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Merge pull request #198 from Neurosim-lab/development
PR from development to master - VERSION 0.6.8
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@@ -75,6 +75,7 @@ Requires NEURON with Python and MPI support. | |
| * **netpyne/utils.py**: utility python methods (eg. to import cell parameters) | ||
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| Please cite as: "Salvador Dura-Bernal, Padraig Gleeson, Cliff C Kerr, Samuel Neymotin, William W Lytton. (2017). Neurosim-lab/NetPyNE: v0.6.7 [Data set]. Zenodo. http://doi.org/10.5281/zenodo.290623" | ||
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| For further information please contact: [email protected] | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,3 +1,3 @@ | ||
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| __version__ = '0.6.7' | ||
| __version__ = '0.6.8' | ||
| __gui__ = True # global option to enable/disable graphics |
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| Original file line number | Diff line number | Diff line change |
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@@ -8,10 +8,11 @@ | |
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| import datetime | ||
| from itertools import product | ||
| from itertools import izip, product | ||
| from popen2 import popen2 | ||
| from time import sleep | ||
| import imp | ||
| from netpyne import specs | ||
| from neuron import h | ||
| pc = h.ParallelContext() # use bulletin board master/slave | ||
| if pc.id()==0: pc.master_works_on_jobs(0) | ||
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@@ -30,15 +31,18 @@ def runJob(script, cfgSavePath): | |
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| class Batch(object): | ||
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| def __init__(self, cfgFile='cfg.py', netParamsFile='netParams.py'): | ||
| def __init__(self, cfgFile='cfg.py', netParamsFile='netParams.py', params=None): | ||
| self.batchLabel = 'batch_'+str(datetime.date.today()) | ||
| self.cfgFile = cfgFile | ||
| self.netParamsFile = netParamsFile | ||
| self.params = [] | ||
| self.saveFolder = '/'+self.batchLabel | ||
| self.method = 'grid' | ||
| self.runCfg = {} | ||
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| self.params = [] | ||
| if params: | ||
| for k,v in params.iteritems(): | ||
| self.params.append({'label': k, 'values': v}) | ||
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| def save(self, filename): | ||
| import os | ||
| basename = os.path.basename(filename) | ||
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@@ -55,10 +59,13 @@ def save(self, filename): | |
| dataSave = {'batch': self.__dict__} | ||
| if ext == 'json': | ||
| import json | ||
| #from json import encoder | ||
| #encoder.FLOAT_REPR = lambda o: format(o, '.12g') | ||
| print('Saving batch to %s ... ' % (filename)) | ||
| with open(filename, 'w') as fileObj: | ||
| json.dump(dataSave, fileObj, indent=4, sort_keys=True) | ||
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| def run(self): | ||
| if self.method in ['grid','list']: | ||
| # create saveFolder | ||
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@@ -86,88 +93,171 @@ def run(self): | |
| cfgModule = imp.load_source(cfgModuleName, self.cfgFile) | ||
| self.cfg = cfgModule.cfg | ||
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| # iterate over all param combinations | ||
| if self.method == 'grid': | ||
| # iterate over all param combinations | ||
| labelList, valuesList = zip(*[(p['label'], p['values']) for p in self.params]) | ||
| valueCombinations = product(*(valuesList)) | ||
| indexCombinations = product(*[range(len(x)) for x in valuesList]) | ||
| elif self.method == 'list': | ||
| pass | ||
| groupedParams = False | ||
| for p in self.params: | ||
| if 'group' not in p: | ||
| p['group'] = False # by default set linear to False | ||
| elif 'group' == True: | ||
| groupedParams = True | ||
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| labelList, valuesList = zip(*[(p['label'], p['values']) for p in self.params if p['group'] == False]) | ||
| valueCombinations = list(product(*(valuesList))) | ||
| indexCombinations = list(product(*[range(len(x)) for x in valuesList])) | ||
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| if groupedParams: | ||
| labelListGroup, valuesListGroup = zip(*[(p['label'], p['values']) for p in self.params if p['group'] == True]) | ||
| valueCombGroups = izip(*(valuesListGroup)) | ||
| indexCombGroups = izip(*[range(len(x)) for x in valuesListGroup]) | ||
| else: | ||
| valueCombGroups = [(0,)] # this is a hack -- improve! | ||
| indexCombGroups = [(0,)] | ||
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| # if using pc bulletin board, initialize all workers | ||
| if self.runCfg.get('type', None) == 'mpi': | ||
| for iworker in range(int(pc.nhost())): | ||
| pc.runworker() | ||
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| for iComb, pComb in zip(indexCombinations, valueCombinations): | ||
| for i, paramVal in enumerate(pComb): | ||
| paramLabel = labelList[i] | ||
| if isinstance(paramLabel, tuple): | ||
| container = getattr(self.cfg, paramLabel[0]) | ||
| container[paramLabel[1]] = paramVal | ||
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| #if 1: | ||
| #for iComb, pComb in zip(indexCombinations, valueCombinations): | ||
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| for iCombG, pCombG in zip(indexCombGroups, valueCombGroups): | ||
| for iCombNG, pCombNG in zip(indexCombinations, valueCombinations): | ||
| if groupedParams: # temporary hack - improve | ||
| iComb = iCombG+iCombNG | ||
| pComb = pCombG+pCombNG | ||
| else: | ||
| setattr(self.cfg, paramLabel, paramVal) # set simConfig params | ||
| print str(paramLabel)+' = '+str(paramVal) | ||
| iComb = iCombNG | ||
| pComb = pCombNG | ||
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| # save simConfig json to saveFolder | ||
| simLabel = self.batchLabel+''.join([''.join('_'+str(i)) for i in iComb]) | ||
| self.cfg.simLabel = simLabel | ||
| self.cfg.saveFolder = self.saveFolder | ||
| cfgSavePath = self.saveFolder+'/'+simLabel+'_cfg.json' | ||
| self.cfg.save(cfgSavePath) | ||
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| # skip if output file already exists | ||
| jobName = self.saveFolder+'/'+simLabel | ||
| if self.runCfg.get('skip', False) and glob.glob(jobName+'.json'): | ||
| print 'Skipping job %s since output file already exists...' % (jobName) | ||
| else: | ||
| # hpc torque job submission | ||
| if self.runCfg.get('type',None) == 'hpc_torque': | ||
| print iComb, pComb | ||
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| # read params or set defaults | ||
| sleepInterval = self.runCfg.get('sleepInterval', 1) | ||
| sleep(sleepInterval) | ||
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| numproc = self.runCfg.get('numproc', 1) | ||
| script = self.runCfg.get('script', 'init.py') | ||
| walltime = self.runCfg.get('walltime', '00:30:00') | ||
| queueName = self.runCfg.get('queueName', 'default') | ||
| nodesppn = 'nodes=1:ppn=%d'%(numproc) | ||
| for i, paramVal in enumerate(pComb): | ||
| paramLabel = labelList[i] | ||
| if isinstance(paramLabel, tuple): | ||
| container = self.cfg | ||
| for ip in range(len(paramLabel)-1): | ||
| if isinstance(container, specs.SimConfig): | ||
| container = getattr(container, paramLabel[ip]) | ||
| else: | ||
| container = container[paramLabel[ip]] | ||
| container[paramLabel[-1]] = paramVal | ||
| else: | ||
| setattr(self.cfg, paramLabel, paramVal) # set simConfig params | ||
| print str(paramLabel)+' = '+str(paramVal) | ||
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| command = 'mpiexec -np %d nrniv -python -mpi %s simConfig=%s' % (numproc, script, cfgSavePath) | ||
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| output, input = popen2('qsub') # Open a pipe to the qsub command. | ||
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| jobString = """#!/bin/bash | ||
| #PBS -N %s | ||
| #PBS -l walltime=%s | ||
| #PBS -q %s | ||
| #PBS -l %s | ||
| #PBS -o %s.run | ||
| #PBS -e %s.err | ||
| cd $PBS_O_WORKDIR | ||
| echo $PBS_O_WORKDIR | ||
| %s""" % (jobName, walltime, queueName, nodesppn, jobName, jobName, command) | ||
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| # Send job_string to qsub | ||
| input.write(jobString) | ||
| print jobString+'\n' | ||
| input.close() | ||
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| # pc bulletin board job submission (master/slave) via mpi | ||
| # eg. usage: mpiexec -n 4 nrniv -mpi batch.py | ||
| elif self.runCfg.get('type',None) == 'mpi': | ||
| jobName = self.saveFolder+'/'+simLabel | ||
| print 'Submitting job ',jobName | ||
| # master/slave bulletin board schedulling of jobs | ||
| pc.submit(runJob, self.runCfg.get('script', 'init.py'), cfgSavePath) | ||
| # set simLabel and jobName | ||
| simLabel = self.batchLabel+''.join([''.join('_'+str(i)) for i in iComb]) | ||
| jobName = self.saveFolder+'/'+simLabel | ||
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| # skip if output file already exists | ||
| if self.runCfg.get('skip', False) and glob.glob(jobName+'.json'): | ||
| print 'Skipping job %s since output file already exists...' % (jobName) | ||
| elif self.runCfg.get('skipCfg', False) and glob.glob(jobName+'_cfg.json'): | ||
| print 'Skipping job %s since cfg file already exists...' % (jobName) | ||
| else: | ||
| # save simConfig json to saveFolder | ||
| self.cfg.simLabel = simLabel | ||
| self.cfg.saveFolder = self.saveFolder | ||
| cfgSavePath = self.saveFolder+'/'+simLabel+'_cfg.json' | ||
| self.cfg.save(cfgSavePath) | ||
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| # hpc torque job submission | ||
| if self.runCfg.get('type',None) == 'hpc_torque': | ||
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| # read params or set defaults | ||
| sleepInterval = self.runCfg.get('sleepInterval', 1) | ||
| sleep(sleepInterval) | ||
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| numproc = self.runCfg.get('numproc', 1) | ||
| script = self.runCfg.get('script', 'init.py') | ||
| walltime = self.runCfg.get('walltime', '00:30:00') | ||
| queueName = self.runCfg.get('queueName', 'default') | ||
| nodesppn = 'nodes=1:ppn=%d'%(numproc) | ||
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| command = 'mpiexec -np %d nrniv -python -mpi %s simConfig=%s' % (numproc, script, cfgSavePath) | ||
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| output, input = popen2('qsub') # Open a pipe to the qsub command. | ||
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| jobString = """#!/bin/bash | ||
| #PBS -N %s | ||
| #PBS -l walltime=%s | ||
| #PBS -q %s | ||
| #PBS -l %s | ||
| #PBS -o %s.run | ||
| #PBS -e %s.err | ||
| cd $PBS_O_WORKDIR | ||
| echo $PBS_O_WORKDIR | ||
| %s""" % (jobName, walltime, queueName, nodesppn, jobName, jobName, command) | ||
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| # Send job_string to qsub | ||
| input.write(jobString) | ||
| print jobString+'\n' | ||
| input.close() | ||
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| # hpc torque job submission | ||
| elif self.runCfg.get('type',None) == 'hpc_slurm': | ||
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| # read params or set defaults | ||
| sleepInterval = self.runCfg.get('sleepInterval', 1) | ||
| sleep(sleepInterval) | ||
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| allocation = self.runCfg.get('allocation', 'csd403') # NSG account | ||
| nodes = self.runCfg.get('nodes', 1) | ||
| coresPerNode = self.runCfg.get('coresPerNode', 1) | ||
| email = self.runCfg.get('email', '[email protected]') | ||
| folder = self.runCfg.get('folder', '.') | ||
| script = self.runCfg.get('script', 'init.py') | ||
| walltime = self.runCfg.get('walltime', '00:30:00') | ||
| numproc = nodes*coresPerNode | ||
| command = 'ibrun -np %d nrniv -python -mpi %s simConfig=%s' % (numproc, script, cfgSavePath) | ||
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| jobString = """#!/bin/bash | ||
| #SBATCH --job-name=%s | ||
| #SBATCH -A %s | ||
| #SBATCH -t %s | ||
| #SBATCH --nodes=%d | ||
| #SBATCH --ntasks-per-node=%d | ||
| #SBATCH -o %s.run | ||
| #SBATCH -e %s.err | ||
| #SBATCH --mail-user=%s | ||
| #SBATCH --mail-type=end | ||
| source ~/.bashrc | ||
| cd %s | ||
| %s | ||
| wait | ||
| """ % (jobName, allocation, walltime, nodes, coresPerNode, jobName, jobName, email, folder, command) | ||
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| # Send job_string to qsub | ||
| # output, input = popen2('sbatch') # Open a pipe to the qsub command. | ||
| # input.write(jobString) | ||
| print 'Submitting job ',jobName | ||
| print jobString+'\n' | ||
| # input.close() | ||
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| batchfile = '%s.sbatch'%(jobName) | ||
| with open(batchfile, 'w') as text_file: | ||
| text_file.write("%s" % jobString) | ||
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| #subprocess.call | ||
| output, pinput = popen2('sbatch '+batchfile) # Open a pipe to the qsub command. | ||
| pinput.close() | ||
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| # pc bulletin board job submission (master/slave) via mpi | ||
| # eg. usage: mpiexec -n 4 nrniv -mpi batch.py | ||
| elif self.runCfg.get('type',None) == 'mpi': | ||
| jobName = self.saveFolder+'/'+simLabel | ||
| print 'Submitting job ',jobName | ||
| # master/slave bulletin board schedulling of jobs | ||
| pc.submit(runJob, self.runCfg.get('script', 'init.py'), cfgSavePath) | ||
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| # wait for pc bulletin board jobs to finish | ||
| try: | ||
| while pc.working(): | ||
| sleep(1) | ||
| pc.done() | ||
| #pc.done() | ||
| except: | ||
| pass | ||
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