Segmentation fault

Dear all,

Apologies for what seems to be a somewhat common and non-specific error. I have previously built DL_POLY on a person computer with no problem, but I have recently tried installing it on my work computer. When I try to run a simulation I am getting:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7fed2bd10d21 in ???
#1 0x7fed2bd0fef5 in ???
#2 0x7fed2b99620f in ???
#3 0x7ffffe4cf004 in ???
Segmentation fault (core dumped)

I believe I have built it correctly as when I try to run a simulation with rvdw and cutoff values that exceed 1/2 cell width, an OUTPUT file is generated describing the failure (as expected). However, when all settings are theoretically correct, an empty OUTPUT file is produced and nothing else. These files have worked on previous runs on my personal computer, so I don’t believe there is an input problem.

Looking in the email archives for similar issues, I found a user experienced similar situation that was result of stack limit.

using $ ulimit -a

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 7823
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 7823
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

The suggested fix was $ ulimit -s unlimited.
which resulted in this for me:

-bash: ulimit: stack size: cannot modify limit: Invalid argument

I believe I was able to overwrite with:

sudo prlimit --stack=unlimited --pid $$; ulimit -s unlimited

resulting in:

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 7823
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 7823
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

However, this has still not fixed the failure to run.

Does anyone have any suggestions to fix this? Is it due to limited resources or restrictions being a work-networked PC?

Apologies for the long-winded email, I thought it would help narrow down the issue.

Thanks,

Daniel

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Hi Daniel,

can you drop me the inputs at [email protected]

Is that machine a windows machine with bash on windows?

Regards,
Alin

Hi Alin,

I’ve just sent them and yes, it is bash on windows.