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Interactive Sessions

Interactive Sessions

Accessing files from cbsunt246 within a script or interactive session on the cluster

The old cbsunt246 server has already been mounted onto the new cbsubscb16 cluster server. To access any file, just use the prefix /fs/cbsunt246 before the rest of the path /workdir/...

Ex: accessing a cbsunt246 file within an salloc interactive session

# log into the cluster
ssh ikk23@cbsulogin2.tc.cornell.edu

# request an interactive session
salloc --nodes=1 --ntasks=1 --mem=1G --partition=short --time=00:10:00

# navigate to repo on cbsunt246
cd /fs/cbsunt246/workdir/shad/shad-lcwgs/

# mount server
/programs/bin/labutils/mount_server cbsunt246 /workdir

# do some computation
touch new_file.txt # will be stored on the cbsunt246 server

# exit the interactive job
exit

Note: you might get the message that the server has already been mounted.

Ex: accessing a cbsunt246 file within a SLURM script.

trial_job.sh
#! /usr/bin/env bash

## #SBATCH --ntasks=1
## #SBATCH --mem=1G
## #SBATCH --partition=short
## #SBATCH --job-name=trial_job
## #SBATCH --output=trial_job.txt

# Make temporary working directory
USER=ikk23
WORKDIR=/workdir/${USER}/${SLURM_JOB_ID}
mkdir $WORKDIR

# Mount the cbsunt246 server
/programs/bin/labutils/mount_server cbsunt246 /workdir

# Copy a file from the old server into the scratch directory
cp /fs/cbsunt246/workdir/shad/shad-lcwgs/sample_lists/error_contigs.txt $WORKDIR

# Do some computing in the scratch directory: 
# ex here: print the first 2 lines of the file and save it to a new file
cd $WORKDIR
cat error_contigs.txt | awk 'NR==1 || NR==2' > first_two_lines_error_contigs.txt

# Copy output to a directory in the old server
cp first_two_lines_error_contigs.txt /fs/cbsunt246/workdir/shad/shad-lcwgs/

# Remove the scratch directory
rm -rf $WORKDIR
Cluster StructureJob Arrays