add passive jobs

ginolhac · Aug 30, 2021 · 4120cd4 · 4120cd4
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diff --git a/chip-seq.pdf b/chip-seq.pdf
diff --git a/docs/index.md b/docs/index.md
@@ -177,7 +177,7 @@ Each node has
 On an interactive session, use the command `htop` to see if the memory is not full. If the system is swapping (using hard drives for memory storage)
 it becomes super slow and eventually stalled.
 
-For passive jobs, you can join a computing node by using the `sjoin nodeid jobid` command. Where `nodeid` and `jobid` can be autocomplemented by <key>TAB</key>
+For passive jobs, you can join a computing node by using the `sjoin nodeid jobid` command. Where `nodeid` and `jobid` can be autocomplemented by <key>TAB</key>. See page [help](https://hpc-docs.uni.lu/jobs/submit/#sjoin)
 
 ### Cores
 

diff --git a/docs/workflow.md b/docs/workflow.md
@@ -19,14 +19,16 @@ Shortly, a container with all the necessary tools, softwares and all libraries a
 
 ### Book resources on iris
 
-`si` is a shortcut for booking a short interactive session (30 minutes, 1 core).
+`si` is a shortcut for booking a short **interactive** session (30 minutes, 1 core).
 
 But, we can alter the time for one hour with `-t` and ask for more cores with `-c`. Example below:
 
 ```
 si -t 1:00:00 -c 6
 ```
 
+Interactive sessions are limited to maximum 2 hours. See at the bottom how to submitted **passive** jobs.
+
 #### (Optional) 
 
 Two nodes were reserved for this course. This will work if you have a student accounts or if you are part of the Department of Life Sciences.
@@ -40,4 +42,47 @@ and for Friday:
 
 ```
 si -t 1:0:0 -c 6 --reservation=aginolhac-teaching-20210903
-```
+```
+
+### Submit passive jobs
+
+It consists in two steps:
+
+- create a file `launcher.sh` at the root of your snakemake that contains the following lines:
+
+```bash
+#!/bin/bash -l
+#SBATCH -N 1
+#SBATCH -J JOB_NAME
+#SBATCH --mail-type=begin,end,fail
+#SBATCH [email protected]
+#SBATCH --ntasks-per-node=1
+#SBATCH --mem-per-cpu=4096
+#SBATCH -c 12
+#SBATCH --time=0-06:00:00
+#SBATCH -p batch
+
+module load tools/Singularity
+conda activate snakemake
+
+srun snakemake --use-singularity --singularity-args "-B /scratch/users/aginolhac:/scratch/users/aginolhac" -j 12
+
+```
+
+You need to update the `JOB_NAME` and your email address. You can also delete those 3 lines (line 3 to 5) if you are interested into this monitoring.
+
+The duration (here 6 hours) and number of cores can be adapted to your needs.
+
+- run the submission with 
+
+```bash
+sbatch launcher.sh
+```
+
+your job will be queued and start whenever it's possible and according to the [fairshare](https://hpc-docs.uni.lu/slurm/fairsharing/).
+
+You can monitor your scheduling with `squeue -la -u $USER`
+
+
+See also the HPC team [tutorial](https://ulhpc-tutorials.readthedocs.io/en/latest/basic/scheduling/).
+