Merge pull request #1349 from vferat/dev-docs

Add a HPC troubleshooting section to the documentation

Author: oesteban

docs/source/usage.rst

@@ -102,16 +102,8 @@ This will separate *DataLad* management from *MRIQC*'s operation,
 which can be an effective way of debugging issues and averting
 erroneous conditions.
 
-Command line interface
-----------------------
-.. argparse::
-   :ref: mriqc.cli.parser._build_parser
-   :prog: mriqc
-   :nodefault:
-   :nodefaultconst:
-
-Running mriqc on HPC clusters
------------------------------
+Running *MRIQC* on HPC with *Singularity*/*Apptainer*
+-----------------------------------------------------
 We have profiled cores and memory usages with the *resource profiler*
 tool of *Nipype*.
 
@@ -140,6 +132,56 @@ on ds030 of OpenfMRI:
   the 1-task example, a rule of thumb may be that each task takes around
   1GB of memory.
 
+Known issues with HPC
+.....................
+
+#. No internet access
+
+    The container needs to download the templates from the internet.
+    If the container does not have internet access, you can download the
+    templates manually using the ``templateflow`` library:
+    
+    .. code-block:: python
+
+      import templateflow.api
+      templateflow.api.TF_S3_ROOT = 'http://templateflow.s3.amazonaws.com'
+      templateflow.api.get('MNI152NLin2009cAsym') # change template if needed
+
+    then provide the templates to the container by mounting the ``templateflow`` home directory and setting the ``TEMPLATEFLOW_HOME`` environment variable:
+
+    .. code-block:: bash
+
+      apptainer run -v /path/to/templateflow:/path/to/templates --env TEMPLATEFLOW_HOME=/path/to/templates ...
+
+#. Socket error:
+
+    When running multiple instances of MRIQC on a HPC, you may encounter the following error:
+
+    .. code-block:: python
+
+      OSError: [Errno 98] Address already in use
+
+    To solve this issue, you can try to isolate the container network from the host network by using the ``--network none`` option.
+
+    .. code-block:: bash
+
+      apptainer run --net --network none ...
+
+    This solution might prevent the container from accessing the internet and downloading templates.
+    In this case, you can download the templates manually and provide access to the downloaded files as explained in the previous section.
+
+    .. code-block:: bash
+
+      apptainer run --net --network none -v /path/to/templateflow:/path/to/templates --env TEMPLATEFLOW_HOME=/path/to/templates ...
+
+Command line interface
+----------------------
+.. argparse::
+   :ref: mriqc.cli.parser._build_parser
+   :prog: mriqc
+   :nodefault:
+   :nodefaultconst:
+  
 .. topic:: References
 
   .. [BIDS] `Brain Imaging Data Structure <http://bids.neuroimaging.io/>`_