Error running CLI modules on multi-user linux system

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1

I have my moving, reference, and transform nodes loaded into slicer. I specify the parameters and hit Run, it fails with this errors (on Brains Resample, but same error occurs with Resample Vector/Scalar module as well).

Resample Image (BRAINS) command line:

slicer:0x2aad09cdc130 --processinformationaddress 0x27938e8 --inputVolume slicer:0xe6b0b0#vtkMRMLScalarVolumeNode1 --referenceVolume slicer:0xe6b0b0#vtkMRMLScalarVolumeNode4 --outputVolume slicer:0xe6b0b0#vtkMRMLScalarVolumeNode6 --pixelType float --warpTransform /tmp/Slicer/EHHFB_vtkMRMLLinearTransformNodeG.h5 --interpolationMode Linear --defaultValue 0 --numberOfThreads -1

HDF5-DIAG: Error detected in HDF5 (1.8.17) thread 0:
#000: /home/kitware/Dashboards/Package/Slicer-480-package/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c line 439 in H5Fis_hdf5(): unable open file
major: File accessibilty
minor: Not an HDF5 file
#001: /home/kitware/Dashboards/Package/Slicer-480-package/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5Fint.c line 554 in H5F_is_hdf5(): unable to open file
major: Low-level I/O
minor: Unable to initialize object
#002: /home/kitware/Dashboards/Package/Slicer-480-package/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 993 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: /home/kitware/Dashboards/Package/Slicer-480-package/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FDsec2.c line 339 in H5FD_sec2_open(): unable to open file: name = ‘/tmp/Slicer/EHHFB_vtkMRMLLinearTransformNodeG.h5’, errno = 2, error message = ‘No such file or directory’, flags = 0, o_flags = 0
major: File accessibilty
minor: Unable to open file

While SLicer has some log files in the /tmp/Slicer folder, there is indeed no /tmp/Slicer/EHHFB_vtkMRMLLinearTransformNodeG.h5 file. But I already loaded the transform into Slicer. Any ideas? This is on Centos 7.2 with Slicer 4.8.0.

2

Does your user have write access to /tmp/Slicer?

3

Yes. (apparently that is too short of answer for discourse to accept it on its own, so here is my attempt to make it ‘meaningful’)

4

What if you try Prefer Executable CLIs?

image

5

Turned out to be multi-user issue. /tmp is writable by everyone, but Slicer directory last time generated some other user.

Anyways, on Linux I think it would make sense to default to home to $HOME/tmp or something of that sort.

6

It is a known issue (https://issues.slicer.org/view.php?id=4340), it just never got fixed. Would you like to give it a try and change how the temp directory name is generated by default?

7

Unfortunately I don’t have the skills. I wouldn’t know even where to start. As the bug description says, if you know what the issue is, it is avoidable.

8

Submitted pull request with proposed fix: https://github.com/Slicer/Slicer/pull/834

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9

The fix is integrated into Slicer-4.9 version.

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