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

[Pablo C. <pc...@cn...>]

Hi Juha, I haven't seen this before.

Hope Xmipp guys can help here.


On 22/11/20 23:34, Juha Huiskonen wrote:
> 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)
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*