Difference between revisions of "JUSTUS2/Software/Singularity"
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= Examples = |
= Examples = |
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| − | Run a GROMACS container: |
+ | Run a GROMACS container using Singularity: |
<pre> |
<pre> |
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$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace |
$ WORKSPACE=`ws_allocate gromacs 3` # allocate workspace |
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$ cd $WORKSPACE # change to workspace |
$ cd $WORKSPACE # change to workspace |
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| − | $ singularity pull gromacs-2020_2.sif docker://nvcr.io/hpc/gromacs:2020.2 # pull container from NGC |
+ | $ singularity pull gromacs-2020_2.sif docker://nvcr.io/hpc/gromacs:2020.2 # pull container from NGC |
$ cp -r /opt/bwhpc/common/chem/gromacs/examples/ ./bwhpc-examples/ # copy example to workspace |
$ cp -r /opt/bwhpc/common/chem/gromacs/examples/ ./bwhpc-examples/ # copy example to workspace |
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$ cd ./bwhpc-examples # move into example directory |
$ cd ./bwhpc-examples # move into example directory |
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Revision as of 03:35, 20 March 2021
| 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 |
1 Description
Singularity is a container platform.
2 License
Singularity is free, open-source software released under the 3-clause BSD license. Please read the license for additional information about Singularity.
3 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
4 Examples
Run a GROMACS container using Singularity:
$ 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/gromacs/examples/ ./bwhpc-examples/ # copy example to workspace $ cd ./bwhpc-examples # move into example directory $ sbatch gromacs-2020.2_gpu.slurm # submit job $ squeue # obtain JOBID $ scontrol show job <JOBID> # check state of job $ ls # when job finishes the results will be visible in this directory
