Comments (7)
My complete workflow (including preparing singularity images for execution, and invoking them on NSG-HPC) is documented in the README.md I will keep updating that file as I make more debugging progress.
Plans, manually upload image data pnp_latest-2017-05-19-f1d9712ba440.img
to Comet using web portal, launch job from webportal.
Invoke the singularity in bootstrap mode using a configuration script such as:
nu.def
sudo singularity bootstrap pnp_latest-2017-05-19-f1d9712ba440.img nu.def
See if I can configure the launch of singularity+Comet to basically execute that statement, using pnp_latest-2017-05-19-f1d9712ba440.img nu.def
, which I will manually upload to the portal.
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bump. ^^
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After today's discussion about the simpler pathway to from docker 2 singularity, I was motivated to follow through with it. However I noticed that using the pattern:
http://singularity.lbl.gov/docs-docker
sudo singularity create --size 4000 tensorflow.img
sudo singularity import tensorflow.img docker://tensorflow/tensorflow:latest
But substituting in relevant variable names to our neuronunit build context:
sudo singularity create --size 4000 pnp.img
sudo singularity import pnp.img docker://pnp
Causes the error below (with singularity on native ubuntu):
Error getting tags using url https://registry-1.docker.io/v2/library/pnp/tags/list
Bootstrap initialization
No bootstrap definition passed, updating container
Executing Prebootstrap module
Executing Postbootstrap module
ERROR: Container does not contain the valid minimum requirement of /bin/sh
This has been fixed in the development branch of singularity:
apptainer/singularity#421
Which probably involves building it from source, which involves its own technical obstacles.
This is the proposed solution (only requires a docker installation), singularity is not even needed its very verbose but its all in one line:
https://github.com/singularityware/docker2singularity
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On my Mac I had this problem (long irrelevant code blocks replaced by ...
):
vagrant@vagrant-ubuntu-trusty-64:~$ sudo singularity create --size 10000 neuronunit.img
Creating a new image with a maximum size of 10000MiB...
...
Done.
vagrant@vagrant-ubuntu-trusty-64:~$ sudo singularity import neuronunit.img
...
Extracting /home/vagrant/.singularity/docker/sha256:7719a427e59f2abb32c0722f1bfb670a6c4a7339c0e8d2fffc19a8eb3ae2d606.tar.gz
tar: opt/conda/lib/icu/current: Cannot create symlink to ‘56.1’: File exists
tar: Exiting with failure status due to previous errors
ERROR:python:Error extracting image: /home/vagrant/.singularity/docker/sha256:7719a427e59f2abb32c0722f1bfb670a6c4a7339c0e8d2fffc19a8eb3ae2d606.tar.gz
ERROR: Aborting with RETVAL=1
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@russelljjarvis
But it looks like Singularity 2.3 has now been released (as of May 31st) so if I rename my old singularity-vm
directory, and then do:
mkdir singularity-vm
cd singularity-vm
vagrant init singularityware/singularity-2.3
vagrant up
vagrant ssh
i.e. Option 1 on the Mac instructions page
then inside the Vagrant container do:
singularity --version
(should be 2.3 with some suffix)
then do:
singularity create --size 10000 neuronunit.img
singularity import neuronunit.img docker://scidash/neuronunit:latest
It seems to complete without error. Then I do:
singularity shell neuronunit.img
and
python -c "import neuronunit"
and it seems to work.
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AOK.
from neuronunit.
Probably not useful in light of so many HPC resources providing Docker support.
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Related Issues (20)
- newer test class for passive elephant tests breaks parallelism in dask, in the case of brian2 backend. HOT 4
- Documenting all Score edge cases that break optimization gradients HOT 3
- A document Notice to debug set PARALLEL_CONFIDENT=False
- Test Suites should be dictionaries not lists. HOT 7
- Use standardized units throughout
- Sciunit judge no longer works with static Models. How can I opt of using the ProtocolToFeaturesTest? HOT 8
- Druckmann Tests are not proper tests
- Confirm that NeuronUnits jNeuromLB backend really can be regarded as a ground truth. HOT 7
- NU test.protocol should be flat or more predictable to traverse.
- Major NU interface redesigns could come with interface diagrams.
- documentation chapters of NeuronUnit should be upgraded to Unit Tests via pytest-ipynb
- 2.5 different code locations that determine sim_length need to be collapsed into one.
- Duplicated content injected current test protocol/parameter
- Installation Fails on Windows HOT 1
- create branch optimization based on dev, that I can merge pull requests into. HOT 2
- Migrate away from travis HOT 2
- Merge error in backend __init__.py HOT 2
- Missing closing ' HOT 1
- Relax constraints on install requirements HOT 1
- unresolved merge conflict in requirements.txt
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