PROBLEM IN RUNNING LIGGGHTS IN PARALLEL

Submitted by ninazbh on Wed, 07/05/2017 - 22:51

Hi,

I am trying to run my liggghts code in parallel on ubuntu 16.04 but I get the following error:

[Ubuntu:29563] *** Process received signal ***
[Ubuntu:29563] Signal: Segmentation fault (11)
[Ubuntu:29563] Signal code: Address not mapped (1)
[Ubuntu:29563] Failing at address: (nil)
[Ubuntu:29563] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7ff9090a64b0]
[Ubuntu:29563] [ 1] /lib/x86_64-linux-gnu/libc.so.6(fclose+0x4)[0x7ff9090de264]
[Ubuntu:29563] [ 2] liggghts[0x99f123]
[Ubuntu:29563] [ 3] liggghts[0x9a05e0]
[Ubuntu:29563] [ 4] liggghts[0xa00927]
[Ubuntu:29563] [ 5] liggghts[0xa0232d]
[Ubuntu:29563] [ 6] liggghts[0xa1cb72]
[Ubuntu:29563] [ 7] liggghts[0x9b5e61]
[Ubuntu:29563] [ 8] liggghts[0x9b0116]
[Ubuntu:29563] [ 9] liggghts[0x4702b1]
[Ubuntu:29563] [10] liggghts[0x470ab5]
[-Ubuntu:29563] [11] liggghts[0x412476]
[Ubuntu:29563] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff909091830]
[Ubuntu:29563] [13] liggghts[0x413319]
[Ubuntu:29563] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 29563 on node -Ubuntu exited on signal 11 (Segmentation fault).

previously, I did not have this problem. I tried to run the codes that I ran before without any issues but now I have the problem. Also, the code runs properly in serial.

I would appreciate any help in this matter.

Thanks,
Nina

Forums:

arnom's picture

arnom | Thu, 07/06/2017 - 10:17

Hi Nina,
can you please post your full case (or upload it somewhere) so that we can have a look at it?
Cheers,
Arno

DCS team member & LIGGGHTS(R) core developer

ninazbh | Fri, 07/07/2017 - 16:19

Hi Arno,

Thank you for your comment.

I changed something in my previous codes, and they again ran successfully. However, the following code gives me the same error. this code starts with reading from a restart file. Could you please let me know where I can upload the code. It needs the restart file and the STL files for the meshes. I can also post the main part of the code if the other parts are not required.

thanks,
Nina

govind | Thu, 07/20/2017 - 09:03

Any specific implementation to run scripts in parallel ?

I am following this command in terminal but does not work :
mpirun -np 4 /home/USER/LIGGGHTS-PUBLIC/src/lmp_fedora -in in.FILE

Govind

govind | Thu, 07/20/2017 - 15:17

Now I am able to run in parallel but with different error. Its says that :

ERROR: Invalid dump style

Here is the dump command :

dump dmp all custom/vtk 10000 post/dump*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius