- ready to go ---------------
# review time limit (or number of requested nodes) for the planned run,
# probably make own copy and edit it
cp /scratch/work/project/open-19-3/simulators_runOnCluster.cmd simulators_runOnCluster.cmd
vim simulators_runOnCluster.cmd

# run through your copy of the aux batch that sets up scheduling & accounting for you
mkdir run2; cd run2
# now in ....../BUILD/run2
#
. ../simulators_runOnCluster.cmd ../mitogen \
    -c ../../config-synthHeLa/standard_masks/config-synthHela.ini \
    -g ../../config-synthHeLa/standard_masks/initialII.ics \
    \| tee log.txt

# notes:
. operator executes content of the file in the running shell (not in a new one as with scripts)
..._runOnCluster.cmd creates a script runCmd*.sh to be executed in the cluster,
one can use it again to rerun the simulation anytime later
..._runOnCluster.cmd submits this script as a job into the cluster for you,
after the job is over, two files (MG*.o* and MG*.e*) are created in the folder where job was submitted (this folder),
the files contain stdout and stderr outputs from the runCmd* script

# inspect job status
qstat -u yourLogin