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[Klaus Thoeni <question187904@xxxxxxxxxxxxxxxxxxxxx>]

New question #187904 on Yade:
https://answers.launchpad.net/yade/+question/187904

Hi Guys,

I currently got access to a Red Hat cluster (Red Hat Enterprise Linux Server release 6.2 (Santiago)). I asked the admin to install all the libraries listed on our webpage under

https://yade-dem.org/doc/installation.html#prerequisities

I compiled the code and after fixing some includes everything looked good. However, I can't load or save simulations. Here the error yade gives me:

Yade [1]: O.load('01_netonly.xml.bz2')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/kt748/YADE-bzr/install/lib/yade-bzr2999/py/yade/__init__.pyc in <module>()
----> 1 
      2 
      3 
      4 
      5 

RuntimeError: stream error


When running yade --test I got the following output:

geotech-r710-3-TMP: yade --test
Math: Matrix3 operations ... ok
Math: Quaternion operations ... ok
Math: Vector2 operations ... ok
Math: Vector3 operations ... ok
Core: correct types are instantiated ... ok
Core: dispatcher ctors with functors ... ok
Core: Attr::hidden ... ok
Core: InteractionLoop special ctor ... ok
Core: invalid attribute access raises AttributeError ... ok
Core: Attr::noSave ... ERROR
Core: ParallelEngine special ctor ... ok
Core: class ctor's attributes ... ok
Core: Attr::triggerPostLoad ... ok
Core: dispatcher and functor type mismatch is detected ... ok
Bodies: erased bodies are None in python ... ok
Bodies: Iterator silently skips erased ones ... ok
Bodies: Iteration ... ok
Bodies: len(O.bodies) ... ok
Bodies: Negative index counts backwards (like python sequences). ... ok
I/O: All classes can be saved and loaded with boost::serialization ... WARNING: cannot open files used for capillary law, all forces will be null. Instructions on how to download and install them is found here : https://yade-dem.org/wiki/CapillaryTriaxialTest.
FAIL
Loop: dead engines are not run ... ok
Loop: O.engines can be modified inside the loop transparently. ... ok
Loop: substepping ... ok
Material+State: CpmMat returns CpmState when asked for newAssocState ... ok
Material+State: throws when body has material and state that don't work together. ... ok
Material+State: throws when body has material but NULL state. ... ok
Material: find by index or label; KeyError raised for invalid label. ... ok
Material: iteration over O.materials ... ok
Material: len(O.materials) ... ok
Material: negative index counts backwards. ... ok
Material: shared_ptr's makes change in material immediate everywhere ... ok
Material: shared_ptr's are preserved when saving/loading ... ERROR
PBC: degenerate cell raises exception ... ok
PBC: homothetic cell deformation adjusts particle velocity ... ok
PBC: utils.kineticEnergy considers only fluctuation velocity, not the velocity gradient ... ok
PBC: L3Geom computes incident velocity correctly ... ok
PBC: ScGeom computes incident velocity correctly ... ok
PBC: setBox modifies hSize correctly ... ok
PBC: chaing trsf changes hSize0, but does not modify hSize ... ok
PBC: velGrad changes hSize but not hSize0, accumulates in trsf ... ok
Clump: ids and flags consistency ... ok
Clump: mass, centroid, intertia ... ok
Clump: velocities of member assigned by NewtonIntegrator ... ok
CohesiveChain: velocity/positions tested in transient dynamics and equilibrium state ... ok
Doctest: yade.eudoxos.IntrSmooth3d ... ok
Doctest: yade.pack.SpherePack_toSimulation ... ok
Doctest: yade.plot.addAutoData ... ok
Doctest: yade.plot.addData ... ok
Doctest: yade.plot.plot ... ok
Doctest: yade.plot.saveDataTxt ... ok
Doctest: yade.utils.SpherePWaveTimeStep ... ok
Doctest: yade.utils.saveVars ... /home/kt748/YADE-bzr/install/lib/yade-bzr2999/py/yade/utils.py:55: UserWarning: Overwriting yade.params.something which already exists.
  if mark in yade.params.__dict__: warnings.warn('Overwriting yade.params.%s which already exists.'%mark)
ok
Doctest: yade.utils.sphere ... ok
Doctest: yade.utils.typedEngine ... ok

======================================================================
ERROR: Core: Attr::noSave
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kt748/YADE-bzr/install/lib/yade-bzr2999/py/yade/tests/wrapper.py", line 86, in testNoSave
    O.saveTmp(quiet=True)
RuntimeError: unregistered class

======================================================================
ERROR: Material: shared_ptr's are preserved when saving/loading
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kt748/YADE-bzr/install/lib/yade-bzr2999/py/yade/tests/core.py", line 150, in testSharedAfterReload
    O.saveTmp(quiet=True); O.loadTmp(quiet=True)
RuntimeError: unregistered class

======================================================================
FAIL: I/O: All classes can be saved and loaded with boost::serialization
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kt748/YADE-bzr/install/lib/yade-bzr2999/py/yade/tests/core.py", line 79, in testSaveAllClasses
    self.assert_(len(failed)==0,'Failed classes were: '+' '.join(failed))
AssertionError: Failed classes were: BoundaryController Collider Dem3DofGeom ElastMat FrictMat FrictPhys GenericSpheresContact IntrCallback MindlinPhys PeriodicEngine Recorder ScGeom Sphere TriaxialStressController

----------------------------------------------------------------------
Ran 54 tests in 65.778s

FAILED (failures=1, errors=2)
******************** SOME TESTS FAILED ********************
Yade: error exit.

Anyone knows what the problem could be? Maybe boost? On my local machines I am using boost version 1.42 and 1.46 whereas the Red Hat cluster uses 1.41. Well, the documentation tells us 1.35 or later. I have no idea. I would really appreciate if someone can tell me what's going wrong.

Thanks,
Klaus


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