# Error running CLI modules on multi-user linux system

**URL:** <https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367>\
**Category:** Support\
**Created:** [November 3, 2017, 7:53pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367 "2017-11-03T19:53:47Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [November 3, 2017, 7:53pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/1 "2017-11-03T19:53:47Z")

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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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 3, 2017, 9:03pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/2 "2017-11-03T21:03:43Z")

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

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [November 3, 2017, 9:22pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/3 "2017-11-03T21:22:19Z")

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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’)

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [November 3, 2017, 9:35pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/4 "2017-11-03T21:35:23Z")

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What if you try Prefer Executable CLIs?

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/d/fd7ade17b3effb89248a374b403cb41ae97ea3ed.png)

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [November 3, 2017, 10:17pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/5 "2017-11-03T22:17:56Z")

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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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 3, 2017, 10:35pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/6 "2017-11-03T22:35:23Z")

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It is a known issue ([https://issues.slicer.org/view.php?id=4340](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?

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [November 3, 2017, 11:09pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/7 "2017-11-03T23:09:45Z")

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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.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 4, 2017, 3:20am UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/8 "2017-11-04T03:20:46Z")

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Submitted pull request with proposed fix: [https://github.com/Slicer/Slicer/pull/834](https://github.com/Slicer/Slicer/pull/834)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [November 4, 2017, 7:48pm UTC](https://discourse.slicer.org/t/error-running-cli-modules-on-multi-user-linux-system/1367/9 "2017-11-04T19:48:31Z")

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The fix is integrated into Slicer-4.9 version.