[scipion-users] module compiled as little endian, but detected different endianness at runtime

[Juha H. <juh...@gm...>]

Hi all,

I have an issue running Xmipp protocol_align_volume_and_particles.py  from
Scipion.

RuntimeError: FATAL: module compiled as little endian, but detected
different endianness at runtime

It seems there's an issue with the installation.  Any tips how to fix it?
The full error is below

Best wishes,
Juha


00054:   STARTED: alignVolumeStep, step 2, time 2020-11-23 00:26:33.446121
00055:   xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm  --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt
00056:   RuntimeError: FATAL: module compiled as little endian, but
detected different endianness at runtime
00057:
/projappl/project_2000637/apps/scipion/3.0/software/em/xmipp/bin/xmipp_volume_align:
line 3: 39299 Segmentation fault
 $XMIPP_HOME/bin/xmipp_volume_align_prog "$@"
00058:   Traceback (most recent call last):
00059:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 188, in run
00060:       self._run()
00061:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 239, in _run
00062:       resultFiles = self._runFunc()
00063:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 235, in _runFunc
00064:       return self._func(*self._args)
00065:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/xmipp3/protocols/protocol_align_volume_and_particles.py",
line 153, in alignVolumeStep
00066:       self.runJob("xmipp_volume_align", args)
00067:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py",
line 1339, in runJob
00068:       self._stepsExecutor.runJob(self._log, program, arguments,
**kwargs)
00069:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/executor.py",
line 66, in runJob
00070:       process.runJob(log, programName, params,
00071:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
line 53, in runJob
00072:       return runCommand(command, env, cwd)
00073:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/utils/process.py",
line 68, in runCommand
00074:       check_call(command, shell=True, stdout=sys.stdout,
stderr=sys.stderr,
00075:     File
"/projappl/project_2000637/apps/Anaconda-3.0/envs/.scipion3env/lib/python3.8/subprocess.py",
line 364, in check_call
00076:       raise CalledProcessError(retcode, cmd)
00077:   subprocess.CalledProcessError: Command 'xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm  --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
returned non-zero exit status 139.
00078:   Protocol failed: Command 'xmipp_volume_align --i1
Runs/005027_XmippProtAlignVolumeParticles/extra/refVolume.vol --i2
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolume.vol --apply
Runs/005027_XmippProtAlignVolumeParticles/extra/inputVolumeAligned.vol
--frm  --copyGeo
Runs/005027_XmippProtAlignVolumeParticles/extra/transformation-matrix.txt'
returned non-zero exit status 139.
00079:   FAILED: alignVolumeStep, step 2, time 2020-11-23 00:26:34.625143
00080:   ------------------- PROTOCOL FAILED (DONE 2/4)