Determine BioFormats2Raw computational requirements

[ErinWeisbart]

Trying two methods to determine optimal setup/computational requirements:

1. Download all files onto EBS volume
2. Use S3FS to pull images from S3

Starting with 1)
I have an EBS volume mounted as /ebs_tmp with 2.5x size of plate with all images downloaded to it.
Enter shell in docker, allowing access to ebs_tmp:
sudo docker run -it --rm --entrypoint /bin/sh -v ~/ebs_tmp:/ebs_tmp openmicroscopy/bioformats2raw:latest
Run bioformats2raw:
sh /opt/bioformats2raw/bin/bioformats2raw /ebs_tmp/PLATE/Images/Index.idx.xml /ebs_tmp/images_zarr/PLATE.ome.zarr

[ErinWeisbart]

Ran 1) on

• m5.xlarge (4 vCPUs, 16 GB memory, .192 USD/hr).
  4.5 hrs. Used 98% CPU, 15% memory for duration.
  (Tested both default parameters and with --resolutions 4)
• c5.xlarge (4 vCPUs, 8 GB memory, .17 USD/hr)
  4.5 hrs. Used 97% CPU, 20-30% memory for duration.
  (default parameters)