Problem Regarding Parallel Simulations

Hello everyone,

I have problem using parallel Cassanda.
I have a 8 core machine, CentOS 6.5 and I use gfortran compiler. I've been able to run a serial simulation using Cassandra without any problem, but when I try to run a parallel simulation I run into this error:

Segmentation fault (core dumped)

This is how I compiled the code:

1- In src diectory I run:
make -f Makefile.gfortran.openMP

2- I copy the created executable file to Examples/GEMC/Methane directory, and I run:
export OMP_NUM_THREADS=8
./cassandra_gfortran_openMP.exe methane.inp

And it gives an error: Segmentation fault (core dumped)

I would appreciate if anybody can help me.

Thank you,

-Mostafa

Mostafa,

Thank you for reporting the issue. Could you provide more details on the ensemble and system you are trying to simulate? Also, could you look at the end of the log file *.log and let us know the output?

Jindal

Jindal,

Thank you for your response. I used the methane GEMC system which can be found in the Example directory (481 methane molecules at 175K)
Here is the end of the log file:
.
.
.

*** Completed assigning intramolecular scaling factors ***

There are 1 different atom types in the system
1 CH4_UA


species number and name: 1 methane_UA_TraPPE.mcf
Name number

---

---

CH4_UA 1


*** Creating VDW interaction table ***
Mixing rule used is: LB

Atom 1 Atom 2 epsilon (amu A^2/ps^2) sigma (A)
CH4_UA CH4_UA 123.0542 3.7300

*** Completed construction of VDW interaction table ***


*** Creating exclusion table ***

species atom1 atom2 vdw scale q-q scale
1 1 1 0.000 0.000

*** Completed construction of exclusion table ***


***** Reading seed info *********

The starting seed s1 is: 153587801

****** Finished loading the seed ********

**** Simulation temperature information ****
Temperature assigned to box 1 is 175.000 K

Temperature assigned to box 2 is 175.000 K

*** Finished loading information for temperature ****


********* Move Probability Info******
Translation probability is 0.988000

Maximum displacement width for species 1 in box 1 is 0.15000

Maximum displacement width for species 1 in box 2 is **********


Probability for volume move is 0.002000

Maximum volume displacement for box in GEMC_NVT simulation is
200.000

Volume moves will be performed in actual volumes

Probability for particle swap is 0.010000

Insertion will be carried out for species 1
using the reservoir sampling

Total number of exchangeable species is 1


Probabilties of swap for individual boxes not specified
Defaulting to uniform probabilities

******** Box pair selection probabilities *********

1 1 0.000000
1 2 1.000000
2 1 1.000000
2 2 1.000000
***** Finished reading the move probability info *****
Number of moves is : 3


***** reading CBMC info *********

Writing out CBMC_Info
kappa for first bead insertion 12
kappa for rotational bias 0
kappa for dihedral selection 12

Smaller cutoff for CBMC for box 1 6.50
Smaller cutoff for CBMC for box 2 6.50
****** finished loading CBMC_Info ********

Thermodynamic quantities will written at every 1000 MC steps.

Coordinates will be written at every 10000 MC steps.

movie header file for box 1 is methane_H.box1
movie_XYZ file for box 1 is methane_box1.xyz

Mostafa,
Hi,
I have the same problem with parallel simulation but the serial simulation run just fine, i think the problem is with volume attempt in parallel version,
set the probabilities to
# Prob_Translation
0.988
0.15
1.0_DP

# Prob_Volume
0.0001
200.0

# Prob_Swap
0.0119

and run your simulation again, it works fine , but when the number of steps or volume probability increase , the error appear.

Javad

Javad,
Than you for your response. I changed my input file as you instructed, but I still encounter the same error.

Hi Mostafa, I am pretty sure that the problem is due the stack size.
First check the current value:
% ulimit -s
and then try to increase it to something huge to check if this is the problem e.g. use the command:
% ulimite -s unlimited
If this works you can specify what is a critical value of the stack (just using unlimited when you run cassandra I think it will not be a problem)