Unblur movie alignment

[mcianfrocco]

Need to update unblur script to run with bash and also setting variables correctly.

csh script as it is currently written:

#!/usr/bin/env bash
setenv  OMP_NUM_THREADS 1
 > MotionCorr/job081/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames_unblur.log  << EOF
Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en.frames.mrc
1
MotionCorr/job081/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames.mrc
MotionCorr/job081/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames_shifts.txt
0.6
YES
1.3
200
0
NO
NO
EOF

[mcianfrocco]

Also need to consider if aligned movies already exist in bucket - perhaps delete if they do? Or kill move alignment. Not sure.

[mcianfrocco]

Relion looks like it wants the shell to be csh, so I cant run relion comands, instead need to write out a bash script that looks like this:

#!/usr/bin/env bash
export  OMP_NUM_THREADS=1
/home/EM_Packages/unblur_1.0.2/bin/unblur_openmp_7_17_15.exe > MotionCorr/job082/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames_unblur.log  << EOF
Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en.frames.mrc
40
MotionCorr/job082/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames.mrc
MotionCorr/job082/Micrographs/17jan31b_CSB-Nucl_00021gr_00001sq_00002hl_00002en_frames_shifts.txt
0.6
YES
1.3
200
0
NO
NO
EOF

[mcianfrocco]

On m4.4xlarge instances - can only run 2 x 2.2 GB movies for unblur - > memory requirement? the machine has 64 GB, which means that I need ~4 x (size of movie in GB) per thread, which is 8 in this case.

[mcianfrocco]

Back at it!

To try:
-running running on x1 instances with RAID0 formatted
-could possibly do 1 unblur per thread of machine
-instance can fit 128 x 8 GB movies into RAID0.
-if instance is split 3 ways -> 84 threads running unblur (42 movies at a time); 22 uploading; 22 downloading
--> should finish ~3 hours if 5 min / movie

[mcianfrocco]

Need tasket for all unblur movie alignments