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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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symbol lookup error ... undefined symbol on Gadi #222

Closed penguian closed 4 years ago

penguian commented 4 years ago

When running a rescaled version of the 1deg_jra55_ryf of ACCESS-OM2 on Gadi, from directory /scratch/fp0/pcl900/access-om2/access-om2-gadi-repro-flags-fixed/control/1deg_jra55_ryf, using /g/data3/hh5/public/apps/miniconda3/envs/analysis3-20.01/bin/payu from conda/analysis3-unstable in /g/data3/hh5/public/modules, this results in the error:

/scratch/fp0/pcl900/access-om2/work/1deg_jra55_ryf/atmosphere/yatm_59c9cb4-modified.exe: symbol lookup error: /scratch/fp0/pcl900/access-om2/work/1deg_jra55_ryf/atmosphere/yatm_59c9cb4-modified.exe: undefined symbol: netcdf_mp_nf90_open_

A workaround is to add 

-v MODULE_VERSION=v4.3.0,MODULEPATH=/g/data3/hh5/public/modules:/apps/Modules/restricted-modulefiles/z00:/opt/Modules/modulefiles:/opt/Modules/v4.3.0/modulefiles:/apps/Modules/modulefiles

to qsub-flags in config.yaml.

aekiss commented 4 years ago

This is a duplicate of this issue - let's consolidate discussion there https://github.com/payu-org/payu/issues/221