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Commit d1519dad authored by Fanny Wegner's avatar Fanny Wegner
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Update file UNIX_HPC_cheat_sheet.md

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......@@ -97,10 +97,11 @@ fi
```
## Running Singularity containers
Running a container called `my_software_container` that contains a command called `my_software`
Running a container called `my_software_container` that contains a command called `my_software` (on a computation node)
```bash
my_software_container.sif my_software [parameters]
srun my_software_container.sif my_software [parameters]
```
......@@ -134,15 +135,29 @@ In a script `myjob.sh`:
#SBATCH --error=[name]_%j.err
# load any required modules
module load [module name]
module load singularityce
command1
command2
command3
srun my_software_container.sif my_software [parameters]
```
Submit script as job to the computing nodes:
```bash
sbatch myjob.sh
```
## Managing jobs
```bash
# show queue of jobs submitted by a specified user
squeue -u [username]
# show queue of jobs submitted by a specified user, with customised output field (including job name!)
squeue -u [username] -O JobID,UserName,Name,State,NumCPUs,MinMemory,TimeUsed,TimeLimit,Nodelist
scancel [jobid] # cancels jobs
```
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