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scilus / dmriqc_flow

A Nextflow pipeline for diffusion MRI quality check
MIT License
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Cannot run current versions of dmriqc-flow using container #28

Open araikes opened 1 month ago

araikes commented 1 month ago

Hi @arnaudbore,

Moving this here as requested. I get the following when using scilus-flows_1.5.0.sif built from DockerHub:

singularity run /groups/adamraikes/singularity_images/scilus-flows_1.5.0.sif  dmriqc-flow --help

==========
== CUDA ==
==========

CUDA Version 11.7.1

Container image Copyright (c) 2016-2022, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

This container image and its contents are governed by the NVIDIA Deep Learning Container License.
By pulling and using the container, you accept the terms and conditions of this license:
https://developer.nvidia.com/ngc/nvidia-deep-learning-container-license

A copy of this license is made available in this container at /NGC-DL-CONTAINER-LICENSE for your convenience.

WARNING: The NVIDIA Driver was not detected.  GPU functionality will not be available.
   Use the NVIDIA Container Toolkit to start this container with GPU support; see
   https://docs.nvidia.com/datacenter/cloud-native/ .

/opt/nvidia/nvidia_entrypoint.sh: line 67: /usr/bin/dmriqc-flow: Permission denied
/opt/nvidia/nvidia_entrypoint.sh: line 67: exec: /usr/bin/dmriqc-flow: cannot execute: Permission denied
arnaudbore commented 1 month ago

Hello @araikes , our flows and singularities are not meant to be used like this and there is no entry point in our containers that will allow you to do something like this. Always use our flow using nextflow combined with singularity (or docker). Hope it helps! Arnaud

araikes commented 1 month ago

How is the scilus-flows container supposed to be used? I thought the point of that container was to be a prebuilt setup for running flows without needing nextflow installed.

Based on the documentation on the container's repo, the following should work:

docker run <scilus-flows image> tractometry-flow <args> and would be analagous to singularity run <scilus-flows image> dmriqc-flow <args> which I have been able to get to work on another system and which previously worked on this system until the most recent time I went to use it when I got the permissions error.