hpc documentation

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
======= Singularity on Caviness ======

===== Build a Singularity container =====

There are several ways to get a Singularity container onto Caviness, but here are the two to consider using if reproducibility is important.

  * You can build a Singularity container from a Docker or Singularity Hub on Caviness.
  * You can build a container on your local system and copy it to Caviness.

==== Build a Singularity container from Docker or Singularity Hub Registry ====

Caviness does not support Docker, but you can build a Singularity container from an existing Docker container or from a Singularity Hub container regsitry. Starting on the head node, load the Singularity software into your environment using VALET, and build your container.

=== Docker Hub example ===

<code>
$ vpkg_require singularity
$ singularity build tensorflow.simg docker://tensorflow/tensorflow
</code>

=== Singularity Hub example ===

<code>
$ vpkg_require singularity
$ singularity build hello-world.simg shub://vsoch/hello-worldw
</code>

More details on this can be found in the [[http://singularity.lbl.gov/quickstart|Singularity User Guide]].

One example of a container registry is [[https://biocontainers.pro/registry/#/]].

==== Build a container on your local system ====

You can build your Singularity container on your local system, installing the singularity program if you need to.  For more information on how to do this, see the [[http://singularity.lbl.gov/quickstart|Singularity web site]].   Copy your container to Caviness using the usual file transfer methods. See the [[abstract:caviness:transfer|Transferring files to/from Caviness]] for more information.

===== Execute your Singularity container through SLURM =====

Once your container is on Caviness you can run it. Containers must run on Caviness' compute nodes, not on the head node. Remember you must specify a **[[abstract:caviness:app_dev:compute_env#using-workgroup-and-directories|workgroup]]** before running any jobs on Caviness, then use either the ''salloc'' or ''sbatch'' command to get access to a compute node.  See the [[abstract:caviness:runjobs:runjobs|Running Jobs on Caviness]] for more information on SLURM and using Caviness' compute nodes.

==== Inside your interactive session or your batch job you must first issue the command ====

<code>
vpkg_require singularity
</code>

Then you can use the singularity commands to execute your container, like the example below.

<code>
[traine@login01 ~]$ workgroup -g it_css
[(it_css:traine)@login01 ~]$ salloc --ntasks=1 --cpus-per-task=4
salloc: Granted job allocation 844
salloc: Waiting for resource configuration
salloc: Nodes r00n45 are ready for job
[traine@r00n45 ~]$ vpkg_require singularity
Adding package `singularity/2.5.1` to your environment
[traine@r00n45 ~]$ singularity shell tensorflow.simg 
Singularity: Invoking an interactive shell within container...

Singularity tensorflow.simg:~> tensorboard --help
usage: tensorboard [-h] [--logdir PATH] [--host ADDR] [--port PORT]
                   [--purge_orphaned_data BOOL] [--reload_interval SECONDS]
                   [--db URI] [--inspect] [--tag TAG] [--event_file PATH]
                   [--path_prefix PATH] [--window_title TEXT]
                   [--max_reload_threads COUNT]
                   [--samples_per_plugin SAMPLES_PER_PLUGIN]
                   [--master_tpu_unsecure_channel ADDR]
                   [--debugger_data_server_grpc_port PORT]
                   [--debugger_port PORT]

TensorBoard is a suite of web applications for inspectinng and understanding
your TensorFlow runs and graphs. https://github.com/tensorflow/tensorboard

Singularity tensorflow.simg:~> grep Cpus_allowed_list /proc/$$/status
Cpus_allowed_list:	0-3
Singularity tensorflow.simg:~> exit
exit
[traine@r00n45 ~]$
</code>

==== Troubleshooting ====

=== Locale error ===

If you experience the error below after starting a particular shell container, then it is likely due to your current locale not being supported in this particular container's shell.  

<code bash>
[traine@r00n45 ~]$ vpkg_require singularity
Adding package `singularity/2.5.1` to your environment
[traine@r00n45 ~]$ singularity shell tensorflow.simg
Singularity: Invoking an interactive shell within container...

Singularity tensorflow.simg:~> tensorboard --help
Traceback (most recent call last):
  File "/usr/local/bin/tensorboard", line 11, in <module>
    sys.exit(run_main())
  File "/usr/local/lib/python2.7/dist-packages/tensorboard/main.py", line 48, in run_main
    program.setup_environment()
  File "/usr/local/lib/python2.7/dist-packages/tensorboard/program.py", line 57, in setup_environment
    util.setup_logging()
  File "/usr/local/lib/python2.7/dist-packages/tensorboard/util.py", line 50, in setup_logging
    locale.setlocale(locale.LC_ALL, '')
  File "/usr/lib/python2.7/locale.py", line 581, in setlocale
    return _setlocale(category, locale)
locale.Error: unsupported locale setting
</code>

Once you start the container shell, check which locale's are supported by using the ''locale -a'' command:

<code bash>
Singularity tensorflow.simg:~> locale -a
locale: Cannot set LC_CTYPE to default locale: No such file or directory
locale: Cannot set LC_MESSAGES to default locale: No such file or directory
locale: Cannot set LC_COLLATE to default locale: No such file or directory
C
C.UTF-8
POSIX
</code>

Of course in this particular case, the locale setting for account ''traine'' is defined as ''en_US.UTF-8'' which is not supported in this shell.  To fix the situation, simply set the ''LANG'' locale to one that is supported before starting the container shell.

<code bash>
[traine@r00n45 ~]$ vpkg_require singularity
Adding package `singularity/2.5.1` to your environment
[tainne@r00n45 ~]$ LANG=C.UTF-8 singularity shell tensorflow.simg
Singularity: Invoking an interactive shell within container...

Singularity tensorflow.simg:~> tensorboard --help
usage: tensorboard [-h] [--logdir PATH] [--host ADDR] [--port PORT]
                   [--purge_orphaned_data BOOL] [--reload_interval SECONDS]
                   [--db URI] [--inspect] [--tag TAG] [--event_file PATH]
                   [--path_prefix PATH] [--window_title TEXT]
                   [--max_reload_threads COUNT]
                   [--samples_per_plugin SAMPLES_PER_PLUGIN]
                   [--master_tpu_unsecure_channel ADDR]
                   [--debugger_data_server_grpc_port PORT]
                   [--debugger_port PORT]

TensorBoard is a suite of web applications for inspectinng and understanding
your TensorFlow runs and graphs. https://github.com/tensorflow/tensorboard

[[ lots of additional information displayed for optional arguments

Singularity tensorflow.simg:~> exit
exit
[traine@r00n45 ~]$
</code>

==== Common Singularity commands ====

Some common commands are listed here. For more information about Singularity, see the [[http://singularity.lbl.gov/quickstart|Singularity web site]]. 

| ''shell'' | Start a shell within your container using the operating system you have set up your container to use.|
| ''exec'' | Run a single command within your container.|
| ''run'' | Run a recipe script you have set up within your container. Using a recipe script forces users of your container to use a pre-established workflow.|
| ''help'' | Provides help on Singularity.|