Hi, all!
Does anyone else see the following behaviour of relion_preprocess?
If the current working directory is on an NFS mount "relion_preprocess --operate_on" runs much slower (>10x). Even if the input/output file itself is stored locally!
Copying the file to local storage and back is still much faster than running directly in the NFS mount dir.
Temporary workaround: Always preprocess locally, with a local directory as working directory:
cd /tmp
cp NFS_MOUNT/input.mrcs .
relion_preprocess --operate_on input.mrcs --o output --norm --bg_radius 205 --white_dust 6 --black_dust 6 --invert_contrast
cp output.mrcs NFS_MOUNT/output.mrcs
Tested with relion 1.1 and relion 1.2beta9
Best regards
--
Matthias Brunner <[log in to unmask]>
PhD student, Marlovits Lab
-Research Institute of Molecular Pathology (IMP)
-Inst of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)
Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
Phone: +43 1 79044 4791
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