Question about EON and vasp

eOn code for long time scale dynamics

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Hongbo
Posts: 8
Joined: Sun May 22, 2022 3:17 pm

Question about EON and vasp

Post by Hongbo »

Dear Professor Graeme Henkelman,

I try to do structural calculation of amorphous MoSx using EON-aKMC. First, I try to run the example of "akmc-cu100mrr-vasp". But I can't run it correctly. Here is the error infomation


Server is locked by pid 135075
Server is locked by pid 135075
Traceback (most recent call last):
File "/public3/home/sc55763/para/eon/bin/eon", line 3, in <module>
main()
File "/public3/home/sc55763/para/eon/eon/main.py", line 24, in main
akmc.main()
File "/public3/home/sc55763/para/eon/eon/akmc.py", line 571, in main
if lock.aquirelock():
File "/public3/home/sc55763/para/eon/eon/locking.py", line 34, in aquirelock
if self.islocked():
File "/public3/home/sc55763/para/eon/eon/locking.py", line 15, in islocked
self.pid = int(f.read().strip())
ValueError: invalid literal for int() with base 10: ''
Traceback (most recent call last):
File "/public3/home/sc55763/para/eon/bin/eon", line 3, in <module>
main()
File "/public3/home/sc55763/para/eon/eon/main.py", line 24, in main
akmc.main()



It seems "ValueError: invalid literal for int() with base 10: ''" is the reason I can't run correctly. But I don't know how to fix it? Which file should be fixed? I attached the complete "akmc-cu100mrr-vasp" files from my account here. Could you please give me some advises?
Hongbo
Posts: 8
Joined: Sun May 22, 2022 3:17 pm

Re: Question about EON and vasp

Post by Hongbo »

It seems the attachment didn't upload successfully. I attach it again here. Could anyone give me any advises? Thank you!
Attachments
akmc-cu100mrr-vasp.tar
(2.59 MiB) Downloaded 48 times
graeme
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Re: Question about EON and vasp

Post by graeme »

I am very interested in getting to the bottom of this, but I'm not able to debug it with the output information. I see a number of worrisome things, but I'm thinking that it may be due to (i) the python environment and (ii) the mpi+vasp setup. I'm going to write you separately and include a student to help sort this out.

One problem is in the jobs/scratch directory, I see:
0_0 0_12 0_24 0_36 0_48 0_60 0_72

so that jobs id's are being incremented by 12 instead of by 1.

In each directory, you can see an error:
/var/spool/slurm/d/job4947970/slurm_script: line 4: /public3/home/sc55763/code/eon/client/eonclient: No such file or directory

this may be related to the error in akmc.log (but I'm not sure):
Eon version svn revision svnversion: /public3/soft/anaconda/Anaconda3-3.7.3-wjl/lib/libuuid.so.1: no version information available (required by /lib64/libapr-1.so.0)
and this could also be related to the other error:
ValueError: invalid literal for int() with base 10: ''

Anyway, again, I'll contact you off the forum to discuss how to sort this out.
Hongbo
Posts: 8
Joined: Sun May 22, 2022 3:17 pm

Re: Question about EON and vasp

Post by Hongbo »

Thank you for your reply. You can log in my accout of High Performance Computing to check the problem. I have sent you my account and password by email.
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