JUSTUS2/Software/Singularity: Difference between revisions

From bwHPC Wiki
Jump to navigation Jump to search
 
(33 intermediate revisions by 2 users not shown)
Line 2: Line 2:
|-
|-
! Description !! Content
! Description !! Content
|-
| module load
| ---
|-
| Availability
| [[BwForCluster_JUSTUS_2]]
|-
|-
| License
| License
Line 31: Line 25:
= Usage =
= Usage =


== Availability ==
<pre>
Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module, but you must use a compute node i.e. via an [[BwForCluster_JUSTUS_2_Slurm_HOWTO#How_to_submit_an_interactive_job.3F|interactive job]]
Usage: singularity [global options...]


The binary ''singularity'' is main program of the container platform.
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


To get help using Singularity execute the following command:
Available Commands:
<pre>
build Build a Singularity image
$ singularity --help
cache Manage the local cache
</pre>
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


Furthermore, a man page is available and can be accessed by typing:
Examples:
<pre>
$ singularity help <command> [<subcommand>]
$ singularity help build
$ man singularity
$ singularity help instance start
</pre>
</pre>


For additional information about how to use Singularity, please consult the [https://sylabs.io/docs/ documentation].


== Batch jobs with containers ==
== Batch jobs with containers ==
Line 105: Line 69:
singularity exec [options] <container> <command>
singularity exec [options] <container> <command>
</pre>
</pre>

<font color=red>Keep in mind that other modules you may have loaded will not be available inside the container.</font>


=== Using GPUs ===
=== Using GPUs ===
Line 115: Line 81:
#SBATCH --gres=gpu:1
#SBATCH --gres=gpu:1
[…]
[…]

module load your/singularity/version #(not needed on JUSTUS 2, but could be necessary on other system)


cd your/workspace
cd your/workspace
Line 155: Line 119:
<pre>
<pre>
$ srun --nodes=1 --exclusive --gres=gpu:2 --pty bash
$ srun --nodes=1 --exclusive --gres=gpu:2 --pty bash
$ WORKSPACE=`ws_allocate npc 3`
$ WORKSPACE=`ws_allocate ngc 3`
$ cd $WORKSPACE
$ cd $WORKSPACE
$ export NGC_IMAGE_DIR=$(pwd)
$ export NGC_IMAGE_DIR=$(pwd)
Line 163: Line 127:
2) PyTorch container
2) PyTorch container
<pre>
<pre>
$ module load ngc/.numlib
$ module load ngc/numlib
$ module load 20.12-py3
$ module load 20.12-torch-py3
$ python3
$ python3
>>> import torch
>>> import torch
Line 170: Line 134:
>>> print(x)
>>> print(x)
>>> quit()
>>> quit()
$ module unload 20.12-py3
$ module unload 20.12-torch-py3
$ module unload ngc/.numlib
$ module unload ngc/numlib
</pre>
</pre>
'''Note:''' Use the container in the same manner as an interactive shell.
'''Note:''' Use the container in the same manner as an interactive shell.
Line 177: Line 141:
3) LAMMPS container
3) LAMMPS container
<pre>
<pre>
$ module load ngc/.chem
$ module load ngc/chem
$ module load 29Oct2020
$ module avail
$ module load 29Oct2020-lammps
$ wget https://lammps.sandia.gov/inputs/in.lj.txt
$ wget https://lammps.sandia.gov/inputs/in.lj.txt
$ export SINGULARITY_BINDPATH=$(pwd)
$ 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 \
$ 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
comm device binsize 2.8
$ module unload 29Oct2020
$ module unload 29Oct2020-lammps
$ module unload ngc/.chem
$ module unload ngc/chem
</pre>
</pre>
'''Note:''' Use <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">SINGULARITY_BINDPATH=<PATH></span> to mount the directory with the input file.
'''Note:''' Use <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">SINGULARITY_BINDPATH=<PATH></span> to mount the directory with the input file.




Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/.numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/.chem</span> for chemistry programs can be selected.
Currently, <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/numlib</span> for numeric libraries and <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">module load ngc/chem</span> for chemistry programs can be selected.


== Batch jobs with containers on JUSTUS 2 ==
== Batch jobs with containers on JUSTUS 2 ==
Line 195: Line 160:
Run a GROMACS container with Singularity as a batch job:
Run a GROMACS container with Singularity as a batch job:
<pre>
<pre>
$ salloc --ntasks=1 # obtain compute node
$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace
$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace
$ cd $WORKSPACE # change to workspace
$ cd $WORKSPACE # change to workspace
Line 213: Line 179:
* [https://en.wikipedia.org/wiki/Singularity_(software) Wikipedia article (english)]
* [https://en.wikipedia.org/wiki/Singularity_(software) Wikipedia article (english)]
----
----
[[Category:Scientific_Applications]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]

Latest revision as of 11:49, 23 April 2024

Description Content
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

Availability

Singularity is directly available on all compute nodes (but not on the login nodes). You do not have to load a module, but you must use a compute node i.e. via an interactive job

The binary singularity is main program of the container platform.

To get help using Singularity execute the following command:

$ singularity --help

Furthermore, a man page is available and can be accessed by typing:

$ man singularity

For additional information about how to use Singularity, please consult the documentation.

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:

#!/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>

Keep in mind that other modules you may have loaded will not be available inside the container.

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 ngc 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-torch-py3
$ python3
>>> import torch
>>> x = torch.randn(2,3)
>>> print(x)
>>> quit()
$ module unload 20.12-torch-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 avail
$ module load 29Oct2020-lammps
$ 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-lammps
$ 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:

$ salloc --ntasks=1                                                         # obtain compute node
$ 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.

Useful links