Troubleshooting

Container building

Singularity cache and tmp

Cache directory Error: “FATAL: While performing build: conveyor failed to get: Error writing blob: write /tmp/bundle-temp-<bundlenumber>/oci-put-blob<blobnumber>>: no space left on device”

Solution: Declare the variables SINGULARITY_CACHEDIR and SINGULARITY_TMPDIR before your singularity build command as follows:

mkdir /path/to/singularity_images/SINGCACHE && mkdir /path/to/singularity_images/TMPSING
SINGULARITY_CACHEDIR=/path/to/singularity_images/SINGCACHE SINGULARITY_TMPDIR=/path/to/singularity_images/SINGTMP singularity build yourimage.sif docker://organization/image:tag

SquashFS-tools

SquashFS-tools Error: FATAL: Unable to create build: while searching for mksquashfs: exec: “mksquashfs”: executable file not found in $PATH

Solution: Compile squashfs-tools locally from GitHub - https://github.com/plougher/squashfs-tools and add to PATH temporarily as follows

cd /path/to/singularity_images/
git clone https://github.com/plougher/squashfs-tools.git
cd squashfs-tools/squashfs-tools
make
export PATH=$PATH:/path/to/singularity_images/squashfs-tools/squashfs-tools

Container running

TemplateFlow

BIDS-Apps failing due to failed attempt to retrieve TemplateFlow images from the web:

.....
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='templateflow.s3.amazonaws.com', port=443): Max retries exceeded with url: /tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab5a2c700>: Failed to establish a new connection: [Errno 110] Connection timed out'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
  self.run()
File "/opt/conda/lib/python3.8/multiprocessing/process.py", line 108, in run
  self._target(*self._args, **self._kwargs)
File "/opt/conda/lib/python3.8/site-packages/smriprep/cli/run.py", line 581, in build_workflow
  retval["workflow"] = init_smriprep_wf(
File "/opt/conda/lib/python3.8/site-packages/smriprep/workflows/base.py", line 166, in init_smriprep_wf
  single_subject_wf = init_single_subject_wf(
File "/opt/conda/lib/python3.8/site-packages/smriprep/workflows/base.py", line 400, in init_single_subject_wf
  anat_preproc_wf = init_anat_preproc_wf(
File "/opt/conda/lib/python3.8/site-packages/smriprep/workflows/anatomical.py", line 376, in init_anat_preproc_wf
  brain_extraction_wf = init_brain_extraction_wf(
File "/opt/conda/lib/python3.8/site-packages/niworkflows/anat/ants.py", line 198, in init_brain_extraction_wf
  tpl_target_path, common_spec = get_template_specs(
File "/opt/conda/lib/python3.8/site-packages/niworkflows/utils/misc.py", line 78, in get_template_specs
  tpl_target_path = get_template(in_template, **template_spec)
File "/opt/conda/lib/python3.8/site-packages/templateflow/conf/__init__.py", line 31, in wrapper
  return func(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/templateflow/api.py", line 79, in get
  _s3_get(filepath)
File "/opt/conda/lib/python3.8/site-packages/templateflow/api.py", line 222, in _s3_get
  r = requests.get(url, stream=True)
File "/opt/conda/lib/python3.8/site-packages/requests/api.py", line 75, in get
  return request('get', url, params=params, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/requests/api.py", line 61, in request
  return session.request(method=method, url=url, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/requests/sessions.py", line 542, in request
  resp = self.send(prep, **send_kwargs)
File "/opt/conda/lib/python3.8/site-packages/requests/sessions.py", line 655, in send
  r = adapter.send(request, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/requests/adapters.py", line 516, in send
  raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='templateflow.s3.amazonaws.com', port=443): Max retries exceeded with url: /tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab5a2c700>: Failed to establish a new connection: [Errno 110] Connection timed out'))

Fix use your own pre-downloaded templateflow directory:

ls /path/to/singularity_images/templateflow
  tpl-Fischer344  tpl-MNI152NLin2009cAsym  tpl-MNIInfant         tpl-PNC
  tpl-fsaverage   tpl-MNI152NLin2009cSym   tpl-MNIPediatricAsym  tpl-RESILIENT
  tpl-fsLR        tpl-MNI152NLin6Asym      tpl-NKI               tpl-UNCInfant
  tpl-MNI152Lin   tpl-MNI152NLin6Sym       tpl-OASIS30ANTs       tpl-WHS

export TEMPLATEFLOW_HOST_HOME=/path/to/singularity_images/templateflow
SINGULARITY_ENVTEMPLATEFLOW_HOME=/opt/templateflow
SINGULARITY_ENVTEMPLATEFLOW_HOME=/opt/templateflow singularity run --nv -B ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITY_ENVTEMPLATEFLOW_HOME},./bids:/data,./bids/derivatives/smriprep:/out,/path/to/singularity_images/license.txt:/opt/freesurfer/license.txt /path/to/singularity_images/smriprep-fastsurfer_dev.sif /data/ /out/ --fs-license-file /opt/freesurfer/license.txt participant --participant-label sub-<participantIDhere>