[Hpc-forum] cp2k pecsen

[Rőczei Gábor]

Kedves János,

Sajnos nem tudom, hogy miért történik ez. Nem ismerem ezt a programot kellő mértékben.

A CC-hez hozzá adtam a hpc-forum-os levelező listánkat. Remélem, hogy nem haragszik emiatt. Abban bízok, hogy hátha valaki más tudni fogja a megoldást.

cp2k log részlet:

 Number of electrons:                                                        512
 Number of occupied orbitals:                                                256
 Number of molecular orbitals:                                               256

 Number of orbital functions:                                               1472
 Number of independent orbital functions:                                   1472

 Extrapolation method: initial_guess
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
forrtl: severe (71): integer divide by zero
MPI: MPI_COMM_WORLD rank 2 has terminated without calling MPI_Finalize()
MPI: aborting job

SGE submit fájl tartalma:

#! /bin/bash
#$ -S /bin/bash -V -cwd -j y
#Change below if you want to submit the job with a different name 
#$ -N cp2k
#Refer to this number later in the script as $NSLOTS
#$ -pe mpi 16 
#Turn the below on if you want exclusive nodes
##$ -l exclusive=true
jobname=NVT.inp
CP2KHOME=/home/stirling/cp2k/exe/Linux-ia64-intel
RESDIR=./
MPI_GROUP_MAX=64
export MPI_GROUP_MAX

mpirun -np $NSLOTS $CP2KHOME/cp2k.popt  $jobname >& ${jobname%.*}.out 

Gábor

On 2012.09.20., at 15:16, janos.daru at chemres.hu wrote:

> Kedves Gabor!
> 
> A program mostmar elindul koszonom.
> Az MPI-al azonban itt is vannak gondjaink:
> 
> Extrapolation method: initial_guess
> forrtl: severe (71): integer divide by zero
> (...)
> forrtl: severe (71): integer divide by zero
> MPI: MPI_COMM_WORLD rank 2 has terminated without calling MPI_Finalize()
> MPI: aborting job
> 
> Rakerestem a hibara es a kovetkezot talaltam, esetleg segithet:
> 
> 2) you seem to have a severe problem with the parallelization software you
> have installed. please contact your sys admit to get some information
> about that. The part of the makefile which generates parallel executables
> usually runs straightforwardly. All you have to do is set the $MPI shell
> variable correctly (in your .$SHELL-rc file) and use the appropriate
> precompiler options (in your makefile) and parallelization tools (on you
> computer system).
> 
> Megprobalna kerem renbe tenni ezt a dolgot? Hasonlo hiba volt debrecenben
> is emaitt ott 12-vel tudtunk csak futni. A elvileg cp2k nagyon jol skalaz
> a processzorok szamaval, igy mi ki tudnank hasznalni, hogy Onok nem egy
> clustert, hanem egy szuperszamitogepet uzemeltetnek pl nehany 128
> processoros jobbal.
> 
> Segitseget elore is koszonom,
> 
> Janos
> 
> 
> 
>> Kedves János,
>> 
>> Szerintem erre a változtatásra volt szükség:
>> 
>> vserver:/home/daru/skalazodas/16 # diff -u tmp.qsub.old tmp.qsub
>> --- tmp.qsub.old	2012-09-20 12:57:11.598086664 +0200
>> +++ tmp.qsub	2012-09-20 12:57:28.862086184 +0200
>> @@ -10,4 +10,4 @@
>> CP2KHOME=/home/stirling/cp2k/exe/Linux-ia64-intel
>> RESDIR=./
>> 
>> -time mpirun $CP2KHOME/cp2k.popt  $jobname >& ${jobname%.*}.out
>> +time mpirun -np $NSLOTS $CP2KHOME/cp2k.popt  $jobname >&
>> ${jobname%.*}.out
>> vserver:/home/daru/skalazodas/16 #
>> 
>> Gábor
>> 
>> On 2012.09.20., at 12:47, janos.daru at chemres.hu wrote:
>> 
>>> Kedves Gabor!
>>> 
>>> 
>>> Megprobalkoztam a Pecsi gepen a cp2k futtatasaval. A kovetkezo hibat
>>> kapom:
>>> MPI: '/home/stirling/cp2k/exe/Linux-ia64-intel/cp2k.popt' is not a legal
>>> hostname
>>> 
>>> A submit file:
>>> /home/daru/skalazodas/16/tmp.qsub
>>> 
>>> ebben a mappaban talalhato az input es az output is.
>>> 
>>> Szeretnek erdeklodni,hogy mi a hiba, es hogy lehetne a programot futasra
>>> birni.
>>> 
>>> Segitseget elore is nagyon koszonom,
>>> 
>>> Janos