docstring for Batch (#780)

update grid and util for sge
suny-downstate-medical-center · Oct 19, 2023 · 2b58255 · 2b58255
1 parent f013bc9
commit 2b58255
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Showing 3 changed files with 42 additions and 7 deletions.
diff --git a/netpyne/batch/batch.py b/netpyne/batch/batch.py
@@ -75,9 +75,38 @@ def tupleToStr(obj):
 # -------------------------------------------------------------------------------
 class Batch(object):
     """
-    Class for/to <short description of `netpyne.batch.batch.Batch`>
-
-
+    Class that handles batch simulations on NetPyNE.
+    Relevant Attributes:
+        batchLabel : str
+            The label of the batch used for directory/file naming of batch generated files.
+        cfgFile : str
+            The path of the file containing the `netpyne.simConfig.SimConfig` object
+        cfg : `netpyne.simConfig.SimConfig`
+            The `netpyne.simConfig.SimConfig` object
+        N.B. either cfg or cfgFile should be specified #TODO: replace with typechecked single argument
+        netParamsFile : str
+            The path of the file containing the `netpyne.netParams.NetParams` object
+        netParams : `netpyne.netParams.NetParams`
+            The `netpyne.netParams.NetParams` object
+        N.B. either netParams or netParamsFile should be specified #TODO: replace with typechecked single argument
+        initCfg : dict
+            params dictionary that is used to modify the batch cfg prior to any algorithm based parameter modifications
+        saveFolder : str
+            The path of the folder where the batch will be saved (defaults to batchLabel)
+        method : str
+            The algorithm method used for batch
+        runCfg : dict
+            Keyword: Arg dictionary used to generate submission templates (see utils.py)
+        evolCfg : dict #TODO: replace with algoCfg? to merge with optimCfg
+            Keyword: Arg dictionary used to define evolutionary algorithm parameters (see evol.py)
+        optimCfg : dict #TODO: replace with algoCfg? to merge with evolCfg
+            Keyword: Arg dictionary used to define optimization algorithm parameters
+            (see asd_parallel.py, optuna_parallel.py, sbi_parallel.py)
+        params : list
+            Dictionary of parameters to be explored per algorithm (grid, evol, asd, optuna, sbi)
+            (see relevant algorithm script for details)
+        seed : int
+            Seed for random number generator for some algorithms
     """
 
     def __init__(
@@ -88,19 +117,23 @@ def __init__(
         netParams=None,
         params=None,
         groupedParams=None,
-        initCfg={},
+        initCfg=None,
         seed=None,
     ):
         self.batchLabel = 'batch_' + str(datetime.date.today())
         self.cfgFile = cfgFile
         self.cfg = cfg
         self.netParams = netParams
-        self.initCfg = initCfg
+        if initCfg:
+            self.initCfg = initCfg
+        else:
+            self.initCfg = {}
         self.netParamsFile = netParamsFile
         self.saveFolder = '/' + self.batchLabel
         self.method = 'grid'
         self.runCfg = {}
         self.evolCfg = {}
+        self.optimCfg = {}
         self.params = []
         self.seed = seed
         if params:

diff --git a/netpyne/batch/grid.py b/netpyne/batch/grid.py
@@ -340,7 +340,7 @@ def gridSubmit(batch, pc, netParamsSavePath, jobName, simLabel, processes, proce
             'walltime': walltime,
             'vmem': '32G',
             'queueName': 'cpu.q',
-            'cores': 1,
+            'cores': 2,
             'pre': '', 'post': '',
             'mpiCommand': 'mpiexec',
             #'log': "~/qsub/{}".format(jobName)
@@ -350,7 +350,7 @@ def gridSubmit(batch, pc, netParamsSavePath, jobName, simLabel, processes, proce
         sge_args.update(batch.runCfg)
 
         #(batch, pc, netParamsSavePath, jobName, simLabel, processes, processFiles):
-        sge_args['command'] = '%s -n $NSLOTS nrniv -python -mpi %s simConfig=%s netParams=%s' % (
+        sge_args['command'] = '%s -n $NSLOTS -hosts $(hostname) nrniv -python -mpi %s simConfig=%s netParams=%s' % (
             sge_args['mpiCommand'],
             script,
             cfgSavePath,

diff --git a/netpyne/batch/utils.py b/netpyne/batch/utils.py
@@ -459,6 +459,8 @@ def jobPathAndNameForCand(index):
             elif type == 'hpc_sge':
                 executer = 'qsub'
                 queueName = args.get('queueName', 'default')
+                command = '%s -n $NSLOTS -hosts $(hostname) %s -python -mpi %s simConfig=%s netParams=%s' % (
+                    mpiCommand, nrnCommand, script, cfgSavePath, netParamsSavePath)
                 jobString = jobStringHPCSGE(
                     jobName, walltime, queueName, nodes, coresPerNode, jobPath, custom, command
                 )