diff --git a/slurm-gcp/SampleSlurmJobs/helloworld_singularity.slrm b/slurm-gcp/SampleSlurmJobs/helloworld_singularity.slrm new file mode 100644 index 0000000..8101a41 --- /dev/null +++ b/slurm-gcp/SampleSlurmJobs/helloworld_singularity.slrm @@ -0,0 +1,21 @@ +#!/bin/bash +#SBATCH --partition debug +#SBATCH --nodes 1 +#SBATCH --ntasks-per-node 1 +#SBATCH --mem-per-cpu 2G +#SBATCH --time 1-0:00:00 +#SBATCH --job-name singularity-helloworld +#SBATCH --output hellowrold-singularity-%J.log + +date +hostname + +module load singularity + +echo "================================================ " +echo "download image" +singularity pull shub://singularityhub/hello-world +echo "Executing the hello-world image" +singularity run ./hello-world_latest.sif +echo "================================================ " + diff --git a/slurm-gcp/SampleSlurmJobs/jupyter_launch.slrm b/slurm-gcp/SampleSlurmJobs/jupyter_launch.slrm new file mode 100644 index 0000000..38bcfa9 --- /dev/null +++ b/slurm-gcp/SampleSlurmJobs/jupyter_launch.slrm @@ -0,0 +1,30 @@ +#!/bin/bash +#SBATCH --partition debug +#SBATCH --nodes 1 +#SBATCH --ntasks-per-node 1 +#SBATCH --mem-per-cpu 4G +#SBATCH --time 2-0:00:00 +#SBATCH --job-name jupyter-notebook-tunnel +#SBATCH --output jupyter-notebook-tunnel-%J.log + +# get tunneling info +XDG_RUNTIME_DIR="" +# port=$(shuf -i8080-8084 -n1) +port=8080 +node=$(hostname -s) +ip=$(hostname -i) +user=$(whoami) +cluster=$(hostname -f) + +# print tunneling instructions jupyter-log +echo -e " +CloudShell port forward command for WebPreview +gcloud compute ssh ${node} -- -A -t -l ${user} -f -N -L ${port}:${ip}:${port} +" + +module load miniconda + +# DON'T USE ADDRESS BELOW. +# DO USE TOKEN BELOW +jupyter-notebook --no-browser --port=${port} --ip=${ip} + diff --git a/slurm-gcp/scripts/install_miniconda.sh b/slurm-gcp/scripts/install_miniconda.sh new file mode 100644 index 0000000..e2a2140 --- /dev/null +++ b/slurm-gcp/scripts/install_miniconda.sh @@ -0,0 +1,27 @@ +conda_version=4.9.2 +wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh +chmod +x /tmp/miniconda.sh +/tmp/miniconda.sh -b -p /apps/miniconda/$conda_version -f +/apps/miniconda/$conda_version/bin/conda install jupyter -y + +#conda_version=$( /apps/miniconda/bin/conda --version | awk '{print $2}') +mkdir -p /apps/modulefiles/miniconda +bash -c "cat > /apps/modulefiles/miniconda/${conda_version}" << CONDA_MODULEFILE +#%Module1.0##################################################################### +## +## modules miniconda/conda_version +## +## modulefiles/miniconda/conda_version +## +proc ModulesHelp { } { + global version modroot + puts stderr "miniconda/$conda_version - sets the environment for miniconda" +} +module-whatis "Sets the environment for using miniconda" +# for Tcl script use only +set topdir /apps/miniconda/$conda_version +set version $conda_version +set sys linux86 +prepend-path PATH /apps/miniconda/$conda_version/bin +CONDA_MODULEFILE +