Update the way parallelization is configured #651
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- Update the --parallel_subjects* flags and rename them to --parallel* (brun_fastsurfer.sh, long_fastsurfer.sh) - Update the "old" --parallel flag (making it legacy, removing from documentation everywhere incl. all examples, but also from the "functionality of the scripts") - Update the way --threads works for surface reconstruction. Before: run_fastsurfer.sh fixes --threads value, if --parallel is set; Now: run_fastsurfer.sh does nothing to the threads value for surface reconstruction, but recon-surf.sh has 2 values for threads: for joint parts and for parallel hemisphere parts; if threads is >= 2 parallel hemispheres is automatically activated and the number of threads available to each parallel hemisphere is halved. - Update the documentation throughout.
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m-reuter
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Feb 6, 2025
Docker/README.md
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| @@ -27,8 +27,7 @@ docker run --gpus all -v /home/user/my_mri_data:/data \ | |||
| --rm --user $(id -u):$(id -g) deepmi/fastsurfer:latest \ | |||
| --fs_license /fs_license/license.txt \ | |||
| --t1 /data/subjectX/t1-weighted.nii.gz \ | |||
| --sid subjectX --sd /output \ | |||
| --parallel | |||
| --sid subjectX --sd /output | |||
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Don't we have to put threads to 2 in order to have parallel behaviour?
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Definitely, I mean, we can also put 2 threads as the default ....
I just removed the --parallel flags because those are not really wanted/needed any more.
m-reuter
reviewed
Feb 6, 2025
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| ### Single parallel pipeline | ||
| This mode is ideal for CPU-based processing for segmentation. It will process segmentations and surfaces in series | ||
| in the same process, but multiple cases are processed at the same time. | ||
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| ```bash | ||
| $FASTSURFER_HOME/brun_fastsurfer.sh --parallel_subjects 4 --threads 2 --parallel | ||
| $FASTSURFER_HOME/brun_fastsurfer.sh --parallel 4 --threads 2 |
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for same behaviour as before threads would need to be 4?
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Yes, but the text below is updated to reflect the behavior as "requested".
m-reuter
reviewed
Feb 6, 2025
… the logfile exists. Append those messages to the logfile once the logfile is created. Cleanup of the temporary logfile. (Don't care if the temporary logfile gets messages, but run_fastsurfer.sh is terminated because of a different error. It is only a temporary file that is very small.)
…md and Docker/README.md. Also remove some outdated information in Docker/README.md.
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Update the
--parallel_subjects*flags and rename them to--parallel*(brun_fastsurfer.sh,long_fastsurfer.sh)Update the "old"
--parallelflag (making it legacy, removing from documentation everywhere incl. all examples, but also from the "functionality of the scripts")Update the way
--threadsworks for surface reconstruction. Before:run_fastsurfer.shfixes--threadsvalue, if--parallelis set; Now:run_fastsurfer.shdoes nothing to the threads value for surface reconstruction, but recon-surf.sh has 2 values for threads: for joint parts and for parallel hemisphere parts; if threads is >= 2 parallel hemispheres is automatically activated and the number of threads available to each parallel hemisphere is halved.Update the documentation throughout.