UT theoretical chemistry code forum

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?

It seems the attachment didn't upload successfully. I attach it again here. Could anyone give me any advises? Thank you!

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.

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.