Hi Experts
After upgrading to 1.0.12, I can run AROMA with 2mm grid but faced another problem.
Sometimes the pipeline will stop with the following error.
Is it to do with my memory setting or some other issue with my docker?
Thank you very much!
180508-02:54:36,135 workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_005_wf.func_preproc_ses_postdose_task_MID_run_02_wf.ica_aroma_wf.ica_aroma" (/root/src/fmriprep/work/fmriprep_wf/single_subject_005_wf/func_preproc_ses_postdose_task_MID_run_02_wf/ica_aroma_wf/ica_aroma)
Traceback (most recent call last):
File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
load_entry_point('fmriprep==1.0.12', 'console_scripts', 'fmriprep')()
File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 314, in main
fmriprep_wf.run(**plugin_settings)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run
self._clean_queue(jobid, graph, result=result))
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 644, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 520, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/interfaces/report_base.py", line 69, in _run_interface
self._generate_report()
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/interfaces/segmentation.py", line 153, in _generate_report
noise_components_file=self._noise_components_file
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/viz/utils.py", line 489, in plot_melodic_components
import pylab as plt
File "/usr/local/miniconda/lib/python3.6/site-packages/pylab.py", line 1, in <module>
from matplotlib.pylab import *
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/pylab.py", line 230, in <module>
import matplotlib.finance
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/finance.py", line 46, in <module>
cachedir = get_cachedir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 336, in wrapper
ret = func(*args, **kwargs)
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 692, in _get_cachedir
return _get_config_or_cache_dir(_get_xdg_cache_dir())
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 657, in _get_config_or_cache_dir
return _create_tmp_config_dir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 577, in _create_tmp_config_dir
tempdir = tempfile.gettempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 296, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 231, in _get_default_tempdir
dirlist)
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/root/src/fmriprep/work/fmriprep_wf/single_subject_005_wf/func_preproc_ses_postdose_task_MID_run_02_wf/ica_aroma_wf/ica_aroma']
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 480, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 648, in _run_command
_save_resultfile(result, outdir, self.name)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/utils.py", line 246, in save_resultfile
savepkl(resultsfile, result)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/utils/filemanip.py", line 686, in savepkl
pkl_file = gzip.open(filename, 'wb')
File "/usr/local/miniconda/lib/python3.6/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/local/miniconda/lib/python3.6/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
OSError: [Errno 30] Read-only file system: '/root/src/fmriprep/work/fmriprep_wf/single_subject_005_wf/func_preproc_ses_postdose_task_MID_run_02_wf/ica_aroma_wf/ica_aroma/result_ica_aroma.pklz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, 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 484, in run
os.remove(hashfile_unfinished)
OSError: [Errno 30] Read-only file system: '/root/src/fmriprep/work/fmriprep_wf/single_subject_005_wf/func_preproc_ses_postdose_task_MID_run_02_wf/ica_aroma_wf/ica_aroma/_0x5ef8f1d1cbe38d826e7ab25181d3afc7_unfinished.json'
Sentry is attempting to send 1 pending error messages
Waiting up to 10 seconds
Press Ctrl-C to quit
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 178, in main
_serve_one(s, listener, alive_r, handler)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 212, in _serve_one
code = spawn._main(child_r)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/__init__.py", line 14, in <module>
import matplotlib
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1182, in <module>
rcParams = rc_params()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1015, in rc_params
fname = matplotlib_fname()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 825, in matplotlib_fname
configdir = _get_configdir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 680, in _get_configdir
return _get_config_or_cache_dir(_get_xdg_config_dir())
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 657, in _get_config_or_cache_dir
return _create_tmp_config_dir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 577, in _create_tmp_config_dir
tempdir = tempfile.gettempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 296, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 231, in _get_default_tempdir
dirlist)
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/root/src/fmriprep']
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 178, in main
_serve_one(s, listener, alive_r, handler)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 212, in _serve_one
code = spawn._main(child_r)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/__init__.py", line 14, in <module>
import matplotlib
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1182, in <module>
rcParams = rc_params()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1015, in rc_params
fname = matplotlib_fname()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 825, in matplotlib_fname
configdir = _get_configdir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 680, in _get_configdir
return _get_config_or_cache_dir(_get_xdg_config_dir())
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 657, in _get_config_or_cache_dir
return _create_tmp_config_dir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 577, in _create_tmp_config_dir
tempdir = tempfile.gettempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 296, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 231, in _get_default_tempdir
dirlist)
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/root/src/fmriprep']
180508-02:54:37,261 workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_005_wf.func_preproc_ses_postdose_task_MID_run_01_wf.ica_aroma_wf.melodic" (/root/src/fmriprep/work/fmriprep_wf/single_subject_005_wf/func_preproc_ses_postdose_task_MID_run_01_wf/ica_aroma_wf/melodic)
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 178, in main
_serve_one(s, listener, alive_r, handler)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/forkserver.py", line 212, in _serve_one
code = spawn._main(child_r)
File "/usr/local/miniconda/lib/python3.6/multiprocessing/spawn.py", line 115, in _main
self = reduction.pickle.load(from_parent)
File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/__init__.py", line 14, in <module>
import matplotlib
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1182, in <module>
rcParams = rc_params()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 1015, in rc_params
fname = matplotlib_fname()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 825, in matplotlib_fname
configdir = _get_configdir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 680, in _get_configdir
return _get_config_or_cache_dir(_get_xdg_config_dir())
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 657, in _get_config_or_cache_dir
return _create_tmp_config_dir()
File "/usr/local/miniconda/lib/python3.6/site-packages/matplotlib/__init__.py", line 577, in _create_tmp_config_dir
tempdir = tempfile.gettempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 296, in gettempdir
tempdir = _get_default_tempdir()
File "/usr/local/miniconda/lib/python3.6/tempfile.py", line 231, in _get_default_tempdir
dirlist)
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/root/src/fmriprep']
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.6/multiprocessing/util.py", line 254, in _run_finalizers
finalizer()
File "/usr/local/miniconda/lib/python3.6/multiprocessing/util.py", line 186, in __call__
res = self._callback(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.6/shutil.py", line 474, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/usr/local/miniconda/lib/python3.6/shutil.py", line 432, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/usr/local/miniconda/lib/python3.6/shutil.py", line 430, in _rmtree_safe_fd
os.unlink(name, dir_fd=topfd)
OSError: [Errno 30] Read-only file system: 'listener-26fd5vq5'
ERRO[11815] Error waiting for container: driver "overlay2" failed to remove root filesystem for 6c8ccce64cc5717be1722693426116efa9b628ad09ded4e4df0f2ddd207f644a: remove /var/lib/docker/overlay2/ad136cfcd9fc47e4e88b3a92ac0719957673b0ece722e9ef2fedcec8e3f0e2dc/diff/out: read-only file system
fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/0f88cf74aef455a07eb67b57cb59c3fbd4a9ac821f4d65dbe1193717ee39111a-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/4ced0a5b510e8e1b429f73c4bbb7674607e769e5529c33a842d55fa047c2912e-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/bd3e6395094ee40ad0f99ba8b28095374c1fa329381627a41d63688f3d286c21-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/15d8085ffa6668d16b7e32d7d9e4ff9ed72343a947b5cde36db2a2991e0f3ec1-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/7e459ccd2e362cb187d8e867550f842512f1ece03b53a83753b934ad5e9ef924-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/fd4070f5c79583e8688fc06d3d0c5b5723e0c99400c71f20dae0f17708151889-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/6454ef1efb4080ef3c276886eae76b57161d330a058af9eedfc8926af43f6242-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/b371ab2b2676543b0fd07e6089152c19e72055cb5ff5dffd7e185273e4df8fff-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/1811197f2952951432e2815167ffee47f3f12e79e50f1ba27524b915e21ce1f8-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/51146d6659b56f6b98e7f33c19c76d47a68fc8bce54acf77ccb4840f9ffe2519-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/319e44c33e434583810761b9d465bf8b5be2e62b809bdba133bad567a9f2d8b9-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/56e97bee14fae7e5996e482627d5033e7b11d97b81fd2460076296de7221f297-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/28c1f23c5fcef5b1f2d5fc80b8c397e5f364eff096210817dc9059fb614ec171-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/7133d20c0423f69679b212cadab60977a3e96819ebcd4de3be34f82c413812af-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/e45552fe490c9a2748ddcceed81a385d1f0d3dfee24f46a9aeb47fe262f92242-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/8aca2c5b3a8e28e0c20fa98a0f08085a683139cec2ddf6fa40a50d6185447fc6-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/6ec33b6eaa07aef8d03e54f0a86a1a4b96d1a4df679b259f6c77322d86d30c2c-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/0085dbb0c5cb1df6f214a6fa460abe4e19da7f641543ba742911ae8573efd94b-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/299870502be215a79bd426dd1feb3bc0c2a00a5b83120269f8388b82831943d7-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/3382d0a63787f93674d2349c2c5af4a7d19235342c76bc3a96d7e00aecde806b-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/bc4d0007b7fc008a234981eef1b6ca4dabd06e75f64c33df1d1517acfeb42fad-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/3b99560ca075a1669f0953365647614d87e9abfb3b9721aca517be13520cca55-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/aaa2ba73421616cdb520b34f0387621fe77dd2f69ba1a4189bc7264cf435437b-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/2154a4a61843195af36dbb58e0de034857ec894742576bf8a448d52dd7546305-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/accd5bfe2dd242645169c8834f0e5692ff02f5635104ed64c895cc3b58c3f524-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/2f8dbfd1c6dc15bf1da479f9ffb9440fedc4fd6de5671f289fd5a804f2ea161f-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/0b63efd3c0093f184d3f43b2f089e31004a3e524bc3c9509b7119ac116da0e47-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/10d9aaaac3833764f776f5fb3ff8b96b6ff53e032665ffa789ea91fd46d58367-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/cb2c51a20d6b59b38f32bcd5b70d133ef8c73235c77605ab3dd1d91b18edb146-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
docker: Error response from daemon: mkdir /var/lib/docker/overlay2/0f700579ad76df51af2f2d5d8f6c515d61056c483a17c22da65024de643f815c-init: read-only file system.
See 'docker run --help'.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?