how to submit job for eon with vasp

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cjinf0614
Posts: 1
Joined: Thu Sep 12, 2019 6:39 am

how to submit job for eon with vasp

Post by cjinf0614 » Thu Sep 12, 2019 8:22 am

Dear Eon developers,
I am learning how to use eon with vasp. I'm interested in the example/akmc-cu100mrr-vasp. I can submit the eon job, but when it requires the vasp to run, the jobs/in directory is empty and the scripts in jobs/scratch are not submitted to the cluster. can you give advice on how to make it work? Thanks.

The akmc.log is as:

2019-09-12 14:25:37 INFO:akmc: Eon version unknown
2019-09-12 14:25:37 WARNING:statelist: State list path does not exist; Creating: .//states/
2019-09-12 14:25:37 WARNING:superbasinscheme: Superbasin path does not exist, creating .//superbasins/
2019-09-12 14:25:38 INFO:explorer: Registering results
2019-09-12 14:25:38 INFO:explorer: Processed 0 results
2019-09-12 14:25:38 DEBUG:explorer: Registered 0.0 results per second
2019-09-12 14:25:38 INFO:explorer: Queue contains 0 searches
2019-09-12 14:25:38 INFO:explorer: Making 12 process searches
2019-09-12 14:25:44 INFO:explorer: Created 12 searches
2019-09-12 14:25:44 DEBUG:explorer: Created 2.05376451319 searches per second
2019-09-12 14:25:44 DEBUG:superbasinscheme: writing
2019-09-12 14:25:44 INFO:akmc: Currently in state 0 with confidence 0.000000
2019-09-12 14:25:44 DEBUG:akmc: KMC finished in 0.000509023666382 seconds
2019-09-12 14:25:44 DEBUG:akmc: 0.00 KMC steps per second
2019-09-12 14:25:44 DEBUG:superbasinscheme: writing


Attachments are the script I used for my cluster, which uses lsf as the job manager. I submit job with the akmc-eon.lsf.

The queued_jobs.sh is:
#!/bin/sh
bjobs | awk '$1~/^[0-9]/ {print $1}'

The cancel_job.sh is:
#!/bin/sh
bkill $@

Best,
Jinfan Chen
Attachments
vasp.lsf.txt
(218 Bytes) Downloaded 34 times
runvasp.sh.txt
(107 Bytes) Downloaded 32 times
akmc-eon.lsf.txt
(117 Bytes) Downloaded 33 times
akmc.lsf.txt
(123 Bytes) Downloaded 33 times
submit_job.sh.txt
(53 Bytes) Downloaded 28 times

graeme
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Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
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Re: how to submit job for eon with vasp

Post by graeme » Thu Oct 10, 2019 8:41 pm

Hi Jinfan,

First, apologies for the slow response. I have been distracted by an update of our codes from python2 -> 3, which is hopefully now almost done.

So, there are a few odd things about your input files. First, the eon program should be run directly on the master node - not through the queuing system. The eon program will queue up your eonclient jobs with the submit_job.sh script that you provide. For sge, I use a script:

#!/bin/sh
qsub -V -b y -j y -o ll_out -S /bin/bash -N "$1" -wd "$2" -pe mpi24 24 ~/code/eon/client/eonclient | awk '{print $3}'

Then, the eonclient program will run vasp directly using the runvasp.sh script. Again, I use:

#!/bin/sh
mpirun -np 24 vasp

As I mentioned for the eon server, the vasp executable should not be submitted via the queue - it is launched from the eonclient (which is run from the queue).

If you need additional help, a .tar.gz of the entire initial input files would be good. I could get it set up for our clusters as an example.

And, if it would make sense and if you are willing to give me access to the machine, I could help with the submit script files for your environment.

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