problem with aKMC

[mahdishirazi]

Hi
I want to run akmc_sample and I set up the whole path
After execute ./akmc.pl I faced with the below error

----------------------------------------------------------------------------------------------
Script directory is /gpfs/sfiwork/mahdis/kMC/akmc_sample/
Read config file: ===========================================================
MaxJobs = 10, SearchesAlgo = dimer.
Assuming a prefactor of 1.0e12/s (skip calculation).

Using kdbquery results, if they exist.
Reading old job information: Found 0 running jobs.
Read state pool information: No old states available.
===========================================================
Number of states: 0.
Reading akmc.dat: NONE. It hasn't started yet
Initialize the first configuration ...
There is one initial min and no states.
Check the minimization status.
Warning from SubmitJobs: in min, just tried to submit a job in min, but it failed. Better check it(marked as 2bsubmitted)
===========================================================
This aKMC simulation is at step 0.
===========================================================
-----------------------------------------------------------------------------------------------------------------------
I will be happy if there is anybody who can help me.
Best Regards
Mahdi

[xulijun2]

It looks like there is something wrong with your submission script.
akmc_submit.pl is the mandatory name for submitting jobs to the queue in cluster computers.
You can do the following checking:
in the min folder just created by the script, try to submit the job directly from there by hand:
type akmc_submit.pl and press enter.
If the submission script works, you should be able to submit the job in folder "min".
If you encounter the same problem, try to fix your akmc_submit.pl until it works in manual submission.

by the way, you should have three scripts ready in the same vtstscripts folder: akmc_submit.pl, akmc_check.pl and akmc_kill.pl. Check their functions in the manual or webpage http://theory.cm.utexas.edu/vtsttools/akmc/

Try to submit, check and kill a job with those three scripts and make sure they work before running akmc.pl

[mahdishirazi]

Hi
I did what ever you said. I copied three scripts in min directory and run them.
I think that main problem is jobID. I checked the akmc_submit.pl and every line as below
----------------------------------------------------------------------------------------------------------------
eval '(exit $?0)' && eval 'exec perl -S $0 ${1+"$@"}' && eval 'exec perl -S $0 $argv:q' if 0;
#;-*- Perl -*-
###################################################################################################
#This script submits a job from the current working directory and return a jobid (in numbers only).
#if somehow the submission fails, "2bsubmitted" must be returned as the jobid.
###################################################################################################
if(-e "INCAR" && -e "KPOINTS" && -e "POTCAR" && -e "akmc.sub"){
chomp($line=`qsub -l nodes=2 -N test -q walton akmc.sub | tail -1`);
print "$line\n";
$line=~s/^\s+//;
print "$line\n";
@line=split(/\s+/,$line);
print "$line\n";
$jobID=$line[2];
print "$line[2], $jobID\n";
}else{
die "Error signal from submit.pl";
}
print "$jobID\n";
if(!($jobID=~/^\d+$/)){
print "2bsubmitted";
}
-----------------------------------------------------------------------
in the $jobID=$line[2]; I do not have any output. when we submit job, jobID is like "80156.sfi400". I do not know perl language! what should I do for this line?
thanks a million
mahdi