Singularity
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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:
- Run Docker on a laptop or personal desktop on to create the image.
- Tag the image and and push it to the repository.
- 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]])