Hi all,
I am trying to run a simulation in LAMMPS (Parallel Executable). And
all of a sudden I got an error message which I did not find in previous
occasions. I am posting the error message along with some earlier parts.
LAMMPS (21 Feb 2013)
Scanning data file ...
4 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (-0.1 -0.1 -0.1) to (25 25 0.1)
2 by 1 by 1 MPI processor grid
8061 atoms
10548 bonds
5274 angles
Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
981 atoms in group inner
1805 atoms in group outer
1 atoms in group bead
6255 atoms in group 2
Setting up run ...
Hi all,
I am trying to run a simulation in LAMMPS (Parallel Executable). And
all of a sudden I got an error message which I did not find in previous
occasions. I am posting the error message along with some earlier parts.
LAMMPS (21 Feb 2013)
Scanning data file ...
4 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (-0.1 -0.1 -0.1) to (25 25 0.1)
2 by 1 by 1 MPI processor grid
8061 atoms
10548 bonds
5274 angles
Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
981 atoms in group inner
1805 atoms in group outer
1 atoms in group bead
6255 atoms in group 2
Setting up run ...
=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
While searching about the error in web I found that it is probably due
to some reason related with 'mpich2' and due to stack overflow..
May be this is a more technical error rather than normal bugs. But I
couldn't able to fix the issue.
this report is far too generic and there is not enough information to
draw any conclusions.
you should try running the same input on a different machine with the
same (or newer) version of lammps.
you should try to determine, if the problem happens only in parallel
or also with the serial version
you should try to generate a core dump and then get a stack trace
using a debugger (i gave a detailed description of how to do this
several times on this mailing list, so it should be somewhere in the
mailing list archives).
if that all leads to no tangible evidence, you can post your
complete(!) input deck to the mailing list here and see if somebody
else can track it down.
axel.
Hi all,
I am trying to run a simulation in LAMMPS (Parallel Executable).
And
all of a sudden I got an error message which I did not find in previous
occasions. I am posting the error message along with some earlier
parts.
LAMMPS (21 Feb 2013)
Scanning data file ...
4 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (-0.1 -0.1 -0.1) to (25 25 0.1)
2 by 1 by 1 MPI processor grid
8061 atoms
10548 bonds
5274 angles
Finding 1-2 1-3 1-4 neighbors ...
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
16 = max # of 1-4 neighbors
20 = max # of special neighbors
981 atoms in group inner
1805 atoms in group outer
1 atoms in group bead
6255 atoms in group 2
Setting up run ...
=====================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
While searching about the error in web I found that it is probably due
to some reason related with 'mpich2' and due to stack overflow..
May be this is a more technical error rather than normal bugs. But I
couldn't able to fix the issue.
this report is far too generic and there is not enough information to
draw any conclusions.
you should try running the same input on a different machine with the
same (or newer) version of lammps.
you should try to determine, if the problem happens only in parallel
or also with the serial version
you should try to generate a core dump and then get a stack trace
using a debugger (i gave a detailed description of how to do this
several times on this mailing list, so it should be somewhere in the
mailing list archives).
if that all leads to no tangible evidence, you can post your
complete(!) input deck to the mailing list here and see if somebody
else can track it down.
axel.
I have tried all sorts of possibilities that Axel opined in
the earlier post.
It's running in my Fujitsu cluster and also in CRAY. And even
in my work station its also running.
But the problem arises when I am trying to run it in more than 6
processors. In all cases the error message which I have posted before
is coming out with an additional error ' SEGMENTATION FAULT'.
But the examples code which have been provided in the LAMMPS example
directory are running for any number of processors.
Is there anything wrong with my input script ?
I mean does it depend on some commands in the input script ?
If it is so, kindly render me some solutions.
Thanks,
Saikat
Best,
******************
Saikat Basu
Junior Research Fellow
Department of Solid State Physics
IACS,Kolkata
Kolkata-700032
Ph no- 03324734971(extn- 2114)
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Dr. Axel Kohlmeyer [email protected] http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
Thanking you,
Best,
I have tried all sorts of possibilities that Axel opined in
the earlier post.
It's running in my Fujitsu cluster and also in CRAY. And even
in my work station its also running.
But the problem arises when I am trying to run it in more than 6
processors. In all cases the error message which I have posted before
is coming out with an additional error ' SEGMENTATION FAULT'.
But the examples code which have been provided in the LAMMPS example
directory are running for any number of processors.
Is there anything wrong with my input script ?
how should anybody know? i for one don't have crystal ball or can read
minds. a segmentation fault can be anything. the fact that you can run
the bundled examples hints that you are trying to do something that is
not right.
I mean does it depend on some commands in the input script ?
same question, same answer.
If it is so, kindly render me some solutions.
nobody can provide a solution without knowing what is going on or
being able to reproduce your problem.
you are not making it easy to help you, on the contrary.
axel.