[ase-users] cannot import name minpack2

Marcin Dulak Marcin.Dulak at fysik.dtu.dk
Wed Apr 17 15:33:30 CEST 2013 

Dear Bernd,

On 04/17/2013 10:49 AM, Bernd Hartke wrote:
> Dear ASE users,
> on an openSuSE-12.1 64bitlinux system, I have just installed 
> ASE3.6.0.2515-74.1 from the distro via zypper (as recommended on 
> https://wiki.fysik.dtu.dk/ase/download.html), after installing what 
> was missing from the prerequisites (as listed on the same page). I did 
> have some trouble in testing SciPy, but hoped that that may have 
> beencaused by my inability to installnose1.3.0 properly (for 
> testing)and that this did not affect SciPy itselfand that all this 
> maybe irrelevant anyway since ASE lists SciPy as recommended but not 
> necessary prerequisite.
>
> All ASE tests run fine except hcp.py, which complains about
>    ImportError: cannot import name minpack2
> I am appending the testase.log filebelow.
>
> Is this failure a direct outcome of an incorrectly/incompletely 
> installed SciPy, or is it something else?

Check your scipy installation with:
python -c "from scipy.optimize import minpack2"

I  would just install a python-scipy version from one of the*build*.*opensuse*.org repositories:

yast --remove python-numpy

zypper ar -f http://download.opensuse.org/repositories/devel:/languages:/python/openSUSE_12.1/devel:languages:python.repo

yast -i python-scipy python-matplotlib python-gtk

One needs to get the compatible API versions between scipy and numpy, and because the scipy from the above repo
is very fresh it conflicts with the default opensuse numpy 1.6.1.
I would also exclude python-numpy and python-scipy from updates after installation, by adding the following to /etc/zypp/locks (see http://en.opensuse.org/Libzypp/Locksfile):

solvable_name: python-numpy
match_type: exact
solvable_name: python-scipy
match_type: exact

If you don't want to pollute the system by installing external packages globally you can download the RPMS by hand,
unpack them somewhere under ${HOME} with:
rpm2cpio *.rpm | cpio -idm
and set the required PYTHONPATH.

Best regards,

Marcin

>
> Note that I have no prior experience with python whatsoever, to the 
> point of not knowing how to set PYTHONPATH properly. Confusingly, I 
> note that on my system there are two different python versions (2.7 
> and 3.2, the default one being 2.7), which may or may not have 
> anything to do withthe above failure.
>
> Any hints are very welcome!
>
> Bernd
>
> ------------------------snip----------------------------------
> python 2.7.2 GCC 64bit ELF on Linux x86_64 SuSE 12.1 x86_64
> Ag-Cu100.py (ScriptTestCase) ... ok
> CO2_Au111.py (ScriptTestCase) ... ok
> COCu111_2.py (ScriptTestCase) ... ok
> ag.py (ScriptTestCase) ... ok
> atom.py (ScriptTestCase) ... ok
> bader.py (ScriptTestCase) ... ok
> basin.py (ScriptTestCase) ... ok
> build.py (ScriptTestCase) ... ok
> center.py (ScriptTestCase) ... ok
> cmdline.py (ScriptTestCase) ... ok
> com.py (ScriptTestCase) ... ok
> coverage.py (ScriptTestCase) ... ok
> crystal.py (ScriptTestCase) ... ok
> dihedralconstraint.py (ScriptTestCase) ... ok
> dimer.py (ScriptTestCase) ... ok
> dimer_method.py (ScriptTestCase) ... ok
> distmom.py (ScriptTestCase) ... ok
> emt.py (ScriptTestCase) ... ok
> emt1.py (ScriptTestCase) ... ok
> emt2.py (ScriptTestCase) ... ok
> example.py (ScriptTestCase) ... ok
> geometry.py (ScriptTestCase) ... ok
> h2.py (ScriptTestCase) ... ok
> hcp.py (ScriptTestCase) ... ERROR
> maxwellboltzmann.py (ScriptTestCase) ... ok
> md.py (ScriptTestCase) ... ok
> n2.py (ScriptTestCase) ... ok
> neb.py (ScriptTestCase) ... ok
> neighbor.py (ScriptTestCase) ... ok
> noncollinear.py (ScriptTestCase) ... ok
> properties.py (ScriptTestCase) ... ok
> pull.py (ScriptTestCase) ... ok
> repeat_FixAtoms.py (ScriptTestCase) ... ok
> replay.py (ScriptTestCase) ... ok
> rotate.py (ScriptTestCase) ... ok
> rotate_euler.py (ScriptTestCase) ... ok
> scaled_positions.py (ScriptTestCase) ... ok
> stm.py (ScriptTestCase) ... ok
> strain.py (ScriptTestCase) ... ok
> strain_emt.py (ScriptTestCase) ... ok
> things.py (ScriptTestCase) ... ok
> unitcellfilter.py (ScriptTestCase) ... ok
> vacancy.py (ScriptTestCase) ... ok
> verlet.py (ScriptTestCase) ... ok
> vib.py (ScriptTestCase) ... ok
> vtk_data.py (ScriptTestCase) ... ok
> vtk_pipeline.py (ScriptTestCase) ... ok
> abinit_cmdline.py (ScriptTestCase) ... ok
> castep_interface.py (ScriptTestCase) ... which: no castep in 
> (/home/hartke/vmd/bin:/home/hartke/tinker_v5.1.09/source:/home/hartke/ADF/source/adfhome/bin:/home/hartke/mpich2_install/bin:/opt/intel/composer_xe_2011_sp1.12.361/bin/intel64:/home/hartke/turbomole/TURBOMOLE/scripts:/home/hartke/turbomole/TURBOMOLE/bin/x86_64-unknown-linux-gnu:/home/hartke/orca/orca/x86_exe:/home/hartke/mopac2009:/home/hartke/g09/gv:/home/hartke/jdk1.7.0_15/bin:/opt/pgi/linux86-64/11.9/bin:/home/hartke/vmd/bin:/home/hartke/tinker_v5.1.09/source:/home/hartke/ADF/source/adfhome/bin:/home/hartke/mpich2_install/bin:/opt/intel/composer_xe_2011_sp1.12.361/bin/intel64:/home/hartke/turbomole/TURBOMOLE/scripts:/home/hartke/turbomole/TURBOMOLE/bin/x86_64-unknown-linux-gnu:/home/hartke/orca/orca/x86_exe:/home/hartke/mopac2009:/home/hartke/g09/gv:/home/hartke/jdk1.7.0_15/bin:/opt/pgi/linux86-64/11.9/bin:/usr/lib64/mpi/gcc/openmpi/bin:/home/hartke/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/X11R6/bin:/usr/bin/X11:/opt/kde3/bin:/home/hartke/g09/g09/bsd:/home/hartke/ 
> g09/g09/lo 
> cal:/home/hartke/g09/g09/extras:/home/hartke/g09/g09:/home/hartke/molpro/Molpro/bin:/home/hartke/xmakemol-5.16:/usr/local/dislin/bin:/opt/intel/composer_xe_2011_sp1.12.361/mpirt/bin/intel64:/home/hartke/g09/g09/bsd:/home/hartke/g09/g09/local:/home/hartke/g09/g09/extras:/home/hartke/g09/g09:/home/hartke/molpro/Molpro/bin:/home/hartke/xmakemol-5.16:/usr/local/dislin/bin:/opt/intel/composer_xe_2011_sp1.12.361/mpirt/bin/intel64)
> ok
> ase_rw.py (ScriptTestCase) ... ok
> cmr_rw.py (ScriptTestCase) ... ok
> reactions.py (ScriptTestCase) ... ok
> reactions_run.py (ScriptTestCase) ... ok
> reactions_test.py (ScriptTestCase) ... ok
> reactions_xsimple.py (ScriptTestCase) ... ok
> rw.py (ScriptTestCase) ... ok
> elk_cmdline.py (ScriptTestCase) ... ok
> abinit.py (ScriptTestCase) ... ok
> info.py (ScriptTestCase) ... ok
> magmom.py (ScriptTestCase) ... ok
> netcdf.py (ScriptTestCase) ... ok
> oi.py (ScriptTestCase) ... ok
> oldtraj.py (ScriptTestCase) ... ok
> trajectory.py (ScriptTestCase) ... ok
> v_sim.py (ScriptTestCase) ... ok
> fleur_cmdline.py (ScriptTestCase) ... ok
> jacapo.py (ScriptTestCase) ... ok
> nwchem_cmdline.py (ScriptTestCase) ... ok
> vasp_Al_volrelax.py (ScriptTestCase) ... ok
> vasp_co.py (ScriptTestCase) ... ok
> COCu111.py (ScriptTestCase) ... ok
>
> ======================================================================
> ERROR: hcp.py (ScriptTestCase)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/site-packages/ase/test/__init__.py", line 
> 54, in testfile
> execfile(self.filename, {'display': self.display})
>   File "/usr/lib/python2.7/site-packages/ase/test/hcp.py", line 30, in 
> <module>
>     from scipy.optimize import fmin_bfgs
>   File 
> "/usr/local/lib64/python2.7/site-packages/scipy/optimize/__init__.py", 
> line 146, in <module>
>   File 
> "/usr/local/lib64/python2.7/site-packages/scipy/optimize/optimize.py", 
> line 34, in <module>
>   File 
> "/usr/local/lib64/python2.7/site-packages/scipy/optimize/linesearch.py", 
> line 16, in <module>
> ImportError: cannot import name minpack2
>
> ----------------------------------------------------------------------
> Ran 71 tests in 55.184s
>
> FAILED (errors=1)
>
> ------------------------snap---------------------------------
> -- 
> Prof. Dr. Bernd Hartke             e-mail:hartke at pctc.uni-kiel.de
> Theoretical Chemistry              phone : +49-431-880-2753
> Institute for Physical Chemistry   fax   : +49-431-880-1758
> University of Kielhttp://ravel.pctc.uni-kiel.de/
> Olshausenstrasse 40
> 24098 Kiel
> GERMANY
> ---------------------------------------------------
> NOTE: e-mail address/domain change: phc --> pctc !
> ---------------------------------------------------
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users


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