Fmriprep: indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
DS000115 / sub-31
DS000119 / sub-74
DS000052 / sub-08
DS000121 / sub-04
Seems like a bad interaction between nilearn and the indexed_gzip or memory errors.
Node: fmriprep_wf.single_subject_31_wf.func_preproc_task_letter2backtask_wf.bold_mni_trans_wf.merge
Working directory: /scratch/03763/oesteban/fmriprep-phase1/work/ds000115/fmriprep_wf/single_subject_31_wf/func_preproc_task_letter2backtask_wf/bold_mni_trans_wf/merge
Node inputs:
compress = True
dtype = f4
header_source = /work/03843/crn_plab/stampede2/fmriprep-phase2/data/openfmri/ds000115/sub-31/func/sub-31_task-letter2backtask_bold.nii.gz
ignore_exception = False
in_files = [ ... ]
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 407, in run
self._run_interface()
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 517, in _run_interface
self._result = self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command
result = self._interface.run()
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base.py", line 1088, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/nilearn.py", line 94, in _run_interface
new_nii = concat_imgs(self.inputs.in_files, dtype=self.inputs.dtype)
File "/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 464, in concat_niimgs
memory=memory, memory_level=memory_level))):
File "/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 133, in _iter_check_niimg
dtype=dtype)
File "/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 271, in check_niimg
niimg = load_niimg(niimg, dtype=dtype)
File "/usr/local/miniconda/lib/python3.6/site-packages/nilearn/_utils/niimg.py", line 116, in load_niimg
dtype = _get_target_dtype(niimg.get_data().dtype, dtype)
File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
data = np.asanyarray(self._dataobj)
File "/usr/local/miniconda/lib/python3.6/site-packages/numpy/core/numeric.py", line 583, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 290, in __array__
raw_data = self.get_unscaled()
File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 285, in get_unscaled
mmap=self._mmap)
File "/usr/local/miniconda/lib/python3.6/site-packages/nibabel/volumeutils.py", line 521, in array_from_file
infile.seek(offset)
File "indexed_gzip/indexed_gzip.pyx", line 311, in indexed_gzip.indexed_gzip.IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
bug
oesteban
All 19 comments
@pauldmccarthy Any pointers for how to start debugging this? And any notion whether to treat this as a problem in nilearn, nibabel or indexed_gzip?
effigies
on 26 Oct 2017
Hey guys,
I know nothing about nilearn or nipype - could you give me some pointers on how to set up an equivalent scenario?
For how long has the image been open before this error occurs, and what else has been done with/to it?
What version of indexed_gzip? You can enable debugging by compiling a local version with -DZRAN_VERBOSE. However, it will be very verbose, and probably not of much use to anybody but myself ...
cd path/to/indexed_gzip
python setup.py build_ext -DZRAN_VERBOSE
python setup.py develop
export PYTHONPATH=`pwd`
pauldmccarthy
on 26 Oct 2017
The dependency is indexed_gzip >= 0.6.1, installed via pip.
I'm trying to generate a situation with indexed_gzip enabled that reproduces this, but having trouble.
@oesteban have you verified that the inputs to that Merge node are full size? I'm wondering if there might be a truncation issue.
effigies
on 26 Oct 2017
This seems a problem only in lonestar5. I'll close for now and reopen if it happens again.
oesteban
on 4 Nov 2017
Hey guys,
The latest version of indexed_gzip (0.7.0) drops file handles by default. So if you are able to reproduce/test the problem you were having, try 0.7.0 and see if it makes a difference
Thanks!
pauldmccarthy
on 5 Nov 2017
I got this error in one of the subjects with fmriprep 1.1.8 and indexed_gzip 0.8.7 ... Any suggestions?
Thanks!
MetaD
on 20 Oct 2018
@MetaD can you provide a stack trace, and ideally share the offending image?
pauldmccarthy
on 21 Oct 2018
I just ran the same fmriprep command again with the same input files, but somehow got this error in a different workflow this time.
Error info for the first time:
181020-04:19:43,585 nipype.workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_169_wf.func_preproc_task_face_run_04_wf.bold_t1_trans_wf.bold_to_t1w_transform" (/u/project/cparkins/data/hierarchy/fmriprep/e/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_t1_trans_wf/bold_to_t1w_transform)
Traceback (most recent call last):
File "/u/home/m/mengdu/.local/bin/fmriprep", line 11, in <module>
sys.exit(main())
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/cli/run.py", line 343, in main
fmriprep_wf.run(**plugin_settings)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 162, in run
self._clean_queue(jobid, graph, result=result))
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 224, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/interfaces/itk.py", line 143, in _run_interface
for i, (in_file, in_xfm) in enumerate(zip(in_files, xfms_list))]
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 556, in result_iterator
yield future.result()
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 405, in result
return self.__get_result()
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 357, in __get_result
raise self._exception
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/thread.py", line 55, in run
result = self.fn(*self.args, **self.kwargs)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/interfaces/itk.py", line 262, in _applytfms
runtime = xfm.run().runtime
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/niworkflows/interfaces/fixes.py", line 29, in _run_interface
self.__class__.__name__, __version__))
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/niworkflows/interfaces/utils.py", line 179, in _copyxform
newimg = resampled.__class__(resampled.get_data(), orig.affine, header)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
data = np.asanyarray(self._dataobj)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/numpy/core/numeric.py", line 553, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 293, in __array__
raw_data = self.get_unscaled()
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 288, in get_unscaled
mmap=self._mmap)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/volumeutils.py", line 521, in array_from_file
infile.seek(offset)
File "indexed_gzip/indexed_gzip.pyx", line 430, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
md5-cf10d539e279948a0471da8abb0e1fa3
181021-16:04:03,408 nipype.workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_169_wf.func_preproc_task_face_run_02_wf.bold_t1_trans_wf.merge" (/u/project/cparkins/data/hierarchy/fmriprep/e/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_02_wf/bold_t1_trans_wf/merge)
md5-732a587e35a6f21c3bd3211de62dbc3f
Traceback (most recent call last):
File "/u/home/m/mengdu/.local/bin/fmriprep", line 11, in <module>
sys.exit(main())
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/cli/run.py", line 343, in main
fmriprep_wf.run(**plugin_settings)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 162, in run
self._clean_queue(jobid, graph, result=result))
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 224, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/interfaces/nilearn.py", line 126, in _run_interface
new_nii = concat_imgs(self.inputs.in_files, dtype=self.inputs.dtype)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 449, in concat_niimgs
niimg = check_niimg(niimg, ensure_ndim=ndim)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nilearn/_utils/niimg_conversions.py", line 271, in check_niimg
niimg = load_niimg(niimg, dtype=dtype)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nilearn/_utils/niimg.py", line 116, in load_niimg
dtype = _get_target_dtype(niimg.get_data().dtype, dtype)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
data = np.asanyarray(self._dataobj)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/numpy/core/numeric.py", line 553, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 293, in __array__
raw_data = self.get_unscaled()
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 288, in get_unscaled
mmap=self._mmap)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/volumeutils.py", line 521, in array_from_file
infile.seek(offset)
File "indexed_gzip/indexed_gzip.pyx", line 430, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
I guess fmriprep was perhaps feeding some intermediate results to indexed_gzip, but there are quite a few intermediate files in the work folder and I'm not sure which one it's supposed to be...
MetaD
on 22 Oct 2018
I'm guessing you're using nibabel 2.3.0 - it is worth upgrading to 2.3.1, as there were a couple of bugfixes related to how indexed_gzip is used which could be the reason for this error.
If that doesn't work, it would help if you could identify and share one of the offending files - it's probably best to share it with me by opening an issue over at pauldmccarthy/indexed_gzip.
pauldmccarthy
on 22 Oct 2018
@MetaD your execution environment may also be relevant. For instance, I believe the issue we had before was on NFS shares.
effigies
on 22 Oct 2018
I updated nibabel to 2.3.1 and tried again, but still got that error. This time it also comes with a log file though, so maybe it provides more useful information (see below)? Would it be useful if I share the 406 input files?
@effigies if it's related to the environment, would you expect I also get this error elsewhere? I've been only getting it with one subject (out of 25) every time I run it. I do have a NFS file system though.
Node: fmriprep_wf.single_subject_169_wf.func_preproc_task_face_run_04_wf.bold_t1_trans_wf.bold_to_t1w_transform
Working directory: /u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_t1_trans_wf/bold_to_t1w_transform
Node inputs:
args = <undefined>
copy_dtype = True
default_value = 0.0
dimension = <undefined>
environ = {}
float = True
input_image = ['/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0000.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0001.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0002.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0003.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0004.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0005.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0006.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0007.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0008.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0009.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0010.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0011.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0012.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0013.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0014.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0015.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0016.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0017.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0018.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0019.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0020.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0021.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0022.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0023.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0024.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0025.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0026.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0027.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0028.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_split/vol0029.nii.gz', 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input_image_type = <undefined>
interpolation = LanczosWindowedSinc
interpolation_parameters = <undefined>
invert_transform_flags = <undefined>
num_threads = 8
out_postfix = _trans
output_image = <undefined>
print_out_composite_warp_file = <undefined>
reference_image = /u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_t1_trans_wf/gen_ref/highres001_N4Corrected0_masked_reference.nii.gz
save_cmd = True
transforms = ['/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz', '/u/project/cparkins/data/hierarchy/fmriprep/169/work/fmriprep_wf/single_subject_169_wf/func_preproc_task_face_run_04_wf/bold_hmc_wf/fsl2itk/mat2itk.txt']
Traceback (most recent call last):
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/interfaces/itk.py", line 143, in _run_interface
for i, (in_file, in_xfm) in enumerate(zip(in_files, xfms_list))]
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 556, in result_iterator
yield future.result()
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 405, in result
return self.__get_result()
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/_base.py", line 357, in __get_result
raise self._exception
File "/u/local/apps/python/3.6.1/lib/python3.6/concurrent/futures/thread.py", line 55, in run
result = self.fn(*self.args, **self.kwargs)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/fmriprep/interfaces/itk.py", line 262, in _applytfms
runtime = xfm.run().runtime
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/niworkflows/interfaces/fixes.py", line 29, in _run_interface
self.__class__.__name__, __version__))
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/niworkflows/interfaces/utils.py", line 179, in _copyxform
newimg = resampled.__class__(resampled.get_data(), orig.affine, header)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/dataobj_images.py", line 202, in get_data
data = np.asanyarray(self._dataobj)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/numpy/core/numeric.py", line 553, in asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 356, in __array__
raw_data = self.get_unscaled()
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/arrayproxy.py", line 351, in get_unscaled
mmap=self._mmap)
File "/u/home/m/mengdu/.local/lib/python3.6/site-packages/nibabel/volumeutils.py", line 525, in array_from_file
infile.seek(offset)
File "indexed_gzip/indexed_gzip.pyx", line 430, in indexed_gzip.indexed_gzip._IndexedGzipFile.seek
indexed_gzip.indexed_gzip.ZranError: zran_seek returned error: -1
@MetaD sure, if you could share the offending files, I'll take a look at them.
pauldmccarthy
on 25 Oct 2018
@pauldmccarthy The files are here (input_image in the last error log). Thank you!!
MetaD
on 26 Oct 2018
There seems to be nothing wrong with any of the inputs - they all load fine on my laptop:
import numpy as np
import indexed_gzip as igzip
import nibabel as nib
print(igzip.__version__)
print(nib.__version__)
for f in glob('*.gz'):
i = igzip.IndexedGzipFile(f)
d = nib.volumeutils.array_from_file((82, 82, 60), '<i2', i, 352)
print(f, d.shape, d.min(), d.max())
Does the error always occur with the same subject? Can you try running from a local (non-networked) file system to see if it still occurs?
pauldmccarthy
on 28 Oct 2018
Hmmm interesting... Yes it always happens with this one subject only. My local computer doesn't have enough memory, but I'll try to run it on OpenNeuro and see if that works. Thanks!
MetaD
on 29 Oct 2018
I just realized OpenNeuro doesn't support running fmriprep on it any more. But somehow when I tried for a 4th time on my cluster, it didn't give any error.. Everything is same as before so I have no idea, but maybe we could close this issue for now... Thanks for the help.
MetaD
on 30 Oct 2018
@MetaD OpenNeuro moved to a new storage backend (the old one was tied to the execution backend), so the new execution backend is in progress. There are plans for a limited, stop-gap execution strategy, but I don't know the timeline on that.
Thanks for looking into this, and sorry there wasn't anything "fixable" this time. My suspicion is that there are some weird interactions with random access on NFS, probably cache-related. Hopefully next time we start running into it, we can get a cluster admin who can do some deep digging.
It occurs to me just now that this may be an interaction of NFS caching and persistent nibabel filehandles. I'll open a new PR to remove an outdated setting.
effigies
on 30 Oct 2018
@MetaD indexed_gzip 0.8.8 is now available, which should hopefully fix this issue - could you upgrade and see if that fixes things?
pauldmccarthy
on 23 Nov 2018
@pauldmccarthy I tried again and no error this time :) Thank you!
MetaD
on 29 Nov 2018
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Most helpful comment
@pauldmccarthy I tried again and no error this time :) Thank you!