Memory problem
Posted: Thu Aug 03, 2017 7:52 am
Hi NEURON Forum,
I am simulating a model of ~1500 cells (each having 20-30 variables) for 90 secs, and then vector recording the membrane potential and calcium in each cell at a timestep of 0.1ms.
The simulations run for ~1 hour, and then the python process gets killed. If you look at top, %MEM gets to about 99% before it terminates. I am using the following code to save the recorded vectors for each cell into an array:
Where each cell is from a cell template.
All we are interested in (for the time being) is the calcium and voltage time-series for each cell. Any reason why this might be happening and how to work around this? We were hoping to double (or more) our simulation time, but it looks like we are at our memory limit.
Cheers,
Linford
I am simulating a model of ~1500 cells (each having 20-30 variables) for 90 secs, and then vector recording the membrane potential and calcium in each cell at a timestep of 0.1ms.
The simulations run for ~1 hour, and then the python process gets killed. If you look at top, %MEM gets to about 99% before it terminates. I am using the following code to save the recorded vectors for each cell into an array:
Code: Select all
vecvm = []
vecca = []
for i in range(ncells):
vecvm.append(h.Vector())
vecca.append(h.Vector())
vecvm[i].record(cell[i].soma(0.5)._ref_v)
vecca[i].record(cell[i].soma(0.5)._ref_ca)
...
h.run()
...
for i in range(ncells):
vecvm[i] = np.array(vecvm[i])
All we are interested in (for the time being) is the calcium and voltage time-series for each cell. Any reason why this might be happening and how to work around this? We were hoping to double (or more) our simulation time, but it looks like we are at our memory limit.
Cheers,
Linford