[CP2K:469] Re: mpich? problems on a linux cluster

carlo antonio pignedoli c.pig... at gmail.com
Fri Dec 7 17:10:24 CET 2007


Dear Axel
we are using the normal gigabit.

I did the dmesg and... well I'm not an expert, I got something that
looks like an error.

for the ulimit -a I have

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
file size               (blocks, -f) unlimited
pending signals                 (-i) 38912
max locked memory       (kbytes, -l) 32
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
stack size              (kbytes, -s) 8192
cpu time               (seconds, -t) unlimited
max user processes              (-u) 38912
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

what is your suggestion for a reasonable value.

Thanks a lot

Carlo

On Dec 7, 2007 4:38 PM, Axel <akoh... at gmail.com> wrote:
>
> carlo,
>
> one more thing that may be important: what interconnect
> do you have and is it working correctly under high load?
>
> cp2k is very demanding and i've run across multiple machines
> (myrinet/infiniband) where the MPI runtime settings needed to
> be tweaked to have the job run reliably. i suggest you log into
> the failing node and have a look at the kernel message buffer
> with "dmesg" and see if there is anything suspicious.
>
> the second option when you see segmentation faults with intel
> compilers is the lack of sufficient stack size. for historical
> reasons, the intel fortran frontend allocates temporary arrays
> by default on the stack instead of the heap. please check your
> cluster nodes for whether the stack segment is large enough
> (ulimit -a), and have the sysadmins increase it if needed.
>
> a second option is to reset the stack size from within cp2k, but
> that requires some (ugly?) modifications of the code and they need
> to be in c. i'll put an updated version of those into the files
> section later.
>
> the third options is to use the -heap-arrays flag, which is only
> supported by intel compilers 10.0 and later.
>
> hope that helps,
>    axel.
>
>
>
> On Dec 7, 7:59 am, "carlo antonio pignedoli" <c.pig... at gmail.com>
> wrote:
> > Ciao Teo,
> >
> > we are using the cmkl libraries
> > intel clustertoolkit for linux
> > version 9.1
> >
>
>
> >
>



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