Hi,
I got a similar error for my system:
...
[n020110:27321] *** Process received signal ***
[n020110:27321] Signal: Segmentation fault (11)
[n020110:27321] Signal code: (128)
[n020110:27321] Failing at address: (nil)
[n020110:27321] [ 0] /lib64/libpthread.so.0 [0x38bac0eb70]
[n020110:27321] [ 1]
On 10/10/12 1:33 PM, Ladasky wrote:
Update:
Ladasky wrote
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system
Update:
Ladasky wrote
>
> Justin Lemkul wrote
>> Random segmentation faults are really hard to debug. Can you resume the
>> run
>> using a checkpoint file? That would suggest maybe an MPI problem or
>> something
>> else external to Gromacs. Without a reproducible system and a debugging
>>
On 10/8/12 4:39 AM, Ladasky wrote:
Justin Lemkul wrote
My first guess would be a buggy MPI implementation. I can't comment on
hardware
specs, but usually the random failures seen in mdrun_mpi are a result of
some
generic MPI failure. What MPI are you using?
I am using the OpenMPI package,
Justin Lemkul wrote
> My first guess would be a buggy MPI implementation. I can't comment on
> hardware
> specs, but usually the random failures seen in mdrun_mpi are a result of
> some
> generic MPI failure. What MPI are you using?
I am using the OpenMPI package, version 1.4.3. It's one of t
On 10/7/12 2:15 PM, Ladasky wrote:
Justin Lemkul wrote
Random segmentation faults are really hard to debug. Can you resume the
run
using a checkpoint file? That would suggest maybe an MPI problem or
something
else external to Gromacs. Without a reproducible system and a debugging
backtrace,
Justin Lemkul wrote
> Random segmentation faults are really hard to debug. Can you resume the
> run
> using a checkpoint file? That would suggest maybe an MPI problem or
> something
> else external to Gromacs. Without a reproducible system and a debugging
> backtrace, it's going to be hard to
On 10/5/12 3:03 PM, Ladasky wrote:
Bumping this once before the weekend, hoping to get some help.
I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4. If these errors are a consequence
of a poorly-equilibrated system, I am no longer
Bumping this once before the weekend, hoping to get some help.
I am getting segmentation fault errors at 1 to 2 million cycles into my
production MD runs, using GROMACS 4.5.4. If these errors are a consequence
of a poorly-equilibrated system, I am no longer getting the right kind of
error message
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