Read only file system error


#1

Getting following error:-

Sat Jun 16 01:11:58 2018: Image # 1265, module MeasureObjectIntensity # 6: CPU_time = 1.19 secs, Wall_time = 1.19 secs
Error detected during run of module MeasureTexture
Traceback (most recent call last):
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/pipeline.py”, line 1770, in run_with_yield
self.run_module(module, workspace)
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/pipeline.py”, line 2022, in run_module
module.run(workspace)
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/modules/measuretexture.py”, line 549, in run
statistics += self.run_one(image_name, object_name, scale, workspace)
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/modules/measuretexture.py”, line 628, in run_one
workspace=workspace
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/modules/measuretexture.py”, line 663, in record_measurement
result
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/workspace.py”, line 169, in add_measurement
self.measurements.add_measurement(object_name, feature_name, data)
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/measurement.py”, line 838, in add_measurement
object_name, feature_name, image_set_number, data_type] = data
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/utilities/hdf5_dict.py”, line 494, in setitem
(object_name, feature_name, [num_idx], idxs[3]), [vals])
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/utilities/hdf5_dict.py”, line 541, in setitem
dataset = feature_group[‘data’]
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “/share/apps/CentOS_6.4/anaconda/r-2.3.0/envs/cellprofiler/lib/python2.7/site-packages/h5py/_hl/group.py”, line 169, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5o.pyx”, line 190, in h5py.h5o.open
KeyError: “Unable to open object (File write failed: time = sat jun 16 01:17:11 2018\n, filename = ‘/tmp/cpmeasurementsp6avgy.hdf5’, file descriptor = 12, errno = 30, error message = ‘read-only file system’, buf = 0x5617384c04a8, total write size = 272, bytes this sub-write = 272, bytes actually written = 18446744073709551615, offset = 543848)”
Sat Jun 16 01:11:59 2018: Image # 1265, module MeasureTexture # 7: CPU_time = 311.75 secs, Wall_time = 312.02 secs
Traceback (most recent call last):
File “/share/apps/CentOS_6.4/anaconda/r-2.3.0/envs/cellprofiler/bin/cellprofiler”, line 11, in
load_entry_point(‘CellProfiler’, ‘console_scripts’, ‘cellprofiler’)()
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/main.py”, line 161, in main
run_pipeline_headless(options, args)
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/main.py”, line 738, in run_pipeline_headless
initial_measurements=initial_measurements
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/pipeline.py”, line 1574, in run
initial_measurements=measurements):
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/pipeline.py”, line 1860, in run_with_yield
measurements.flush()
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/measurement.py”, line 383, in flush
self.hdf5_dict.flush()
File “/share/apps/CentOS_6.4/CellProfiler/cellprofiler/utilities/hdf5_dict.py”, line 343, in flush
self.hdf5_file.flush()
File “/share/apps/CentOS_6.4/anaconda/r-2.3.0/envs/cellprofiler/lib/python2.7/site-packages/h5py/_hl/files.py”, line 308, in flush
h5f.flush(self.fid)
File “h5py/_objects.pyx”, line 54, in h5py._objects.with_phil.wrapper
File “h5py/_objects.pyx”, line 55, in h5py._objects.with_phil.wrapper
File “h5py/h5f.pyx”, line 115, in h5py.h5f.flush
RuntimeError: Unable to flush file’s cached information (File write failed: time = sat jun 16 01:17:11 2018
, filename = ‘/tmp/cpmeasurementsp6avgy.hdf5’, file descriptor = 12, errno = 30, error message = ‘read-only file system’, buf = 0x5617384c04a8, total write size = 272, bytes this sub-write = 272, bytes actually written = 18446744073709551615, offset = 543848)

any suggestions on what may have went wrong?

Thanks,
Ved


#2

@vedient, this is a naive question, but do you have write access to your output folder location or the Temporary Folder found in preferences? Have you tried running CellProfiler on a different machine and had success?


#3

Sorry for late reply. I wasn’t having access to temp folder at that time, because of that the issue was coming. It solved now.

Thanks,
Ved