Differences

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--- titan_to_process [2024/02/02 15:43] – Luc Bonnefond
+++ titan_to_process [2024/07/25 12:08] (current) – Luc Bonnefond
@@ Line 8: / Line 8: @@
 ssh <login>@cbi-gateway-01
 ls /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset>
-rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> /mnt/storage/teams/lamour-ruff/Top2-G4/<dataset>
+rsync -avz --progress /mnt/titan2/offloaddata/TemScripting/EF-Falcon/<dataset> /mnt/storage/teams/<your_team_folder>/<project>/<dataset>
 </code>
@@ Line 15: / Line 15: @@
 ==== 2. Convert the EER movies to TIF ====
-Log into **cbi-compute-01** and transfer the scripts <quote>eer2tif_parallel_loop.py</quote>, <quote>eer2tif_parallel.py</quote> and <quote>eer2tif.py</quote> in your **home**
+Log into **cbi-compute-01** and transfer the scripts {{ ::eer2tif_parallel_loop.py |}} and {{ ::eer2tif_parallel.py |}} in your **home**
 <code>
 ssh <login>@cbi-compute-01
 module load relion
-cd /mnt/storage/teams/lamour-ruff/<project>/<dataset>/ #go to the folder with the dataset
+cd /mnt/storage/teams/<your_team_folder>/<project>/<dataset>/ #go to the folder with the dataset
 module load python
 python ~/eer2tif_parallel.py
@@ Line 29: / Line 29: @@
 ==== 3. Begin processing with relion ====
-Load and start relion (from cbi-compute-01 of phantom-node39)
+Load and start relion (from cbi-compute-01 or the team GPU node (phantom-node39 for Lamour-Ruff))
 <code>
 module load relion
@@ Line 41: / Line 41: @@
 === Estimation the camera gain ===
-Estimate the gain with at least 200 movies (redo if needed with a lager number
+Estimate the gain with at least 200 movies (redo if needed with a larger number)
-<code>relion_estimate_gain --i Import/job001/movies.star --j 8 --o estimated_gain.mrc</code>
+<code>relion_estimate_gain --i Import/job001/movies.star --j 8 --max_frames 10000 --random true --o estimated_gain.mrc</code>
+Explanation of options:
+  * --j: number of thread
+  * --max_frames: target number of frames to average (rounded to movies)
+  * --random: randomize the order of input movies before taking subset
 === Job Relion/Motion correction ===
-Specify the dose per frame, the number of patches 5x5m, provide the gain file, and set 20 threads
+Specify the dose per frame, the number of patches 5x5m, provide the gain file, and set several MPI (number of tasks in parallel) and several (as a multiple of the number of frames in the movies) threads (number of cpu per task)