Interactive-Mode-HPC-tutorial

Interactive Mode (HPC) tutorial on Bash

1. Sign in Discovery7 account

$ ssh -Y *******@discovery7.dartmouth.edu

srun manual

$ man srun

2. Set working directory

3. After configuring files, run the interactive mode

$ srun --pty /bin/bash

If the error is

Package bash-completion was not found in the pkg-config search path.
Perhaps you should add the directory containing `bash-completion.pc'
to the PKG_CONFIG_PATH environment variable
No package 'bash-completion' found
bash: /yum: No such file or directory

install the package

$ conda install -c conda-forge bash-completion

Proceed ([y]/n)?

y

4. Interactive Mode

$ srun --pty /bin/bash

if error appears again

ç^Csrun: Cancelled pending job step with signal 2
srun: error: Unable to create step for job 1257531: Job/step already completing or completed

add your file at the end

$ srun --pty /bin/bash snakemake.sbatch

Checking job priorities

$ squeue

Checking all available partitions

$ sinfo

Checking the hostname

$ hostname
discovery7.hpcc.dartmouth.edu

Jobs submitted with srun –pty /bin/bash will be assigned the cluster default values of 1 CPU and 1024MB of memory. The account must also be specified; the job will not run otherwise. If additional resources are required, they can be requested as options to the srun command. The following example job is assigned 2 nodes with 2 CPUS and 4GB of memory each:

srun --nodes=2 --ntasks-per-node=4 --mem-per-cpu=1GB --cpus-per-task=1 --pty /bin/bash

SLURM

If running on the cluster, please edit the cluster.json config file to match your cluster configuration. Once complete, submit the given sbatch file to the cluster.

$ sbatch snakemake.sbatch