[ase-users] Failing Tests Related to Scientific_netcdf

[Robert Wexler]

Dear ASE Users,

I tested my installation and received 4 errors.

My machine specific information is as follows:

platform        Darwin-15.5.0-x86_64-i386-64bit
python-2.7.10   /usr/bin/python
ase-3.11.0      /Users/<username>/ase/ase/
numpy-1.8.0rc1
 /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/
scipy-0.13.0b1
 /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy/
test-dir
 /var/folders/vb/858_vzmn18gc7hd524j0gmf80000gn/T/ase-test-fEK8kI

The 4 errors I received were:

======================================================================
ERROR: niggli.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/<username>/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/Users/<username>/ase/ase/test/niggli.py", line 123, in <module>
    niggli_reduce(conf)
  File "/Users/<username>/ase/ase/build/tools.py", line 631, in
niggli_reduce
    scpos = np.dot(atoms.get_scaled_positions(), np.linalg.inv(C).T)
  File "/Users/<username>/ase/ase/atoms.py", line 1459, in
get_scaled_positions
    fractional = np.linalg.solve(self.cell.T, self.positions.T).T
  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/linalg/linalg.py",
line 380, in solve
    r = gufunc(a, b, signature=signature, extobj=extobj)
ValueError: cannot remove a zero-sized axis from an iterator

======================================================================
ERROR: scientificpython_bug.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/<username>/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/Users/<username>/ase/ase/test/scientificpython_bug.py", line 10,
in <module>
    import Scientific.IO.NetCDF as netcdf
  File "/Library/Python/2.7/site-packages/Scientific/IO/NetCDF.py", line
165, in <module>
    from Scientific_netcdf import *
ImportError: No module named Scientific_netcdf

======================================================================
ERROR: fio/oi.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/<username>/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/Users/<username>/ase/ase/test/fio/oi.py", line 90, in <module>
    write(fname1, atoms, format=format)
  File "/Users/<username>/ase/ase/io/formats.py", line 259, in write
    io.write(filename, images, **kwargs)
  File "/Users/<username>/ase/ase/io/etsf.py", line 12, in write_etsf
    ETSFWriter(filename).write_atoms(atoms)
  File "/Users/<username>/ase/ase/io/etsf.py", line 35, in __init__
    from Scientific.IO.NetCDF import NetCDFFile
  File "/Library/Python/2.7/site-packages/Scientific/IO/NetCDF.py", line
165, in <module>
    from Scientific_netcdf import *
ImportError: No module named Scientific_netcdf

======================================================================
ERROR: jacapo/jacapo.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/<username>/ase/ase/test/__init__.py", line 53, in testfile
    {'display': self.display})
  File "/Users/<username>/ase/ase/test/jacapo/jacapo.py", line 5, in
<module>
    from ase.calculators.jacapo import Jacapo
  File "/Users/<username>/ase/ase/calculators/jacapo/__init__.py", line 3,
in <module>
    from ase.calculators.jacapo.jacapo import *
  File "/Users/<username>/ase/ase/calculators/jacapo/jacapo.py", line 21,
in <module>
    from Scientific.IO.NetCDF import NetCDFFile as netCDF
  File "/Library/Python/2.7/site-packages/Scientific/IO/NetCDF.py", line
165, in <module>
    from Scientific_netcdf import *
ImportError: No module named Scientific_netcdf

I'm not sure what is causing the first error but the second error, i.e.
"ImportError: No module named Scientific_netcdf", seems to be related to my
installation of netCDF and ScientificPython2.8. I used MacPorts to install
netcdf 4.4.1 and received the following output:

<computername>:~ <username>$ sudo port install netcdf
Password:
--->  Computing dependencies for netcdf
--->  Cleaning netcdf
--->  Scanning binaries for linking errors
--->  No broken files found.

Then I tried, however unsuccessfully, to install ScientificPython2.8 and
received the following output:

<computername>:ScientificPython-2.8.1 <username>$ python setup.py build
netCDF not found, the netCDF module will not be built!
If netCDF is installed somewhere on this computer,
please set NETCDF_PREFIX to the path where
include/netcdf.h and lib/netcdf.a are located
and re-run the build procedure.
running build
running build_py
running build_ext
running build_scripts

I located netcdf.h in /opt/local/include/ but was unable to find netcdf.a.
I then modified the variable NETCDF_PREFIX in setup.py with /opt/local but
received the same output upon trying to build.

As a side comment, my main motivation for using ASE is to be able to
perform LAMMPS total energy calculations as part of a Python script. So
perhaps, these errors are insignificant and I can move on without worry. I
would, however, like to get all functionalities of ASE running on my
computer so that I can explore them later.

Does anybody have experience with the problem I am facing and can suggest
ways to correct the errors that show up during testing?

Thank you all so much for you help. I am looking forward to your responses.

Best,
Robert Wexler

---------------------------------------------
Robert B. Wexler
PhD Candidate in Chemistry
University of Pennsylvania, 2018
rwexler at sas.upenn.edu
(215) 801-8741
---------------------------------------------
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