Closed amirhusseinab closed 2 weeks ago
Update:
Setting --omp-nthreads 1 fixes the issue as expected, but the processing time of non-eddy functions is a lot.
This was fixed in #788 (merged yesterday)
I had this issue with 0.22.0 - downloaded today.
I think this is also relevant - on overriding the default eddy with eddy_config.json, in the boilerplate it says: "Groups deviating by more than 4 standard deviations from the prediction had their data replaced with imputed values" I think it is set by ol_nstd argument in eddy_config which I have set to 5 rather than the default 4.
Summary
Running with an eddy_config file to utilize CUDA and mporder results in an error in eddy_cuda step:
Additional details
What were you trying to do?
The command I used:
The config file:
What did you expect to happen?
To have a successful preprocessing :)
What actually happened?
Despite explicitly setting num_threads to 1 in the eddy_config, It prints out:
And later it fails with an error:
In the output log file, the --nthr flag in eddy_cuda is also set to 8.
Reproducing the bug