[ase-users] Installation of ASE-DACAPO On Ubuntu 12.10
Sungsik Kim
sungsik312 at gmail.com
Sun Feb 10 20:48:56 CET 2013
Hello,
I checked "sudo apt-get install python-ase", I think it does not work on
Ubuntu 11.04.
I did
export ASE_TAGS=https://svn.fysik.dtu.dk/projects/ase/tags/
sudo bash -c 'echo "deb
http://widehat.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04 /"
> /etc/apt/sources.list.d/home_dtufys.sources.list'
wget http://widehat.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04/Release.key
&& sudo apt-key add Release.key && rm Release.key
sudo apt-get update
sudo apt-get install python-ase
I did testase again by using
$ bash$ mkdir /tmp/testase.$$; cd /tmp/testase.*$ testase.py 2>&1 |
tee testase.log
Here is the results I got.
no segmentation fault shows anymore. but still having jacapo.py error.
#############################################################################
python 2.7.1+ GCC 4.5.2 64bit ELF on Linux x86_64 Ubuntu 11.04 natty
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) ... ok
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) ... 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) ... /usr/local/bin/dacapo.run
ERROR
nwchem_cmdline.py (ScriptTestCase) ... ok
vasp_Al_volrelax.py (ScriptTestCase) ... ok
vasp_co.py (ScriptTestCase) ... ok
COCu111.py (ScriptTestCase) ... ok
======================================================================
ERROR: jacapo.py (ScriptTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/ase/test/__init__.py", line
54, in testfile
execfile(self.filename, {'display': self.display})
File "/usr/local/lib/python2.7/dist-packages/ase/test/jacapo/jacapo.py",
line 35, in <module>
ft=0.01)
File
"/usr/local/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py",
line 252, in __init__
self.set_nc(nc)
File
"/usr/local/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py",
line 1214, in set_nc
self._set_frame_number()
File
"/usr/local/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py",
line 669, in _set_frame_number
nc = netCDF(self.nc, 'r')
File "/usr/lib/python2.7/dist-packages/Scientific/IO/NetCDF.py", line
177, in NetCDFFile
return apply(_NetCDFFile, args)
IOError: netcdf: NetCDF: Unknown file format
----------------------------------------------------------------------
Ran 71 tests in 47.630s
FAILED (errors=1)
################################################################################
And about Second example - 1.8. Molecular Reaction Barrier
I got different error now. However, it was much better than before.
Here is error I got with some results.
###############################################################################
BFGSLineSearch: 0 14:39:25 -1028.884861 11.6889
BFGSLineSearch: 1 14:43:53 -1029.733777 0.1110
BFGSLineSearch: 2 14:45:05 -1029.733889 0.0227
-1029.73388857
Traceback (most recent call last):
File "skim2.py", line 33, in <module>
mask = FixAtoms([True,True,False])
File "/home/sungsik/ase/ase/constraints.py", line 103, in __init__
'FixAtoms: The indices array contained duplicates. '
ValueError: FixAtoms: The indices array contained duplicates. Perhaps you
wanted to specify a mask instead, but forgot the mask= keyword.
###############################################################################
Thank you
Sincerely
Sungsik
2013/2/10 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
> Hi,
>
> i saw "sudo apt-get install python-ase" in your instructions so assumed
> you configured the dtufys repository:
> https://wiki.fysik.dtu.dk/ase/**download.html#installation-**
> with-package-manager-on-linux<https://wiki.fysik.dtu.dk/ase/download.html#installation-with-package-manager-on-linux>
> Is there any output dacapo produces before the segmentation fault occurs?
> Can you verify if the segmentation fault happens also for the dacapo
> version from the dtufys repository?
> It is not a good idea to run python testase.py from ase/tools directory as
> there are many files produced by the tests.
>
> Best regards,
>
> Marcin
>
> On 02/10/13 19:38, Sungsik Kim wrote:
>
>> sudo apt-get install python-ase
>>
>
>
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