There is probably not enough contiguous virtual memory available

MRCIEU / PHESANT

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

MIT License

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There is probably not enough contiguous virtual memory available #12

Closed jielab closed 4 years ago

jielab commented 4 years ago

Dear all:

Please see the screenshot below. Can you please let me know how to resolve this memory issue?

I used the default "../variable-info/outcome-info.tsv" and "../variable-info/data-coding-ordinal-info.txt" file that comes with the download. Does these two files contain all the variables and data codings existing in the whole UKB dataset, or should I use my own version based on the data that I got from my UKB application?

Thank you very much & best regards, Jie

louise commented 4 years ago

You could try running PHESANT with a larger number of parts (e.g. 200), which should reduce the memory requirements in each part. If you are not already using HPC then that would also help.