Ok, so your problem is identified as a stack size problem. I went into
these limitations using Intel fortran compilers on large data problems.
First, it seems you can increase your stack size as "ulimit -s
unlimited" works (you didn't enforce the system hard limit). The best
way is to set this setting in your .bashrc file so it will works on
every node.
But setting it to unlimited may not be really safe. IE, if you got in a
badly coded recursive function calling itself without a stop condition
you can request all the system memory and crash the node. So set a large
but limited value, it's safer.
I'm managing a cluster and I always set a maximum value to stack size. I
also limit the memory available for each core for system stability. If a
user request only one of the 12 cores of a node he can only access 1/12
of the node memory amount. If he needs more memory he has to request 2
cores, even if he uses a sequential code. This avoid crashing jobs of
other users on the same node with memory requirements. But this is not
configured on your node.
Duke Nguyen a écrit :
On 3/30/13 3:13 PM, Patrick Bégou wrote:
I do not know about your code but:
1) did you check stack limitations ? Typically intel fortran codes
needs large amount of stack when the problem size increase.
Check ulimit -a
First time I heard of stack limitations. Anyway, ulimit -a gives
$ 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) 127368
max locked memory (kbytes, -l) unlimited
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) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
So stack size is 10MB??? Does this one create problem? How do I change
this?
2) did your node uses cpuset and memory limitation like fake numa to
set the maximum amount of memory available for a job ?
Not really understand (also first time heard of fake numa), but I am
pretty sure we do not have such things. The server I tried was a
dedicated server with 2 x5420 and 16GB physical memory.
Patrick
Duke Nguyen a écrit :
Hi folks,
I am sorry if this question had been asked before, but after ten
days of searching/working on the system, I surrender :(. We try to
use mpirun to run abinit (abinit.org) which in turns will call an
input file to run some simulation. The command to run is pretty simple
$ mpirun -np 4 /opt/apps/abinit/bin/abinit < input.files >& output.log
We ran this command on a server with two quad core x5420 and 16GB of
memory. I called only 4 core, and I guess in theory each of the core
should take up to 2GB each.
In the output of the log, there is something about memory:
P This job should need less than 717.175 Mbytes
of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : 69.524 Mbytes ; DEN or POT disk file : 14.240
Mbytes.
So basically it reported that the above job should not take more
than 718MB each core.
But I still have the Segmentation Fault error:
mpirun noticed that process rank 0 with PID 16099 on node biobos
exited on signal 11 (Segmentation fault).
The system already has limits up to unlimited:
$ cat /etc/security/limits.conf | grep -v '#'
* soft memlock unlimited
* hard memlock unlimited
I also tried to run
$ ulimit -l unlimited
before the mpirun command above, but it did not help at all.
If we adjust the parameters of the input.files to give the reported
mem per core is less than 512MB, then the job runs fine.
Please help,
Thanks,
D.
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