JUSTUS2/Software/Singularity
| Description | Content |
|---|---|
| module load | --- |
| Availability | BwForCluster_JUSTUS_2 |
| License | Open-source software, distributed under the 3-clause BSD License. More... |
| Citing | --- |
| Links | Homepage | Documentation |
| Graphical Interface | No |
Description
Singularity is a container platform.
License
Singularity is free, open-source software released under the 3-clause BSD license. Please read the license for additional information about Singularity.
Usage
Usage: singularity [global options...]
Options:
-c, --config string specify a configuration file (for root or unprivileged installation only) (default
"/etc/singularity/singularity.conf")
-d, --debug print debugging information (highest verbosity)
-h, --help help for singularity
--nocolor print without color output (default False)
-q, --quiet suppress normal output
-s, --silent only print errors
-v, --verbose print additional information
--version version for singularity
Available Commands:
build Build a Singularity image
cache Manage the local cache
capability Manage Linux capabilities for users and groups
config Manage various singularity configuration (root user only)
delete Deletes requested image from the library
exec Run a command within a container
help Help about any command
inspect Show metadata for an image
instance Manage containers running as services
key Manage OpenPGP keys
oci Manage OCI containers
plugin Manage Singularity plugins
pull Pull an image from a URI
push Upload image to the provided URI
remote Manage singularity remote endpoints, keyservers and OCI/Docker registry credentials
run Run the user-defined default command within a container
run-help Show the user-defined help for an image
search Search a Container Library for images
shell Run a shell within a container
sif siftool is a program for Singularity Image Format (SIF) file manipulation
sign Attach digital signature(s) to an image
test Run the user-defined tests within a container
verify Verify cryptographic signatures attached to an image
version Show the version for Singularity
Examples:
$ singularity help <command> [<subcommand>]
$ singularity help build
$ singularity help instance start
Batch jobs with containers
Batch jobs utilizing Singularity containers are generally built the same way as all other batch jobs, where the job script contains singularity commands. For example:
Using CPUs
#!/bin/bash # Allocate one node #SBATCH --nodes=1 # Number of program instances to be executed #SBATCH --tasks-per-node=4 # 8 GB memory required per node #SBATCH --mem=16G # Maximum run time of job #SBATCH --time=1:00:00 # Give job a reasonable name #SBATCH --job-name=Singularity # File name for standard output (%j will be replaced by job id) #SBATCH --output=singularity_job-%j.out # File name for error output #SBATCH --error=singularity_job-%j.err cd your/workspace # Run container (two options to start a container) singularity run [options] <container> singularity exec [options] <container> <command>
Using GPUs
#!/bin/bash […] # Allocate one GPU per node #SBATCH --partition=gpu #SBATCH --gres=gpu:1 […] cd your/workspace # Run container (two options to start a container) singularity run --nv [options] <container> singularity exec --nv [options] <container> <command>
Using the flag is advisable, but may be omitted if the correct GPU- and driver-APIs are available on the container.
Examples
Run your first container on JUSTUS 2
Build a TensorFlow container with Singularity and execute a Python command:
# request interactive node with GPUs
$ srun --nodes=1 --exclusive --gres=gpu:2 --pty bash
# create workspace and navigate into it
$ WORKSPACE=`ws_allocate tensorflow 3`
$ cd $WORKSPACE
# build container
$ singularity build tensorflow-20.11-tf2-py3.sif docker://nvcr.io/nvidia/tensorflow:20.11-tf2-py3
# execute Python command
$ singularity exec --nv tensorflow-20.11-tf2-py3.sif python -c 'import tensorflow as tf; \
print("Num GPUs Available: ",len(tf.config.experimental.list_physical_devices("GPU")))'
Note: Ready-to-use containers can be pulled from the NVIDIA GPU CLOUD (NGC) catalog.
NGC environment modules on JUSTUS 2
1) Prepare a workspace to store the container
$ srun --nodes=1 --exclusive --gres=gpu:2 --pty bash $ WORKSPACE=`ws_allocate npc 3` $ cd $WORKSPACE $ export NGC_IMAGE_DIR=$(pwd)
Important: Containers can only run in workspaces.
2) PyTorch container
$ module load ngc/.numlib $ module load 20.12-py3 $ python3 >>> import torch >>> x = torch.randn(2,3) >>> print(x) >>> quit() $ module unload 20.12-py3 $ module unload ngc/.numlib
Note: Use the container in the same manner as an interactive shell.
3) LAMMPS container
$ module load ngc/.chem $ module load 29Oct2020 $ wget https://lammps.sandia.gov/inputs/in.lj.txt $ export SINGULARITY_BINDPATH=$(pwd) $ mpirun -n 2 lmp -in in.lj.txt -var x 8 -var y 8 -var z 8 -k on g 2 -sf kk -pk kokkos cuda/aware on neigh full \ comm device binsize 2.8 $ module unload 29Oct2020 $ module unload ngc/.chem
Note: Use SINGULARITY_BINDPATH=<PATH> to mount the directory with the input file.
Currently, module load ngc/.numlib for numeric libraries and module load ngc/.chem for chemistry programs can be selected.
Batch jobs with containers on JUSTUS 2
Run a GROMACS container with Singularity as a batch job:
$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace $ cd $WORKSPACE # change to workspace $ singularity pull gromacs-2020_2.sif docker://nvcr.io/hpc/gromacs:2020.2 # pull container from NGC $ cp -r /opt/bwhpc/common/chem/ngc/gromacs/ ./bwhpc-examples/ # copy example to workspace $ cd ./bwhpc-examples # change to example directory $ sbatch gromacs-2020.2_gpu.slurm # submit job $ squeue # obtain JOBID $ scontrol show job <JOBID> # check state of job
More batch job examples are located at /opt/bwhpc/common/chem/ngc.