netpyne.batch.utils

Module with helper functions to set up and run batch simulations

Functions:

createFolder(folder)	Function for/to <short description of netpyne.batch.utils.createFolder>
jobStringMPIDirect(custom, folder, command)
jobStringHPCSlurm(jobName, allocation, ...)
jobStringHPCTorque(jobName, walltime, ...)
jobStringHPCSGE(jobName, walltime, vmem, ...)	creates string for SUN GRID ENGINE https://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html recommended optional pre and post commands rsync -a $SGE_O_WORKDIR/ $TMPDIR/ cd $TMPDIR <execute command here> rsync -a --exclude '.run' --exclude '.err' $TMPDIR/ $SGE_O_WORKDIR/
cp(obj[, verbose, die])	Function for/to <short description of netpyne.batch.utils.cp>
dcp(obj[, verbose, die])	Function for/to <short description of netpyne.batch.utils.dcp>
sigfig(X[, sigfigs, SI, sep, keepints])	Function for/to <short description of netpyne.batch.utils.sigfig>
runJob(nrnCommand, script, cfgSavePath, ...)	Function for/to <short description of netpyne.batch.utils.runJob>
evaluator(batch, candidates, args, ngen, pc, ...)

netpyne.batch.utils.createFolder(folder)

Function for/to <short description of netpyne.batch.utils.createFolder>

Parameters:

folder (<type>) – <Short description of folder> Default: required

netpyne.batch.utils.jobStringMPIDirect(custom, folder, command)

netpyne.batch.utils.jobStringHPCSlurm(jobName, allocation, walltime, nodes, coresPerNode, jobPath, email, reservation, custom, folder, command)

netpyne.batch.utils.jobStringHPCTorque(jobName, walltime, queueName, nodes, coresPerNode, jobPath, custom, command)

netpyne.batch.utils.jobStringHPCSGE(jobName, walltime, vmem, queueName, cores, pre, command, post, log, **kwargs)

creates string for SUN GRID ENGINE https://gridscheduler.sourceforge.net/htmlman/htmlman1/qsub.html recommended optional pre and post commands rsync -a $SGE_O_WORKDIR/ $TMPDIR/ cd $TMPDIR <execute command here> rsync -a –exclude ‘.run’ –exclude ‘.err’ $TMPDIR/ $SGE_O_WORKDIR/

netpyne.batch.utils.cp(obj, verbose=True, die=True)

Function for/to <short description of netpyne.batch.utils.cp>

Parameters:

• obj (<type>) – <Short description of obj> Default: required

• verbose (bool) – <Short description of verbose> Default: True Options: <option> <description of option>

• die (bool) – <Short description of die> Default: True Options: <option> <description of option>

netpyne.batch.utils.dcp(obj, verbose=True, die=False)

Function for/to <short description of netpyne.batch.utils.dcp>

Parameters:

• obj (<type>) – <Short description of obj> Default: required

• verbose (bool) – <Short description of verbose> Default: True Options: <option> <description of option>

• die (bool) – <Short description of die> Default: False Options: <option> <description of option>

netpyne.batch.utils.sigfig(X, sigfigs=5, SI=False, sep=False, keepints=False)

Function for/to <short description of netpyne.batch.utils.sigfig>

Parameters:

• X (<type>) – <Short description of X> Default: required

• sigfigs (int) – <Short description of sigfigs> Default: 5 Options: <option> <description of option>

• SI (bool) – <Short description of SI> Default: False Options: <option> <description of option>

• sep (bool) – <Short description of sep> Default: False Options: <option> <description of option>

• keepints (bool) – <Short description of keepints> Default: False Options: <option> <description of option>

netpyne.batch.utils.runJob(nrnCommand, script, cfgSavePath, netParamsSavePath, simDataPath, rankId)

Function for/to <short description of netpyne.batch.utils.runJob>

Parameters:

• script (<type>) – <Short description of script> Default: required

• cfgSavePath (<type>) – <Short description of cfgSavePath> Default: required

• netParamsSavePath (<type>) – <Short description of netParamsSavePath> Default: required

• simDataPath (<type>) – <Short description of simDataPath> Default: required

netpyne.batch.utils.evaluator(batch, candidates, args, ngen, pc, **kwargs)