@@ -186,7 +186,7 @@ the templates that are used, e.g., in the atlas-based brain extraction
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step or spatial normalization.
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Default settings in the Singularity image should get along with the
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- Singularity installation of your system. However, deviations from the
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+ * Singularity* installation of your system. However, deviations from the
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default configurations of your installation may break this
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compatibility. A particularly problematic case arises when the home
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directory is mounted in the container, but the ` $HOME ` environment
@@ -257,7 +257,7 @@ endpoints), then you can try the following:
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--cleanenv fmriprep.simg < fmriprep arguments>
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` ` `
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Otherwise, [some users have succeeded pre-fetching the necessary
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- templates onto the TemplateFlow directory to then bind the folder at
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+ templates onto the * TemplateFlow* directory to then bind the folder at
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execution](https://neurostars.org/t/problems-using-pediatric-template-from-templateflow/4566/15):
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` ` ` Shell
@@ -277,6 +277,27 @@ $ singularity run -B ${TEMPLATEFLOW_HOME:-$HOME/.cache/templateflow}:/templatefl
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--cleanenv fmriprep.simg < fmriprep arguments>
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` ` `
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+ # # *Socket errors* when running parallel processes on HPC
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+
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+ When running multiple instances of a * NiPreps* on HPC, you may encounter
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+ errors like [` nipreps/mriqc#1170` ](https://github.com/nipreps/mriqc/issues/1170):
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+
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+ ` ` ` text
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+ OSError: [Errno 98] Address already in use
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+ ` ` `
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+
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+ To solve this issue, you can try to isolate the container network from
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+ the host network by using the ` --network none` setting of * Singularity* /* Apptainer* :
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+
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+ ` ` ` shell
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+ apptainer run --net --network none ...
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+ ` ` `
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+
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+ This solution prevents the container from accessing the Internet and from
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+ downloading data, for example, templates.
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+ Please follow the previous section' s guidelines to pre-fetch templates
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+ and then making them accessible.
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+
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## Troubleshooting
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Setting up a functional execution framework with Singularity might be
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