files not found in settings/tmp/

[micahwilhelm]

I'm trying to run n-sdm on the Hyperion cluster at the WSL. Unfortunately, v1.0.1 doesn't run out of the box (for me) using the nsdm-project example. There are some files such as n_spe.txt spe_runs.txt which should exist in nsdm-project/settings/tmp/ but the run script cannot find them. Is this a known bug?

nohup bash nsdm.sh > nsdm.out

nsdm.out shows the following errors:

Welcome to this new nsdm-project run 9e9403 Submitted batch job 9542396 cat: /home/wilhelm/nsdm//tmp/nsdm-project/settings/tmp/n_spe.txt: No such file or directory N-SDM settings defined and species occurence data for species disaggregated cat: /home/wilhelm/nsdm//tmp/nsdm-project/settings/tmp/spe_runs.txt: No such file or directory Starting N-SDM run 1 out of runs N-SDM settings updated cat: /home/wilhelm/nsdm//tmp/nsdm-project/settings/tmp/n_spe.txt: No such file or directory expr: syntax error expr: syntax error expr: syntax error expr: syntax error expr: syntax error expr: syntax error expr: syntax error Submitted batch job 9542397 PRE modelling datasets generated sbatch: error: Batch job submission failed: Invalid job array specification GLO data preparation and covariate selection done sbatch: error: Batch job submission failed: Invalid job array specification GLO modelling done sbatch: error: Batch job submission failed: Invalid job array specification GLO ensembling done sbatch: error: Batch job submission failed: Invalid job array specification REG data preparation and covariate selection done sbatch: error: Batch job submission failed: Invalid job array specification REG modelling done sbatch: error: Batch job submission failed: Invalid job array specification REG ensembling and scale nesting done sbatch: error: Batch job submission failed: Invalid job array specification individual FUT GLO predictions done sbatch: error: Batch job submission failed: Invalid job array specification FUT GLO ensembling done sbatch: error: Batch job submission failed: Invalid job array specification individual FUT REG predictions done sbatch: error: Batch job submission failed: Invalid job array specification FUT REG ensembling and scale nesting done sbatch: error: Batch job submission failed: Invalid job array specification Final evaluation done Sacct outputs analysis done ODMAP protocol generated find: 'd2_models/': No such file or directory Main outputs sync to saving location Finished!

If more information is needed please let me know.

[antadde]

These files are generated during the preparation step by "./scripts/nsdm-project/main/0_mainPRE/pre_A.R." Something wrong might have happen, could you check the error file in ./scripts/nsdm-project/main/0_mainPRE/ ?

[micahwilhelm]

Thanks for the tip! The system was not finding the nsdm R package. All is well now.