Update BIO applications

BIO-applications.md

@@ -12,6 +12,83 @@
 - If you get OOM errors ( Out of memory error), this can be due to "general" memory and GPU card "memory" issues (the latter usually mentions "cuda" in the error). You can either increase the memory (--mem=XXX) or you can specifically go for the largest GPU card (merlin-g-015, A500 GPU card with 24GB memory) by using the option `--constraint=gpumem_24gb`.
 - Debugging: In case of errors, go to the folder and check your scripts, the error messages and log files!
 
+
+ 
+**Use case:**
+```
+
+# Available variables:
+#  script_path_abs=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/queue_sub_script.sh
+#  	- the absolute path to the generated submission script
+#  run_cmd=/data/user/benoit_r/cryosparc/cryosparc_worker/bin/cryosparcw run --project P1 --job J8 --master_hostname merlin-l-01.psi.ch --master_command_core_port 39042 > /data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/job.log 2>&1
+#  	- the complete command-line string to run the job
+#  num_cpu=8
+#  	- the number of CPUs needed
+#  num_gpu=1
+#  	- the number of GPUs needed. Note: the code will use this many GPUs
+#    	starting from dev id 0. The cluster scheduler or this script have the
+#    	responsibility of setting CUDA_VISIBLE_DEVICES so that the job code
+#    	ends up using the correct cluster-allocated GPUs.
+#  ram_gb=8.0
+#  	- the amount of RAM needed in GB
+#  job_dir_abs=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8
+#  	- absolute path to the job directory
+#  project_dir_abs=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc
+#  	- absolute path to the project dir
+#  job_log_path_abs=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/job.log
+#  	- absolute path to the log file for the job
+#  worker_bin_path=/data/user/benoit_r/cryosparc/cryosparc_worker/bin/cryosparcw
+#  	- absolute path to the cryosparc worker command
+#  run_args=--project P1 --job J8 --master_hostname merlin-l-01.psi.ch --master_command_core_port 39042
+#  	- arguments to be passed to cryosparcw run
+#  project_uid=P1
+#  	- uid of the project
+#  job_uid=J8
+#  	- uid of the job
+#  job_creator=rb
+#  	- name of the user that created the job (may contain spaces)
+#  cryosparc_username=roger.benoit@psi.ch
+#  	- cryosparc username of the user that created the job (usually an email)
+ 
+#SBATCH --job-name=cryosparc_P1_J8
+#SBATCH --output=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/job.log.out
+#SBATCH --error=/data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/job.log.err
+#SBATCH --ntasks=1
+#SBATCH --threads-per-core=1
+#SBATCH --mem-per-cpu=2000M
+#SBATCH --time=7-00:00:00
+#SBATCH --partition=gpu
+#SBATCH --cluster=gmerlin6
+#SBATCH --gpus=1
+#SBATCH --cpus-per-gpu=4
+ 
+# Print hostname, for debugging
+echo "Job Id: $SLURM_JOBID"
+echo "Host:   $SLURM_NODELIST"
+ 
+export SRUN_CPUS_PER_TASK=$((${SLURM_GPUS:-1} * ${SLURM_CPUS_PER_GPU:-1}))
+srun /opt/psi/Programming/anaconda/2019.07/conda/bin/python -c 'import os; print(f"CPUs:   {os.sched_getaffinity(0)}")'
+ 
+# Make sure this matches the version of cuda used to compile cryosparc
+module purge
+ 
+srun /data/user/benoit_r/cryosparc/cryosparc_worker/bin/cryosparcw run --project P1 --job J8 --master_hostname merlin-l-01.psi.ch --master_command_core_port 39042 > /data/project/bio/benoit/Roger/2024_pRB22_b/20201023_pRB22_b/CS-prb22-b-cryosparc/J8/job.log 2>&1
+ 
+EXIT_CODE=$?
+echo "Exit code: $EXIT_CODE"
+exit $?
+
+```
+
+![image](uploads/a18136b73f7e155782a91e00a26cc820/image.png)
+![image](uploads/9ae914b53c15f046856c613c061c60ce/image.png)
+
+Two solutions: 
+1.) 
+Increase memory as long as it is enough - limits depending on nodes... 
+2.) 
+![image](uploads/d6cb7dfe55369b019cef1b6d06f78132/image.png)
+
 ## Cryosparc
 [Cryosparc official documentation](https://cryosparc.com/docs)
 
@@ -33,6 +110,7 @@
 <img src="uploads/e139c07804105107dd34d92f82028f9f/image.png" alt="drawing" width="300"/>
 
 
+
 ## Alphafold 
 
 [Alphafold repository](https://github.com/google-deepmind/alphafold)