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suny-downstate-medical-center / netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.
http://www.netpyne.org
MIT License
144 stars 135 forks source link

addition of SGE submission script #755

Closed jchen6727 closed 1 year ago

jchen6727 commented 1 year ago

utils, batch modified to support submission to SGE

jchen6727 commented 1 year ago

batch:

netpyne/netpyne/batch. grid and utils to run on HPC SGE (qsub). see jobStringHPCSGE in utils. def jobStringHPCSGE(jobName, walltime, vmem, queueName, cores, custom, command, log, **kwargs): the arguments specified in runCfg include:

        sge_args = {
        # def jobStringHPCSGE(jobName, walltime, vmem, queueName, cores, custom, command)
            'jobName': jobName,
            'walltime': walltime,
            'vmem': '32G',
            'queueName': 'cpu.q',
            'cores': 1,
            'custom': '',
            'mpiCommand': 'mpiexec',
            'log': "~/qsub/{}.run".format(jobName)
        }