Add 2.13 release examples

namd/2.13/get_apoa1.sh

+#!/bin/bash
+
+ggID='1tnn5TgpJHO3WATymQVBngWmx29T0rZfm'
+ggURL='https://drive.google.com/uc?export=download'
+
+if [ ! -f apoa1.tar.gz ]; then
+  echo "Downloading apoa1.tar.gz"
+  curl -sc /tmp/gcokie "${ggURL}&id=${ggID}" >/dev/null
+  getcode="$(awk '/_warning_/ {print $NF}' /tmp/gcokie)"
+  cmd='curl -C - -LOJb /tmp/gcokie "${ggURL}&confirm=${getcode}&id=${ggID}"'
+  eval $cmd
+else
+  echo "apoa1.tar.gz already exists, not downloading"
+fi
+
+if [ ! -d apoa1 ]; then
+  tar xf apoa1.tar.gz
+  echo "apoa1 example directory unpacked"
+else
+  echo "apoa1 directory already exists, not unpacking"
+fi

namd/2.13/multi-node/pbs/namd-apoa1.pbs

+#!/bin/bash
+
+#PBS -N namd_ngc
+#PBS -j oe
+#PBS -l select=4:ncpus=28:ngpus=1
+#PBS -l walltime=00:10:00
+
+set -e; set -o pipefail
+
+# Load required modules
+module load singularity
+
+# Calculate task/process counts
+PBS_TASK_COUNT=$(grep -c . ${PBS_NODEFILE})
+PBS_NODE_COUNT=$(uniq ${PBS_NODEFILE} | wc -l)
+PBS_TASKS_PER_NODE=$(( PBS_TASK_COUNT / PBS_NODE_COUNT ))
+
+# Reserve one CPU core for comm thread
+NAMD_TASKS_PER_NODE=$(( PBS_TASKS_PER_NODE - 1 ))
+NAMD_TASKS_TOTAL=$(( PBS_NODE_COUNT * NAMD_TASKS_PER_NODE ))
+
+# Change to PBS submission directory
+cd ${PBS_O_WORKDIR}
+
+# Download APOA1 example input
+wget -O - https://gitlab.com/NVHCP/ngc-examples/raw/master/namd/2.13/get_apoa1.sh | bash
+INPUT="/host_pwd/apoa1/apoa1.namd"
+
+# Generate charmrun nodelist
+NODELIST=$(pwd)/.nodelist.${PBS_JOBID}
+for host in $(uniq ${PBS_NODEFILE}); do
+  echo "host ${host} ++cpus ${PBS_TASKS_PER_NODE}" >> ${NODELIST}
+done
+
+# singularity alias which will launch charmrun and namd2
+SIMG="$(pwd)/namd_2.13-multinode.simg"
+SINGULARITY="$(which singularity) exec --nv -B $(pwd):/host_pwd ${SIMG}"
+
+# charmrun alias
+SSH="ssh -o PubkeyAcceptedKeyTypes=+ssh-dss -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o LogLevel=ERROR"
+CHARMRUN="charmrun ++remote-shell \"${SSH}\" ++nodelist ${NODELIST} ++scalable-start ++p ${NAMD_TASKS_TOTAL} ++ppn ${NAMD_TASKS_PER_NODE}"
+
+# namd2 alias
+NAMD2="namd2 +setcpuaffinity +idlepoll ${INPUT}"
+
+# Launch parallel namd
+eval "${SINGULARITY} ${CHARMRUN} ${SINGULARITY} ${NAMD2}"
+
+# Cleanup nodelist
+rm ${NODELIST}

namd/2.13/multi-node/slurm/namd-apoa1.slurm

+#!/bin/bash
+
+#SBATCH --nodes 2
+#SBATCH --ntasks=16
+#SBATCH --time 00:10:00
+
+set -e; set -o pipefail
+
+# Load required modules
+module load singularity
+
+# Download APOA1 example input
+wget -O - https://gitlab.com/NVHCP/ngc-examples/raw/master/namd/2.13/get_apoa1.sh | bash
+INPUT="/host_pwd/apoa1/apoa1.namd"
+
+# Generate charmrun nodelist
+NODELIST=$(pwd)/nodelist.${SLURM_JOBID}
+for host in $(scontrol show hostnames); do
+  echo "host ${host} ++cpus ${SLURM_CPUS_ON_NODE}" >> ${NODELIST}
+done
+
+# singularity alias which will launch charmrun and namd2
+SIMG="$(pwd)/namd_2.13-multinode.simg"
+SINGULARITY="$(which singularity) exec --nv -B $(pwd):/host_pwd ${SIMG}"
+
+# charmrun alias
+SSH="ssh -o PubkeyAcceptedKeyTypes=+ssh-dss -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o LogLevel=ERROR"
+CHARMRUN="charmrun ++remote-shell \"${SSH}\" ++nodelist ${NODELIST} ++p ${SLURM_NTASKS} ++ppn ${SLURM_CPUS_ON_NODE}"
+
+# namd2 alias
+NAMD2="namd2 +setcpuaffinity +idlepoll ${INPUT}"
+
+# Launch parallel namd
+eval "${SINGULARITY} ${CHARMRUN} ${SINGULARITY} ${NAMD2}"
+
+# Cleanup nodelist
+rm ${NODELIST}

namd/2.13/multi-node/slurm/namd-apoa1.slurm.orig

+#!/bin/bash
+
+#SBATCH --nodes 2
+#SBATCH --time 00:10:00
+
+# Load the required modules
+module load singularity
+
+echo "Downloading APOA1 Dataset..."
+wget -O - https://gitlab.com/NVHCP/ngc-examples/raw/master/namd/2.13b2/get_apoa1.sh | bash
+
+echo "Generating charmrun hostfile..."
+NODELIST=$(pwd)/nodelist.${SLURM_JOBID}
+for host in $(scontrol show hostnames); do
+  echo "host ${host} ++cpus ${SLURM_CPUS_ON_NODE}" >> ${NODELIST}
+done
+
+SIMG="$(pwd)/namd_2.13b2-multinode.simg"
+SINGULARITY="$(which singularity) exec --nv -B $(pwd):/host_pwd ${SIMG}"
+SSH="ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o LogLevel=ERROR"
+CHARMRUN="charmrun ++remote-shell \"${SSH}\" ++nodelist ${NODELIST} ++scalable-start"
+INPUT="/host_pwd/apoa1/apoa1.namd"
+NAMD2="namd2 +setcpuaffinity +idlepoll ${INPUT} ++ppn ${SLURM_CPUS_ON_NODE}"
+
+echo "Running APOA1 example..."
+eval "${SINGULARITY} ${CHARMRUN} ${SINGULARITY} ${NAMD2} ${INPUT}"
+rm ${NODELIST}

namd/2.13/single-node/docker.sh

+#!/bin/bash
+# Usage: ./docker.sh <gpu count> <image name>
+set -e; set -o pipefail
+
+GPU_COUNT=${1:-1}
+IMG=${2:-"nvcr.io/hpc/namd:2.13-singlenode"}
+
+echo "Downloading APOA1 Dataset..."
+wget -O - https://gitlab.com/NVHCP/ngc-examples/raw/master/namd/2.13/get_apoa1.sh | bash
+INPUT="/host_pwd/apoa1/apoa1.namd"
+
+if [ -f /dev/infiniband ]; then
+    echo "Enabling Infiniband support"
+    IB_DEV="--device=/dev/infiniband --cap-add=IPC_LOCK --net=host"
+fi
+
+DOCKER="nvidia-docker run ${IB_DEV} -it --rm -v ${PWD}:/host_pwd ${IMG}"
+NAMD2="namd2 ${INPUT}"
+
+echo "Running APOA1 example in ${IMG} on ${GPU_COUNT} GPUS..."
+${DOCKER} ${NAMD2}

namd/2.13/single-node/singularity.sh

+#!/usr/bin/env bash
+# Usage: ./singularity.sh <gpu count> <image name>
+set -e; set -o pipefail
+
+GPU_COUNT=${1:-1}
+SIMG=${2:-"namd_2.13-singlenode"}
+
+echo "Downloading APOA1 Dataset..."
+wget -O - https://gitlab.com/NVHCP/ngc-examples/raw/master/namd/2.13/get_apoa1.sh | bash
+INPUT="/host_pwd/apoa1/apoa1.namd"
+
+SINGULARITY="singularity exec --nv -B $(pwd):/host_pwd ${SIMG}"
+NAMD2="namd2 ${INPUT}"
+
+echo "Running APOA1 example in ${SIMG} on ${GPU_COUNT} GPUS..."
+${SINGULARITY} ${NAMD2}