Tag: modules

Using Spyder

Using Spyder

Spyder is available through Anaconda Navigator on the FAS-RC Remote Desktop application on the Open OnDemand dashboard. To access it:

  • go to the VDI dashboard at https://vdi.rc.fas.harvard.edu/pun/sys/dashboard/ (or https://fasseood.rc.fas.harvard.edu/pun/sys/dashboard if you are working on FASSE)
  • start a new Remote Desktop session
  • connect to the Remote Desktop session
  • open a Terminal in the Remote Desktop session and load the relevant Anaconda module. Check https://portal.rc.fas.harvard.edu/p3/build-reports/ for the most up-to-date modules.
    • Examples:
    • if you’re working with Python 2, type the following:
      • module load Anaconda/5.0.1-fasrc02
    • if you’re working with Python 3, type the following:
      • module load Anaconda3/2020.11
  • type the following:
    • anaconda-navigator
  • when Anaconda Navigator loads, you may choose to remain in the “base” environment, or load your preferred environment from the “Applications on” dropdown, or create a new environment using the Environments tab to the left.
  • when you are in the environment you need, click the Launch button under the icon for Spyder.

Screenshots of the process:

Singularity on the cluster

Singularity on the cluster

 

Online Trainings Materials

Introduction

Containerization of workloads has become popular, particularly using Docker. However, Docker is not suitable for HPC applications due to security reasons. There are a couple of alternatives for HPC containers, with Singularity being the one that covers a large set of cases. Singularity has been deployed on the cluster, and can also import Docker containers.
This page provides information on how to use Singularity on the cluster. Singularity enables users to have full control of their operating system environment. This allows a non-privileged user to “swap out” the Linux operating system and environment on the host machine for a Linux OS and computing environment that they can control. For instance, if the host system runs CentOS Linux but your application requires Ubuntu Linux with a specific software stack, you can create an Ubuntu image, install your software into that image, copy the created image to the cluster, and run your application on that host in its native Ubuntu environment.
Singularity leverages the resources of the host system, such as high-speed interconnect (e.g., InfiniBand), high-performance parallel file systems (e.g., Lustre /n/holyscratch01 and /n/holylfs filesystems), GPUs, and other resources (e.g., licensed Intel compilers).
Note for Windows and MacOS: Singularity only supports Linux containers. You cannot create images that use Windows or MacOS (this is a restriction of the containerization model rather than Singularity).

Why Singularity?

There are some important differences between Docker and Singularity:

  • Docker and Singularity have their own container formats.
  • Docker containers may be imported to run via Singularity.
  • Docker containers need root privileges for full functionality which is not suitable for a shared HPC environment.
  • Singularity allows working with containers as a regular user.

Singularity on the cluster

Singularity is available only on the compute nodes on the cluster. Therefore, to use it you need to either start an interactive job or submit a batch-job to the available SLURM queues.
In the below examples we illustrate the interactive use of Singularity in an interactive bash shell.

[user@holylogin01 ~]$ salloc -p test -c 1 -t 00-01:00 --mem=4000
[user@holyseas02 ~]$

Check Singularity version:

[user@holyseas02 ~]$ which singularity
/usr/bin/singularity
[user@holyseas02 ~]$ singularity --version
singularity version 3.1.1-1.el7

The most up-to-date help on Singularity comes from the command itself.

[user@holyseas02 ~]$ singularity --help
Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)
Usage:
  singularity [global options...]
Description:
  Singularity containers provide an application virtualization layer enabling
  mobility of compute via both application and environment portability. With
  Singularity one is capable of building a root file system that runs on any
  other Linux system where Singularity is installed.
Options:
  -d, --debug              print debugging information (highest verbosity)
  -h, --help               help for singularity
  -q, --quiet              suppress normal output
  -s, --silent             only print errors
  -t, --tokenfile string   path to the file holding your sylabs
                           authentication token (default
                           "/n/home12/nweeks/.singularity/sylabs-token")
  -v, --verbose            print additional information
      --version            version for singularity
Available Commands:
  apps        List available apps within a container
  build       Build a Singularity image
  cache       Manage the local cache
  capability  Manage Linux capabilities for users and groups
  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
  pull        Pull an image from a URI
  push        Push a container to a Library URI
  run         Run the user-defined default command within a container
  run-help    Show the user-defined help for an image
  search      Search a Library for images
  shell       Run a shell within a container
  sign        Attach a cryptographic signature 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 
      Additional help for any Singularity subcommand can be seen by appending
      the subcommand name to the above command.

For additional help or support, please visit https://www.sylabs.io/docs/

Getting existing images onto the cluster

Singularity uses container images which you can scp or rsync to the cluster as you would do with any other file. See Copying Data to & from the cluster using SCP or SFTP for more information.
Note: For larger Singularity images, please use the available scratch filesystems, such as /n/holyscratch01/my_lab/username and /n/holylfs/LABS/my_lab/username.
You can also use the pull or build commands to download pre-built images from external resources, such as Singularity Hub (as of April 26th 2021, Singularity Hub is a read-only archive), the Sylabs Container Library or Docker Hub. For instance, you can download a native Singularity image with its default name from Singularity Hub with:

[user@holyseas02 ~]$ singularity pull shub://vsoch/hello-world
 62.32 MiB / 62.32 MiB [================================] 100.00% 43.02 MiB/s 1

The downloaded image file is hello-world_latest.sif.
You can also pull the image with a customized name; e.g., hello.sif:

[user@holyseas02 ~]$ singularity pull --name hello.sif shub://vsoch/hello-world
 62.32 MiB / 62.32 MiB [================================] 100.00% 57.26 MiB/s 1s

Similarly, you can pull images from Docker Hub:

[user@holyseas02 ~]$ singularity pull docker://godlovedc/lolcow
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:9fb6c798fa41e509b58bccc5c29654c3ff4648b608f5daa67c1aab6a7d02c118
...
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: lolcow_latest.sif

See official Singularity documentation for more information.

BioContainers

Cluster nodes automount a CernVM-File System at /cvmfs/singularity.galaxyproject.org/. This provides a universal file system namespace to Singularity images for the BioContainers project, which comprises container images automatically generated from Bioconda software packages. The Singularity images are organized into a directory hierarchy following the convention:

/cvmfs/singularity.galaxyproject.org/FIRST_LETTER/SECOND_LETTER/PACKAGE_NAME:VERSION--CONDA_BUILD

For example:

singularity exec /cvmfs/singularity.galaxyproject.org/s/a/samtools:1.13--h8c37831_0 samtools --help

The Bioconda package index lists all software available in /cvmfs/singularity.galaxyproject.org/, while the BioContainers registry provides a searchable interface.

NOTE: There will be a 10-30 second delay when first accessing /cvmfs/singularity.galaxyproject.org/ on a compute node on which it is not currently mounted; in addition, there will be a delay when accessing a Singularity image on a compute node where it has not already been accessed and cached to node-local storage.

Docker Rate Limiting

Docker rate limits the number of pulls anonymous accounts can make from Docker Hub.  If you hit either an error of Too Many Requests or pull rate limit, you will need to create a Docker account to get a higher limit.  See the Docker documentation for more details.

Working with images

When working with images you could either start an interactive session, or submit a Singularity job to the available queues. For these examples, we will use a hello-world.sif in an interactive bash shell.

[user@holylogin01 ~]$ salloc -p test -c 1 -t 00-01:00 --mem=4000
[user@holyseas02 ~]$ singularity pull --name hello-world.sif shub://vsoch/hello-world
 62.32 MiB / 62.32 MiB [================================] 100.00% 37.63 MiB/s 1s

Shell

With the shell command, you can start a new shell within the container image and interact with it as if it were a small virtual machine. Note that the shell command does not source ~/.bashrc and ~/bash_profile. Therefore, the shell command can be useful if customizations in your ~/.bashrc and ~/bash_profile are applicable only on the host.

[user@holy7c24604 ~]$ singularity shell hello-world.sif
Singularity> pwd
/n/home06/pkrastev/holylfs/pgk/SINGULARITY/vol2
Singularity> ls
funny.sif gcc-7.2.0.sif hello-world.sif hello.sif lolcow.sif ubuntu.sif vsoch-hello-world-master-latest.sif
Singularity> id
uid=56139(pkrastev) gid=40273(rc_admin) groups=40273(rc_admin),10006(econh11),34539(fas_it),34540(cluster_users),402119(solexa_writers),402160(VPN_HELPMAN),402161(RT_Users),402854(wpdocs_users),403083(owncloud),403266(file-isi_microsoft-full-dlg),403284(gitlabint_users),403331(rc_class) 
Singularity>

To exit the container, use the exit command:

Singularity> exit
exit
[user@holy7c24604 ~]$

Commands within a container

You can use the exec command to execute specific commands within the container. For instance, you can run the below command to display information about the native Linux OS of the image:

[user@holyseas02 ~]$ singularity exec hello-world.sif cat /etc/os-release
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

Running containers

Singularity images contain run-scripts that can be triggered with the run command to perform specific actions when the container is run. This can be done either by using the run command, or by calling the container as if it were an executable, i.e.,

[user@holyseas02 ~]$ singularity run hello-world.sif
RaawwWWWWWRRRR!!

or

[user@holyseas02 ~]$ ./hello-world.sif
RaawwWWWWWRRRR!!

Sometimes you may have a container with several apps, each with its own set of run-scripts. You can use the apps command to list the available apps within the container. For instance, if you have an image named my_image.simg which has N apps (app_1, app_2,…, app_N) you can do:

[user@holyseas02 ~]$ singularity apps my_image.sif
app_1
app_2
...
app_N

You can run a particular app with

[user@holyseas02 ~]$ singularity run --app app_2 my_image.sif

GPU example:

First, start an interactive GPU job and then download the Singularity image hello-world.sif:

[user@holylogin01 ~]$ salloc -p gpu --gres=gpu:1 --mem 1000 -n 4 -t 60
[user@holygpu7c26304 ~]$singularity pull --name hello-world.sif shub://vsoch/hello-world

To access Nvidia GPU card driver installed inside of Singularity container you need to use --nv option while executing the container. To verify that you have access to the requested GPUs, run nvidia-smi inside the container:

[user@holygpu7c26304 ~]$ singularity exec --nv hello-world.sif /bin/bash
Singularity> nvidia-smi
 +-----------------------------------------------------------------------------+
| NVIDIA-SMI 396.26 Driver Version: 396.26 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 Tesla K20Xm Off | 00000000:88:00.0 Off | 0 |
| N/A 37C P0 61W / 235W | 0MiB / 5700MiB | 65% Default |
+-------------------------------+----------------------+----------------------+

Accessing files from a container

Files and directories on the cluster are accessible from within the container. By default, directories under /n, $HOME, $PWD, and /tmp are available at runtime inside the container:

[user@holygpu7c26304 singularity_doc_tutorial]$ echo $PWD
/n/holyscratch01/user_lab/Everyone/user/singularity_doc_tutorial
[user@holygpu7c26304 singularity_doc_tutorial]$ echo $HOME
/n/home05/user
[user@holygpu7c26304 singularity_doc_tutorial]$ echo $SCRATCH
/n/holyscratch01
[user@holygpu7c26304 singularity_doc_tutorial]$ singularity exec --nv hello-world.sif /bin/bash
Singularity> echo $PWD
/n/holyscratch01/user_lab/Everyone/user/singularity_doc_tutorial
Singularity> echo $HOME
/n/home05/user
Singularity> echo $SCRATCH
/n/holyscratch01

You can specify additional directories to bind mount into your container with the --bind option. For instance, if you first create a file hello.dat in your /scratch directory on the host system. Then, you can execute from within the container by bind mounting /scratch to the /mnt directory inside the container:

[user@holyseas02 ~]$ echo 'Hello from inside the container!' > /scratch/hello.dat
[user@holyseas02 ~]$ singularity exec --bind /scratch:/mnt hello-world.sif cat /mnt/hello.dat
Hello from inside the container!

Singularity containers as SLURM jobs

You can also use Singularity images within a non-interactive batch script as you would any other command. If your image contains a run-script then you can use singularity run to execute the run-script in the job. You can also use singularity exec to execute arbitrary commands (or scripts) within the image. Below is an example batch-job submission script using the hello-world.sif to print out information about the native OS of the image.

#!/bin/bash
#SBATCH -J singularity_test
#SBATCH -o singularity_test.out
#SBATCH -e singularity_test.err
#SBATCH -p test
#SBATCH -t 0-00:30
#SBATCH -c 1
#SBATCH --mem=4000
# Singularity command line options
singularity exec hello-world.sif cat /etc/os-release

If the above batch-job script is named singularity.sbatch, for instance, the jobs is submitted as usual with sbatch:

[user@holylogin01 ~]$ sbatch singularity.sbatch

Upon the job completion, the STD output is located in the file singularity_test.out.

[user@holylogin01 ~]$ cat singularity_test.out
NAME="Ubuntu"
VERSION="14.04.5 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.5 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"

Building Singularity images

To build Singularity containers, you need root access to the build system. Therefore, you cannot build a Singularity container on the cluster. Depending on whether or not you have an access to a Linux machine, possible options are:

  • If you have a Linux system to which you have root (admin) access, you can install Singularity and build your Singularity containers there. See Install Singularity on Linux for more information.
  • If you don’t have a Linux system you could easily install one in a virtual machine using software like VirtualBox, Vagrant, or VMware. See Install on Windows or Mac for specific Windows or MacOS instructions.
  • You can build a Singularity image from a local Docker image on Windows, Mac, or Linux with the docker2singularity Docker image.

In addition to your own Linux environment, you will also need a definition file to build a Singularity container from scratch. You can find some simple definition files for a variety of Linux distributions in the /example directory of the source code. Detailed documentation about building Singularity container images is available at the Singularity website.

Parallel computing with Singularity

For building Singularity images and running applications with openMP, Mpich, and OpenMPI refer to our Github documentation.

References

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