[moose-generic] Help running Moose in MPI mode

[Linda J <lin...@ca...>]

Hi all,
I am trying to use Moose for some research purposes, so far, I have 
successfully compiled and run for a single node, now I'm planning to run 
on a multinode-cluster or using MPI, but I face a lot of difficulties 
like segmentation faults and aborts.

I built using the following command first,
      make BUILD=mpi
after installing, I ran the scripts like shown below
      mpirun.mpich -np 4 python Demos/squid/squid.py

How to run Moose using MPI?

Below is the output, I got
__________________________________________________________________________________
on node 0, numNodes = 4, numCores = 4
++++Warning: Ignored attempt to set Cm of compartment  to less than 1e-15
Traceback (most recent call last):
   File "Demos/squid/squid.py", line 372, in <module>
     test()
   File "Demos/squid/squid.py", line 366, in test
     model = SquidModel('model')
   File "Demos/squid/squid.py", line 314, in __init__
     self.squid_axon = SquidAxon(path+'/squid_axon')
Warning: Ignored attempt to set Cm of compartment  to less than File 
"Demos/squid/squid.py", line 194, in __init__
1e-15
     self.specific_gl = SquidAxon.defaults['specific_gl']
   File "Demos/squid/squid.py", line 257, in specific_gl
     self.Rm = 1.0/(value * self.area)
ZeroDivisionError: float division by zero
+++++Warning: Ignored attempt to set Cm of compartment  to less than 1e-15
Traceback (most recent call last):
   File "Demos/squid/squid.py", line 372, in <module>
     test()
   File "Demos/squid/squid.py", line 366, in test
+    model = SquidModel('model')
   File "Demos/squid/squid.py", line 314, in __init__
+    self.squid_axon = SquidAxon(path+'/squid_axon')
   File "Demos/squid/squid.py", line 217, in __init__
     SquidAxon.VMAX)
   File "Demos/squid/squid.py", line 81, in setupAlpha
     gate = moose.HHGate(self.path + '/gateX')
Traceback (most recent call last):
   File "Demos/squid/squid.py", line 372, in <module>
ValueError: Parent element does not exist: /model[0]/squid_axon[0]/K[0]
Warning: Ignored attempt to set Cm of compartment  to less than 1e-15    
test()

   File "Demos/squid/squid.py", line 366, in test
Traceback (most recent call last):
     model = SquidModel('model')
   File "Demos/squid/squid.py", line 372, in <module>
   File "Demos/squid/squid.py", line 314, in __init__
     test()
   File "Demos/squid/squid.py", line 366, in test
     self.squid_axon = SquidAxon(path+'/squid_axon')
       File "Demos/squid/squid.py", line 205, in __init__
     model = SquidModel('model')
   File "Demos/squid/squid.py", line 314, in __init__
SquidAxon.VMAX)
     self.squid_axon = SquidAxon(path+'/squid_axon')
   File "Demos/squid/squid.py", line 194, in __init__
       File "Demos/squid/squid.py", line 81, in setupAlpha
self.specific_gl = SquidAxon.defaults['specific_gl']
   File "Demos/squid/squid.py", line 257, in specific_gl
         self.Rm = 1.0/(value * self.area)
ZeroDivisionError: gate = moose.HHGate(self.path + '/gateX')
ValueError: float division by zero
Parent element does not exist: /model[0]/squid_axon[0]/Na[0]
*** Error in `python': free(): invalid size: 0x00007f1816bf58a0 ***
*** Error in `python': free(): invalid size: 0x00007f53f58bd8a0 ***
*** Error in `python': free(): invalid size: 0x00007f2083f898a0 ***
*** Error in `python': free(): invalid size: 0x00007fa02baa98a0 ***

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)

-- 
Regards,
Linda J