FileNotFoundError: Could not find libs.

[noeliaferruz]

Hi guys,

I'm in version 1.0.26. I run: model.viewStates(ligand="resname MOL and noh"). And got the following error: What am I missing?

/nfs/grid/software/hpcc/apps/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)
/nfs/grid/software/hpcc/apps/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)
/nfs/grid/software/hpcc/apps/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)
/nfs/grid/software/hpcc/apps/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)
/nfs/grid/software/hpcc/apps/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)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-5-119f81c50177> in <module>()
      2 #model.load('model-oldsimdata_25+.dat')
      3 os.chdir('/hpc/grid/wip_cmg_wwmc/workspace/groups/neuro_cc/acellera/tmp/proteins/D3R/batches')
----> 4 model.viewStates(ligand="resname MOL and noh")

/path/to/htmd/model.py in viewStates(self, states, statetype, protein, ligand, viewer, mols, numsamples, wrapsel, alignsel)
    395             states = [states]
    396         if mols is None:
--> 397             mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel)
    398         colors = [0, 1, 3, 4, 5, 6, 7, 9]
    399         for i, s in enumerate(states):

/path/to/htmd/model.py in getStates(self, states, statetype, wrapsel, alignsel, alignmol, samplemode, numsamples)
    346         # Removed ncpus because it was giving errors on some systems.
    347         mols = Parallel(n_jobs=1, verbose=11)(delayed(_loadMols)(self, i, rel, molfile, wrapsel, alignsel, refmol)
--> 348                                                   for i, rel in enumerate(relframes))
    349         return np.array(mols, dtype=object)
    350 

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self, iterable)
    798             # was dispatched. In particular this covers the edge
    799             # case of Parallel used with an exhausted iterator.
--> 800             while self.dispatch_one_batch(iterator):
    801                 self._iterating = True
    802             else:

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in dispatch_one_batch(self, iterator)
    656                 return False
    657             else:
--> 658                 self._dispatch(tasks)
    659                 return True
    660 

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in _dispatch(self, batch)
    564 
    565         if self._pool is None:
--> 566             job = ImmediateComputeBatch(batch)
    567             self._jobs.append(job)
    568             self.n_dispatched_batches += 1

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __init__(self, batch)
    178         # Don't delay the application, to avoid keeping the input
    179         # arguments in memory
--> 180         self.results = batch()
    181 
    182     def get(self):

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in __call__(self)
     70 
     71     def __call__(self):
---> 72         return [func(*args, **kwargs) for func, args, kwargs in self.items]
     73 
     74     def __len__(self):

/nfs/grid/software/hpcc/apps/Linux-x86_64-RHEL6/acellera/current/python/lib/python3.5/site-packages/joblib/parallel.py in <listcomp>(.0)
     70 
     71     def __call__(self):
---> 72         return [func(*args, **kwargs) for func, args, kwargs in self.items]
     73 
     74     def __len__(self):

/path/to/htmd/model.py in _loadMols(self, i, rel, molfile, wrapsel, alignsel, refmol)
    522         trajs = np.append(trajs, f.sim.trajectory[f.piece])
    523         frs = np.append(frs, f.frame)
--> 524     mol.read(trajs, frames=frs)
    525     if len(wrapsel) > 0:
    526         mol.wrap(wrapsel)

/path/to/htmd/molecule/molecule.py in read(self, filename, type, skip, frames, append)
    670             self._readPDB(filename, mode='pdbqt')
    671         elif (type is None and firstfile.endswith(".xtc")) or type == "xtc":
--> 672             self._readTraj(filename, skip=skip, frames=frames, append=append)
    673         elif (type is None and firstfile.endswith(".coor")) or type == "coor":
    674             self._readBinCoordinates(filename)

/path/to/htmd/molecule/molecule.py in _readTraj(self, filename, skip, frames, append, mdtraj)
    914                     traj.coords = traj.coords[:, :, frames[i]]
    915                 else:
--> 916                     traj = XTCread(f, frames[i])
    917                 self.fileloc.append([f, int(frames[i])])
    918 

/path/to/htmd/molecule/xtc.py in XTCread(filename, frames)
     52 
     53 def XTCread(filename, frames=None):
---> 54     lib = xtc_lib()
     55     nframes = pack_ulong_buffer([0])
     56     natoms = pack_int_buffer([0])

/path/to/htmd/molecule/xtc.py in xtc_lib()
     35 def xtc_lib():
     36     lib = {}
---> 37     libdir = htmd.home(libDir=True)
     38 
     39     import platform

/path/to/htmd/home.py in home(dataDir, libDir)
     45             return os.path.join(libdir, "pro", platform.system())
     46         else:
---> 47             raise FileNotFoundError('Could not find libs.')
     48     else:
     49         return homeDir

FileNotFoundError: Could not find libs.

[stefdoerr]

@mj-harvey @j3mdamas libs have disappeared again. Something in the conda release?

[mj-harvey]

I don't understand how that could have been released. The tests should have failed. 'll look into it

On 31 May 2016 at 17:03, Stefan notifications@github.com wrote:

@mj-harvey https://github.com/mj-harvey @j3mdamas https://github.com/j3mdamas libs have disappeared again. Something in the conda release?

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[giadefa]

.travis_conda_upload.sh is different between multiscalelan and acellera

On 31 May 2016 at 18:53, M J Harvey notifications@github.com wrote:

I don't understand how that could have been released. The tests should have failed. 'll look into it

On 31 May 2016 at 17:03, Stefan notifications@github.com wrote:

@mj-harvey https://github.com/mj-harvey @j3mdamas https://github.com/j3mdamas libs have disappeared again. Something in the conda release?

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[mj-harvey]

giadefa ellera/htmd is a long way behind multiscalelab/htmd at this point.

On 31 May 2016 at 17:59, giadefa notifications@github.com wrote:

.travis_conda_upload.sh is different between multiscalelan and acellera

On 31 May 2016 at 18:53, M J Harvey notifications@github.com wrote:

I don't understand how that could have been released. The tests should have failed. 'll look into it

On 31 May 2016 at 17:03, Stefan notifications@github.com wrote:

@mj-harvey https://github.com/mj-harvey @j3mdamas https://github.com/j3mdamas libs have disappeared again. Something in the conda release?

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[giadefa]

not really. We only tag via acellera now.

On 31 May 2016 at 19:02, M J Harvey notifications@github.com wrote:

giadefa ellera/htmd is a long way behind multiscalelab/htmd at this point.

On 31 May 2016 at 17:59, giadefa notifications@github.com wrote:

.travis_conda_upload.sh is different between multiscalelan and acellera

On 31 May 2016 at 18:53, M J Harvey notifications@github.com wrote:

I don't understand how that could have been released. The tests should have failed. 'll look into it

On 31 May 2016 at 17:03, Stefan notifications@github.com wrote:

@mj-harvey https://github.com/mj-harvey @j3mdamas https://github.com/j3mdamas libs have disappeared again. Something in the conda release?

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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

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[mj-harvey]

The libraries are all ther and working in 1.0.26. The release couldn't have happened otherwise. Noelia, what's the output of

from htmd import * print( htmd.home() )

Is it what you expect?

if you then do a find under that directory for "libxtc.so" is it found?

what's the output of "file /path/to/libxtc.so" ?

On 31 May 2016 at 18:06, giadefa notifications@github.com wrote:

not really. We only tag via acellera now.

On 31 May 2016 at 19:02, M J Harvey notifications@github.com wrote:

giadefa ellera/htmd is a long way behind multiscalelab/htmd at this point.

On 31 May 2016 at 17:59, giadefa notifications@github.com wrote:

.travis_conda_upload.sh is different between multiscalelan and acellera

On 31 May 2016 at 18:53, M J Harvey notifications@github.com wrote:

I don't understand how that could have been released. The tests should have failed. 'll look into it

On 31 May 2016 at 17:03, Stefan notifications@github.com wrote:

@mj-harvey https://github.com/mj-harvey @j3mdamas https://github.com/j3mdamas libs have disappeared again. Something in the conda release?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/Acellera/htmd/issues/42#issuecomment-222736338 , or mute the thread <

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[noeliaferruz]

The output is:

from htmd import *
print(htmd.home())

Please cite. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery, J. Chem. Theory Comput., 2016, 12 (4), pp 1845-1852. http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049

You are on the latest HTMD version (1.0.26).
/path/to/acellera/current/python/lib/python3.5/site-packages/htmd

It is not what I was expecting, but that's another issue I have to look at. Since Friday we now have two modules, acellera/test, and acellera/current. And we have permissions to update them. But it seems they're still interconverted, whenever I update test, current is also updated, and jupyter seems to open htmd from current...I'll ask here.

However I don't have reading permissions in that folder to do the file command, let me ask:

ferrun@cclnx928-> find /path/to/acellera/current/python/lib/python3.5/site-packages/htmd -name "libxtc.so"
find: `/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/builder/charmmfiles': Permission denied
find: `/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/clustering': Permission denied
find: `/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/lib': Permission denied
find: `/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/parameterize': Permission denied

[mj-harvey]

Ok -- it's the lack of file permissions that is causing the problem.

On 31 May 2016 at 18:53, Noelia Ferruz notifications@github.com wrote:

The output is:

from htmd import * print(htmd.home())

Please cite. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery, J. Chem. Theory Comput., 2016, 12 (4), pp 1845-1852. http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049

You are on the latest HTMD version (1.0.26). /path/to/acellera/current/python/lib/python3.5/site-packages/htmd

It is not what I was expecting, but that's another issue I have to look at. Since Friday we now have two modules, acellera/test, and acellera/current. And we have permissions to update them. But it seems they're still interconverted, whenever I update test, current is also updated, and jupyter seems to open htmd from current...I'll ask here.

However I don't have reading permissions in that folder to do the file command, let me ask:

ferrun@cclnx928-> find /path/to/acellera/current/python/lib/python3.5/site-packages/htmd -name "libxtc.so" find: /path/to/acellera/current/python/lib/python3.5/site-packages/htmd/builder/charmmfiles': Permission denied find:/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/clustering': Permission denied find: /path/to/acellera/current/python/lib/python3.5/site-packages/htmd/lib': Permission denied find:/path/to/acellera/current/python/lib/python3.5/site-packages/htmd/parameterize': Permission denied

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[noeliaferruz]

Ok, thanks a lot One question, is this lack of permission something to fix from my end or your end?

[noeliaferruz]

It was finally fixed from here, not sure what happened with the two new modules, apologies for the incoveniences.