Singularity

From UMIACS
Revision as of 16:33, 5 May 2022 by Mbaney (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

Singularity is a container platform that doesn't elevate the privileges of a user running the container. This is important as UMIACS runs many multi-tenant hosts and doesn't provide administrative control to users on them.

You can find out what the current version is that we provide by running the singularity --version command. If this instead says singularity: command not found please contact staff and we will ensure that the software is available on the host you are looking for it on.

$ singularity --version
singularity version 3.4.2-1.1.el7

Singularity can run a variety of images including its own format and Docker images. To create images, you need to have administrative rights. Therefore, you will need to do this on a host that you have administrative access to (laptop or personal desktop) rather than a UMIACS-supported host.

If you are going to pull large images, you may run out of space in your home directory. We suggest you run the following commands to setup a alternate cache directory.

export WORKDIR=/scratch0/username
export SINGULARITY_CACHEDIR=${WORKDIR}/.cache
mkdir -p $SINGULARITY_CACHEDIR

We do suggest you pull images down into an intermediate file (SIF file) as you then do not have to worry about re-caching the image.

$ singularity pull cuda10.2.sif docker://nvidia/cuda:10.2-devel
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
 25.45 MiB / 25.45 MiB [====================================================] 0s
Copying blob sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
 34.53 KiB / 34.53 KiB [====================================================] 0s
Copying blob sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
 845 B / 845 B [============================================================] 0s
Copying blob sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
 162 B / 162 B [============================================================] 0s
Copying blob sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
 6.88 MiB / 6.88 MiB [======================================================] 0s
Copying blob sha256:902fc5ce82298797e09dc1b28ed942da3892a354321725fad6955ee651557e98
 9.00 MiB / 9.00 MiB [======================================================] 0s
Copying blob sha256:ae1bb79c5cfc1c10948684c3a2964ec7444b19cae7edc487aa474804336b52c1
 184 B / 184 B [============================================================] 0s
Copying blob sha256:fa6605c8fe7a3779c56b4768ac46738f160f005067f22c03e3cf5e87ad5d19d0
 674.37 MiB / 674.37 MiB [==================================================] 8s
Copying blob sha256:0508a679d3397b66fdf6cd56db9a99e2b7af5a8519e9f9534d2dff07779f2482
 783.58 MiB / 783.58 MiB [=================================================] 10s
Copying config sha256:44b5f1390c8715653c6488b3cb4fbee875c30cacadc827b2b4372b18318b2fa0
 7.28 KiB / 7.28 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
2020/04/14 11:52:55  info unpack layer: sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
2020/04/14 11:52:56  info unpack layer: sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
2020/04/14 11:52:56  info unpack layer: sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
2020/04/14 11:52:56  info unpack layer: sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
2020/04/14 11:52:56  info unpack layer: sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
2020/04/14 11:52:57  info unpack layer: sha256:902fc5ce82298797e09dc1b28ed942da3892a354321725fad6955ee651557e98
2020/04/14 11:52:57  info unpack layer: sha256:ae1bb79c5cfc1c10948684c3a2964ec7444b19cae7edc487aa474804336b52c1
2020/04/14 11:52:57  info unpack layer: sha256:fa6605c8fe7a3779c56b4768ac46738f160f005067f22c03e3cf5e87ad5d19d0
2020/04/14 11:53:14  info unpack layer: sha256:0508a679d3397b66fdf6cd56db9a99e2b7af5a8519e9f9534d2dff07779f2482
INFO:    Creating SIF file...
INFO:    Build complete: cuda10.2.sif

Now you can run the local image with the run command or start a shell with the shell command. Please note that if you are in an environment with GPUs and you want to access them inside the container you need to specify the --nv flag.

$ singularity run --nv cuda10.2.sif nvidia-smi -L
GPU 0: GeForce GTX 1080 Ti (UUID: GPU-9ee980c3-8746-08dd-8e14-82fbaf88367e)

Example

We have a gpudocker example workflow using our GitLab as a Docker registry. You can clone the repository and further customize this to your needs. The workflow is:

  1. Run Docker on a laptop or personal desktop on to create the image.
  2. Tag the image and and push it to the repository.
  3. Pull the image down onto one of our workstations/clusters and run it with your data.
$ singularity pull gpudocker.sif docker://registry.umiacs.umd.edu/derek/gpudocker
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
 25.45 MiB / 25.45 MiB [====================================================] 2s
Copying blob sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
 34.53 KiB / 34.53 KiB [====================================================] 0s
Copying blob sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
 845 B / 845 B [============================================================] 0s
Copying blob sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
 162 B / 162 B [============================================================] 0s
Copying blob sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
 6.88 MiB / 6.88 MiB [======================================================] 0s
Copying blob sha256:85386706b02069c58ffaea9de66c360f9d59890e56f58485d05c1a532ca30db1
 8.05 MiB / 8.05 MiB [======================================================] 1s
Copying blob sha256:ee9b457b77d047ff322858e2de025e266ff5908aec569560e77e2e4451fc23f4
 184 B / 184 B [============================================================] 0s
Copying blob sha256:be4f3343ecd31ebf7ec8809f61b1d36c2c2f98fc4e63582401d9108575bc443a
 656.83 MiB / 656.83 MiB [=================================================] 28s
Copying blob sha256:30b4effda4fdab95ec4eba8873f86e7574c2edddf4dc5df8212e3eda1545aafa
 782.81 MiB / 782.81 MiB [=================================================] 37s
Copying blob sha256:b6f46848806c8750a68edc4463bf146ed6c3c4af18f5d3f23281dcdfb1c65055
 100.58 MiB / 100.58 MiB [==================================================] 5s
Copying blob sha256:44845dc671f759820baac0376198141ca683f554bb16a177a3cfe262c9e368ff
 1.47 GiB / 1.47 GiB [====================================================] 1m4s
Copying config sha256:1b2e5b7b99af9d797ef6fbd091a6a2c6a30e519e31a74f5e9cacb4c8c462d6ed
 7.56 KiB / 7.56 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
2020/04/14 12:21:17  info unpack layer: sha256:7ddbc47eeb70dc7f08e410a6667948b87ff3883024eb41478b44ef9a81bf400c
2020/04/14 12:21:18  info unpack layer: sha256:c1bbdc448b7263673926b8fe2e88491e5083a8b4b06ddfabf311f2fc5f27e2ff
2020/04/14 12:21:18  info unpack layer: sha256:8c3b70e3904492c753652606df4726430426f42ea56e06ea924d6fea7ae162a1
2020/04/14 12:21:18  info unpack layer: sha256:45d437916d5781043432f2d72608049dcf74ddbd27daa01a25fa63c8f1b9adc4
2020/04/14 12:21:18  info unpack layer: sha256:d8f1569ddae616589c5a2dabf668fadd250ee9d89253ef16f0cb0c8a9459b322
2020/04/14 12:21:18  info unpack layer: sha256:85386706b02069c58ffaea9de66c360f9d59890e56f58485d05c1a532ca30db1
2020/04/14 12:21:18  info unpack layer: sha256:ee9b457b77d047ff322858e2de025e266ff5908aec569560e77e2e4451fc23f4
2020/04/14 12:21:18  info unpack layer: sha256:be4f3343ecd31ebf7ec8809f61b1d36c2c2f98fc4e63582401d9108575bc443a
2020/04/14 12:21:35  info unpack layer: sha256:30b4effda4fdab95ec4eba8873f86e7574c2edddf4dc5df8212e3eda1545aafa
2020/04/14 12:21:55  info unpack layer: sha256:b6f46848806c8750a68edc4463bf146ed6c3c4af18f5d3f23281dcdfb1c65055
2020/04/14 12:21:58  info unpack layer: sha256:44845dc671f759820baac0376198141ca683f554bb16a177a3cfe262c9e368ff
INFO:    Creating SIF file...
INFO:    Build complete: gpudocker.sif
$ singularity run --nv gpudocker.sif python3 -c 'from __future__ import print_function; import torch; print(torch.cuda.current_device()); x = torch.rand(5, 3); print(x)'
0
tensor([[0.5299, 0.9827, 0.7858],
        [0.2044, 0.6783, 0.2606],
        [0.0538, 0.4272, 0.9361],
        [0.1980, 0.2654, 0.4160],
        [0.1680, 0.8407, 0.0509]])