UT theoretical chemistry code forum

Dear all,
I am trying to run the akmc code using the scripts as suggested. I have modified the three files akmc_submit.pl akmc_check.pl and akmc_kill.pl according to my system. I am running it on a cluster using the LSF queueing system. I tried with the example code and when I try to run it using akmc.pl I get the following error:
Script directory is /home/pg0104/akmc_sample
Read config file: ===========================================================
MaxJobs = 8, 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 tried to submit the akmc_submit.pl manually in the min directory. It does the structural minimization and then stops. The job is submitted as a normal VASP job on the cluster.

I am not sure what needs to be modified for this to work.

Regards,
PG

Hello:
I am still struggling to run the akmc example code as given. I have modified my submission scripts to be compatible with my cluster. I have created a director akmc_sample and copied the files. The akmc.pl and the other akmc submit scripts are all located in the vtsscripts directory. When I try to run akmc.pl in the akmc_sample directory, a min directory is created and the minimization is complete but the job stops after that with the following error.
Script directory is /home/pg0104/vtstscripts
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 ...
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.
===========================================================


Although the minimization is complete, there is an error message. I am not sure why nothing is written to the jobs.dat file and the next step is not proceeding. Is there some other paramters to be modified in the perl script specific to the cluster?

REgards,
PG

Hi, the akmc_submit.pl script should return a digital job ID only. Please try using akmc_submit.pl to manually submit a job and make sure only a digital job ID is the only output if a job is submitted successfully. In your case, the job was submitted, but jobid was not captured by akmc.pl, so no writtings occured to jobs.dat. Please feel free to email me at xulijun@u.washington.edu if you have further questions about akmc scripts. -Lijun

Hello:
I checked the akmc.submit.pl script. We have the LSF queuing system. I changed the script akmc_submit.pl accordingly.
Here is what I get when I submit akmc_submit.pl

bsub <akmc.sub |tail -1
Job <13038> is submitted to default queue <normal>.



Regards,
PG

Hi, akmc_submit.pl should return a digital job ID, which you can use to check your job status.
in your case, you also need to make more changes to force akmc_submit.pl to print nothing but
13038
Your scirpt should look like this: see the difference in "$jobID=substr($line[2], 1, -1);"

if(-e "INCAR" && -e "KPOINTS" && -e "POTCAR" && -e "akmc.sub"){
chomp($line=`qsub akmc.sub | tail -1`);
$line=~s/^\s+//;
@line=split(/\s+/,$line);
$jobID=substr($line[2], 1, -1);
}else{
die "Error signal from submit.pl";
}
print "$jobID\n";
if(!($jobID=~/^\d+$/)){
print "2bsubmitted";
}

by the way, akmc_check.pl 13038 should return the job status such as running, queue, stopped and submitted, and akmc_kill.pl 13038 shall do the killing.

What those three scirpts print is improtant to akmc.pl

There are comment lines about this in the sample scripts.

- Lijun