can travis check RH6 as well

[giadefa]

Some people have RH6 and sometime there are missing libs.

[noeliaferruz]

I guess this is related to the error I am seeing.

Any quick fix/workaround?

Thanks, Noelia

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.flux' detected! Please use 'msmtools.flux' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.generation' detected! Please use 'msmtools.generation' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.dtraj' detected! Please use 'msmtools.dtraj' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.estimation' detected! Please use 'msmtools.estimation' in the future.
  category=PyEMMA_DeprecationWarning)
/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/pyEMMA-2.2-py3.5-linux-x86_64.egg/pyemma/util/_ext/shimmodule.py:131: PyEMMA_DeprecationWarning: Access to a moved module 'pyemma.msm.analysis' detected! Please use 'msmtools.analysis' in the future.
  category=PyEMMA_DeprecationWarning)

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-27-9944f0a767c6> in <module>()
      1 metr2 = Metric(sims2,skip=10)
      2 metr2.projection(MetricDistance('protein and name CA', 'resname MOL and noh', metric='contacts'))
----> 3 data2 = metr2.project()

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/projections/metric.py in project(self)
     54             uqMol = Molecule(molfile)
     55             for proj in self.projectionlist:
---> 56                 proj._precalculate(uqMol)
     57                 #map.append(np.array(proj.getMapping(uqMol), dtype=object))
     58             #map = np.hstack(map)

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/projections/metricdistance.py in _precalculate(self, mol)
     54 
     55     def _precalculate(self, mol):
---> 56         self.precalcsel1 = self._processSelection(mol, self.sel1, self.groupsel1)
     57         self.precalcsel2 = self._processSelection(mol, self.sel2, self.groupsel2)
     58 

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/projections/metricdistance.py in _processSelection(self, mol, sel, groupsel)
    138         if isinstance(sel, str):  # If user passes simple string selections
    139             if groupsel is None:
--> 140                 sel = mol.atomselect(sel)
    141             elif groupsel == 'all':
    142                 sel = self._processMultiSelections(mol, [sel])

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/molecule/molecule.py in atomselect(self, sel, indexes, strict)
    430                                chain=self.chain,
    431                                segname=self.segid, insert=self.insertion, altloc=self.altloc, beta=self.beta,
--> 432                                occupancy=self.occupancy)
    433             if np.sum(s) == 0 and strict:
    434                 raise NameError('No atoms were selected with atom selection "{}".'.format(sel))

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/molecule/vmdparser.py in vmdselection(selection, coordinates, atomname, atomtype, resname, resid, chain, segname, insert, altloc, beta, occupancy, bonds)
     59             cdll.LoadLibrary(os.path.join(libdir, "psprolib.dll"))
     60 
---> 61     parser = cdll.LoadLibrary(os.path.join(libdir, "libvmdparser.so"))
     62 
     63     c_selection = create_string_buffer(selection.encode('ascii'), len(selection) + 1)

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/ctypes/__init__.py in LoadLibrary(self, name)
    423 
    424     def LoadLibrary(self, name):
--> 425         return self._dlltype(name)
    426 
    427 cdll = LibraryLoader(CDLL)

/path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/ctypes/__init__.py in __init__(self, name, mode, handle, use_errno, use_last_error)
    345 
    346         if handle is None:
--> 347             self._handle = _dlopen(self._name, mode)
    348         else:
    349             self._handle = handle

OSError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /path/to/site/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/htmd/lib/basic/Linux/libvmdparser.so)

[mj-harvey]

Can't do Travis builds for RHEL6-er aOSes annoyingly. I can put in a test case that will fail if we inadvertantly push libs that depend on GLIBC_2.14 or later.

[noeliaferruz]

Is there any possible workaround in the meanwhile or library I can load? This error affects both htmd and parameterise so we're stuck at the moment.

Thanks, Noelia

[mj-harvey]

No. I'm working on fixing it now.

On 23 May 2016 at 17:05, Noelia Ferruz notifications@github.com wrote:

Is there any possible workaround in the meanwhile or library I can load? This error affects both htmd and parameterise so we're stuck at the moment.

Thanks, Noelia

— You are receiving this because you were assigned. Reply to this email directly or view it on GitHub https://github.com/Acellera/htmd/issues/39#issuecomment-221018739

https://www.acellera.com

https://twitter.com/acellera?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor https://www.youtube.com/user/acelleracom https://www.linkedin.com/company/acellera https://www.acellera.com/md-simulation-blog-news/ [image: skype:acellera] http://is.gd/1eXkbS

[noeliaferruz]

Thanks, no problem.

[mj-harvey]

Fixed, and added a build test to ensure there's not another release iwth an accidnetal dependency on port RHEL6 glibc