NAMD []

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===== NAMD =====

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

[[http://www.ks.uiuc.edu/Research/namd|NAMD]]

==== Job NAMD on BDW ====

=== Job NAMD multicore (single BDW node) ===

Example script ''slurm-namd-bdw.sh'' to run NAMD multicore on 1 node using 16 cores and at most 32 GB of memory:

<code bash slurm-namd-bdw.sh>
#!/bin/bash
#SBATCH --job-name=NAMD
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --mem=32G
#SBATCH --time=1-00:00:00
#SBATCH --partition=bdw
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/bdw

if [ ! -e "${SLURM_JOB_NAME}.conf" ]; then
    echo "Error: file '${SLURM_JOB_NAME}.conf' not found." 1>&2
    exit 1
fi

namd2 +p ${SLURM_TASKS_PER_NODE} "${SLURM_JOB_NAME}.conf" > "${SLURM_JOB_NAME}.log"
</code>

Submission example:

<code>
sbatch --job-name=t1r1_min1 slurm-namd-bdw.sh
</code>

=== Job NAMD multicore (single BDW node, simplified version) ===

Example script ''slurm-namd-bdw.sh'' to run NAMD multicore on 1 node using 16 cores and at most 32 GB of memory:

<code bash slurm-namd-bdw.sh>
#!/bin/bash
#SBATCH --job-name=t1r1_min1
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --mem=32G
#SBATCH --time=1-00:00:00
#SBATCH --partition=bdw
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/bdw

namd2 +p ${SLURM_TASKS_PER_NODE} t1r1_min1.conf > t1r1_min1.log
</code>

Submission example:

<code>
sbatch slurm-namd-bdw.sh
</code>

=== Job NAMD multicore (single BDW node, exclusive mode) ===

Example script ''slurm-namd.sh'' to run NAMD multicore on 1 node in exclusive mode:

<code bash slurm-namd.sh>
#!/bin/bash
#SBATCH --job-name=NAMD
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --time=1-00:00:00
#SBATCH --partition=bdw
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/bdw

if [ ! -e "${SLURM_JOB_NAME}.conf" ]; then
    echo "Error: file '${SLURM_JOB_NAME}.conf' not found." 1>&2
    exit 1
fi

namd2 +p ${SLURM_TASKS_PER_NODE} "${SLURM_JOB_NAME}.conf" > "${SLURM_JOB_NAME}.log"
</code>

Submission example:

<code>
sbatch --job-name=t1r1_min1 slurm-namd-bdw.sh
</code>

=== Job NAMD multicore (single BDW node, exclusive mode, simplified version) ===

Example script ''slurm-namd-bdw.sh'' to run NAMD multicore on 1 node in exclusive mode:

<code bash slurm-namd-bdw.sh>
#!/bin/bash
#SBATCH --job-name=t1r1_min1
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --time=1-00:00:00
#SBATCH --partition=bdw
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/bdw

namd2 +p ${SLURM_TASKS_PER_NODE} t1r1_min1.conf > t1r1_min1.log
</code>

Submission example:

<code>
sbatch slurm-namd-bdw.sh
</code>

==== Job NAMD on KNL ====

=== Job NAMD multicore (single KNL node) ===

Example script ''slurm-namd-knl.sh'' to run NAMD multicore on 1 KNL node in exclusive mode using 64 cores:

<code bash slurm-namd-knl.sh>
#!/bin/bash
#SBATCH --job-name=NAMD
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=64
#SBATCH --exclusive
#SBATCH --mem=0
#SBATCH --time=1-00:00:00
#SBATCH --partition=knl
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/knl

if [ ! -e "${SLURM_JOB_NAME}.conf" ]; then
    echo "Error: file '${SLURM_JOB_NAME}.conf' not found." 1>&2
    exit 1
fi

namd2 +p ${SLURM_TASKS_PER_NODE} "${SLURM_JOB_NAME}.conf" > "${SLURM_JOB_NAME}.log"
</code>

Submission example:

<code>
sbatch --job-name=t1r1_min1 slurm-namd-knl.sh
</code>

==== Job NAMD on GPU ====

=== Job NAMD multicore (single GPU node) ===

Example script ''slurm-namd-gpu.sh'' to run NAMD multicore on 1 GPU node using 8 cores, 2 GPUs and at most 32 GB of memory:

<code bash slurm-namd-gpu.sh>
#!/bin/bash
#SBATCH --job-name=NAMD
#SBATCH --output=%x.o%j
#SBATCH --error=%x.e%j
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --gres=gpu:2
#SBATCH --mem=32G
#SBATCH --time=1-00:00:00
#SBATCH --partition=gpu
#
# Edit next line
#SBATCH --account=<account>

module load namd/2.12/gpu

if [ ! -e "${SLURM_JOB_NAME}.conf" ]; then
    echo "Error: file '${SLURM_JOB_NAME}.conf' not found." 1>&2
    exit 1
fi

namd2 +p ${SLURM_TASKS_PER_NODE} "${SLURM_JOB_NAME}.conf" > "${SLURM_JOB_NAME}.log"
</code>

Submission example:

<code>
sbatch --job-name=t1r1_min1 slurm-namd-gpu.sh
</code>

Submission example overriding the options specified in the launch script:

<code>
sbatch --job-name=t1r1_min1 --ntasks-per-node=16 --gres=gpu:4 --mem=64G slurm-namd-gpu.sh
</code>
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