[ase-users] Failing Tests Related to Scientific_netcdf
Robert Wexler
robertowexler at gmail.com
Tue Aug 23 00:07:59 CEST 2016
Dear Eric,
Thank you very much for your quick response.
So it seems that when you get SciPy for Python 2.7 from MacPorts, it
automatically installs version 1.8, which has a bug (
https://github.com/numpy/numpy/issues/3847). I was able to solve this error
by reinstalling Python 3.5, SciPy, and Numpy, and selecting python35 as my
primary executable.
I haven't solved the netCDF and ScientificPython issue yet. When/if I do, I
will report back here to this thread.
Thank you again!
Best,
Rob
On Mon, Aug 22, 2016 at 3:49 PM, Eric Hermes <ehermes at chem.wisc.edu> wrote:
> Robert,
>
>
>
> The first error is related to a bug in your installed version of Numpy,
> and the remaining are due to a bug in your installed version of
> ScientificPython (as you have identified). Specifically, according to the
> aptly-named "scientificpython_bug.py" test, ScientificPython version 2.8 or
> greater is required for NetCDF support.
>
>
>
> I am not a Mac user, so I am not intimately familiar with MacPorts, but it
> would appear that when you installed NetCDF it did not build/install the
> static library version (netcdf.a). This appears to be a requested
> enhancement in the MacPorts bug tracker: https://trac.macports.org/
> ticket/51303. I expect your best bet is to manually install NetCDF and
> switch BUILD_SHARED_LIBS on in cmake if you wish to continue using the
> ScientificLinux package. Alternatively, you can use system Python and
> manually install ASE's dependencies following the guide on the ASE wiki
> here: https://wiki.fysik.dtu.dk/ase/install.html.
>
>
>
> Eric
>
>
>
> *From:* ase-users-bounces at listserv.fysik.dtu.dk [mailto:ase-users-bounces@
> listserv.fysik.dtu.dk] *On Behalf Of *Robert Wexler via ase-users
> *Sent:* Monday, August 22, 2016 2:17 PM
> *To:* ase-users at listserv.fysik.dtu.dk
> *Subject:* [ase-users] Failing Tests Related to Scientific_netcdf
>
>
>
> 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
>
> ---------------------------------------------
>
--
Robert Wexler
rlw56 at drexel.edu
robertowexler at gmail.com
(215) 801-8741
------------------------------------------------------------
Drexel University Class of 2013
Chemistry
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