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Whenever I try to run my python 3 script through Paramiko/subprocess I get errors like this:

HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140482549520192:
  #000: ../../../src/H5Dio.c line 170 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: ../../../src/H5Dio.c line 543 in H5D__read(): can't read data
    major: Dataset
    minor: Read failed
  #002: ../../../src/H5Dchunk.c line 2046 in H5D__chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: ../../../src/H5Dchunk.c line 3401 in H5D__chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: ../../../src/H5Z.c line 1351 in H5Z_pipeline(): required filter 'HDF5 JPEG-LS filter' is not registered
    major: Data filters
    minor: Read failed
  #005: ../../../src/H5PL.c line 370 in H5PL_load(): search in paths failed
    major: Plugin for dynamically loaded library
    minor: Can't get value
  #006: ../../../src/H5PL.c line 474 in H5PL__find(): can't open directory
    major: Plugin for dynamically loaded library
    minor: Can't open directory or file

Yet, the following scenarios work just fine:

  • Connecting to the machine through ssh on a Linux terminal and running the script there;
  • Running the script on the machine itself;

I believe I loaded the environment variables just fine, as well as the .bashrc just in case. Does anybody have a clue about this weird behavior?

EDIT: Those relative paths bother me, I'm not sure if that might be the cause.

jruivo
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    The relative paths look like they refer to the path to the C file this code was compiled from, not to anything actually in your code. But it also looks like this is not a Python question at all, or you need to reveal how your Python code ends up calling this C code. – tripleee Apr 09 '19 at 12:25
  • Which Unix commands fail? This is not a reproducible example, can you try to create one? Also, it doesn't look like a Python question at all, but an internal C bug on Paramiko. – smci Apr 09 '19 at 12:29

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