Unable to load simulation output .pkl file
smcelroy97 opened this issue · comments
Scott McElroy commented
am attempting to load a .pkl file from a recent simulation, I am using the current version of netpyne from the development branch
I run sim = netpyne.sim.load(filename)
and get the following error:
Start time: 2023-10-30 15:53:25.737152
Loading file /ddn/smcelroy97/A1model_sm/data/ASSR_test/scott_A1_test_0_0_data.pkl ...
Done; file loading time = 124.88 s
Loading simConfig...
Loading netParams...
Loading net...
Unable to create Python structure: 'tags'
Added NEURON objects to 0 cells
Done; re-instantiate net time = 0.01 s
Loading simData...
Warning: could not find VecStim point process mechanism required for population IC
Creating network of 44 cell populations on 1 hosts...
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[3], line 1
----> 1 sim = netpyne.sim.load('/ddn/smcelroy97/A1model_sm/data/ASSR_test/scott_A1_test_0_0_data.pkl')
File ~/netpyne/netpyne/sim/wrappers.py:444, in load(filename, simConfig, output, instantiate, instantiateCells, instantiateConns, instantiateStims, instantiateRxD, createNEURONObj)
442 pops = sim.net.createPops() # instantiate network populations
443 if instantiateCells:
--> 444 cells = sim.net.createCells() # instantiate network cells based on defined populations
445 if instantiateConns:
446 conns = sim.net.connectCells() # create connections between cells based on params
File ~/netpyne/netpyne/network/network.py:99, in Network.createCells(self)
96 self._setDiversityRanges() # update fractions for rules
98 for ipop in list(self.pops.values()): # For each pop instantiate the network cells (objects of class 'Cell')
---> 99 newCells = ipop.createCells() # create cells for this pop using Pop method
100 self.cells.extend(newCells) # add to list of cells
101 sim.pc.barrier()
File ~/netpyne/netpyne/network/pop.py:86, in Pop.createCells(self)
84 # create cells based on fixed number of cells
85 elif 'numCells' in self.tags:
---> 86 cells = self.createCellsFixedNum()
88 # create cells based on density (optional ynorm-dep)
89 elif 'density' in self.tags:
File ~/netpyne/netpyne/network/pop.py:194, in Pop.createCellsFixedNum(self)
189 else:
190 cellTags['params']['rates'] = [
191 self.tags['dynamicRates']['rates'],
192 self.tags['dynamicRates']['times'],
193 ] # 1D list (same for all)
--> 194 cells.append(self.cellModelClass(gid, cellTags)) # instantiate Cell object
196 if sim.cfg.verbose:
197 print(
198 (
199 'Cell %d/%d (gid=%d) of pop %s, on node %d, '
200 % (i, sim.net.params.scale * self.tags['numCells'] - 1, gid, self.tags['pop'], sim.rank)
201 )
202 )
File ~/netpyne/netpyne/cell/compartCell.py:59, in CompartCell.__init__(self, gid, tags, create, associateGid)
56 self.secLists = Dict() # dict of sectionLists
58 if create:
---> 59 self.create() # create cell
60 if associateGid:
61 self.associateGid()
File ~/netpyne/netpyne/cell/compartCell.py:116, in CompartCell.create(self, createNEURONObj)
114 self.createPyStruct(prop)
115 if createNEURONObj:
--> 116 self.createNEURONObj(
117 prop, propLabel
118 )
File ~/netpyne/netpyne/cell/compartCell.py:352, in CompartCell.createNEURONObj(self, prop, propLabel)
349 sec = self.secs[sectName] # pointer to section
351 if 'geom' in sectParams:
--> 352 self._setGeometryParams(sectName, sectParams, cellType, cellVars)
354 # add distributed mechanisms
355 if 'mechs' in sectParams:
File ~/netpyne/netpyne/cell/compartCell.py:399, in CompartCell._setGeometryParams(self, sectName, sectParams, cellType, cellVars)
397 for geomParamName, geomParamValue in sectParams['geom'].items():
398 if not type(geomParamValue) in [list, dict]: # skip any list or dic params
--> 399 func, vars = CellParams.stringFuncAndVarsForGeom(cellType, sectName, geomParamName)
400 if func:
401 geomParamValue = self.__evaluateCellParamsStringFunc(func, vars, sec, cellVars=cellVars)
File ~/netpyne/netpyne/specs/netParams.py:187, in CellParams.stringFuncAndVarsForGeom(cellType, section, param)
183 @staticmethod
184 def stringFuncAndVarsForGeom(cellType, section, param):
185 from .. import sim
--> 187 funcs = sim.net.params._cellParamStringFuncs
188 return funcs.get(cellType, {}).get(section, {}).get('geom', {}).get(param, (None, []))
AttributeError: 'NetParams' object has no attribute '_cellParamStringFuncs'
Salvador Dura-Bernal commented
@smcelroy97 is this still an issue?
Scott McElroy commented
Sorry just saw this, no all good now!
…On Wed, May 1, 2024 at 3:56 PM Salvador Dura-Bernal < ***@***.***> wrote:
@smcelroy97 <https://github.com/smcelroy97> is this still an issue?
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