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payu-org / payu

A workflow management tool for numerical models on the NCI computing systems
Apache License 2.0
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Issue with manual collating restarts in latest payu #268

Closed rmholmes closed 4 years ago

rmholmes commented 4 years ago

When attempting to manually collate restarts I encounter problems using the latest payu (from conda/analysis3-20.04(analysis3-unstable)):

[rmh561@gadi-login-03 01deg_jra55_ryf]$ pwd
/home/561/rmh561/access-om2/01deg_jra55_ryf
[rmh561@gadi-login-03 01deg_jra55_ryf]$ payu collate --directory=archive/restart643/ocean/^C
[rmh561@gadi-login-03 01deg_jra55_ryf]$ cat 01deg_jra55_r_c.o5869025
laboratory path:  archive/restart643/ocean
binary path:  archive/restart643/ocean/bin
input path:  archive/restart643/ocean/input
work path:  archive/restart643/ocean/work
archive path:  archive/restart643/ocean/archive
payu: Found modules in /opt/Modules/v4.3.0
{'archive/restart643/ocean/archive/01deg_jra55_ryf/output000/ocean': []}
...

It looks like it's getting all those paths wrong for some reason (not picking up shortpath in config.yaml?). I have no problems if I revert to conda/analysis3-20.01(analysis3:default) (in which case it correctly finds laboratory path: /scratch/e14/rmh561/access-om2).

aidanheerdegen commented 4 years ago

Thanks @rmholmes. I have reproduced. Will investigate and push a fix when I figure out the problem.

aidanheerdegen commented 4 years ago

The updated version (1.0.19) has been installed into conda/analysis3-20.04(analysis3-unstable).

I tested it, but please let me know if it has fixed your issue @rmholmes

rmholmes commented 4 years ago

Thanks Aidan. Yes I just tested and it seems to work fine now.