[ase-users] Installation of ASE-DACAPO On Ubuntu 12.10
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Mon Feb 11 10:00:38 CET 2013
Hi,
On 02/11/13 02:17, Sungsik Kim wrote:
> Hello,
>
> I reinstalled Ubuntu 11.04 and installed everything again. Now it
> looks like working.
>
> #########################################################################################
> sudo apt-get install liblapack-dev
> sudo apt-get install libnetcdf-dev
> sudo apt-get install netcdf-bin
> sudo apt-get install fftw-dev
> sudo apt-get install subversion
> sudo apt-get install gfortran
> sudo apt-get install python-scientific
> sudo apt-get install grace
> sudo apt-get install rasmol
> sudo apt-get install gnuplot
> sudo apt-get install python-pexpect
> sudo apt-get install python-vtk
> sudo apt-get install python-matplotlib
> sudo apt-get install python-gnuplot
> svn checkout https://svn.fysik.dtu.dk/projects/ase/trunk ase
> export ASE_TAGS=https://svn.fysik.dtu.dk/projects/ase/tags/
> sudo bash -c 'echo "deb
> http://download.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04
> /" > /etc/apt/sources.list.d/home_dtufys.sources.list'
> wget
> http://download.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04/Release.key
> && sudo apt-key add Release.key && rm Release.key
please do:
sudo apt-get remove python-ase dacapo
Then remove /etc/apt/sources.list.d/home_dtufys.sources.list
and configure the 11.04 repository.
Here is what should work on Ubuntu:
https://listserv.fysik.dtu.dk/pipermail/ase-users/2012-September/001537.html
> sudo apt-get update
> sudo apt-get install python-ase
> svn co https://svn.fysik.dtu.dk/projects/dacapo/trunk dacapo
> sudo apt-get install dacapo
if you install dacapo from the repository there is no need to build it
from sources
> export NETCDF="/usr/lib"
> export DACAPOPATH="$HOME/psp"
> export BLASLAPACK="-L/usr/lib -lnetcdff -lnetcdf -L/usr/lib -lblas
> -llapack -L/usr/lib -lblas -llapack -lgfortran"
> export FFTW="/usr/lib"
> cd ~/dacapo/src
> make gfortran_fnosecond_underscore
> cd
> mkdir psp
> cp -pr dacapo/psp/*/*/*.pseudo psp
> export VTK_TK_WIDGET_PATH=/usr/lib
> export PYTHONPATH=${HOME}/dacapo/Python:${HOME}/ase
> export
> PATH=${HOME}/bin:${HOME}/ase/ase/tools:${HOME}/dacapo/Python/Dacapo/Tools:${PATH}
> export
> DACAPOEXE_SERIAL=${HOME}/dacapo/src/gfortran_fnosecond_underscore_serial/dacapo.run
> ############################################################################################
>
> I think that now I installed dacapo correctly. When doing testase by
> the command on the web, there is no error in jacapo.py anymore.
>
> About the first part of the second example, I got the same error like
> below, 1.8. molecular reaction barriers
> ############################################################################################################
> BFGSLineSearch: 0 18:53:50 -1028.884861 11.6889
> BFGSLineSearch: 1 18:58:19 -1029.733777 0.1135
> BFGSLineSearch: 2 18:59:32 -1029.733890 0.0207
> -1029.73388965
> 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.
> ##################################################################################################################
> I think this is due to mask=FixAtoms([True,True,False]) command line
> on script. So I deleted two lines containing "mask", and am running it
> and waiting for results.
this is a mistake in the tutorial - it should be:
mask = FixAtoms(mask=[True,True,False])
Best regards,
Marcin
> I expect that there will be no error in this run.
> I really appreciate you.
> It was really helpful to me.
> Thanks
>
> Sincerely
>
> Sungsik
>
>
> 2013/2/10 Sungsik Kim <sungsik312 at gmail.com <mailto:sungsik312 at gmail.com>>
>
> Hello,
>
> I checked "sudo apt-get install python-ase", I think it does not
> work on Ubuntu 11.04.
> I did
>
> exportASE_TAGS=https://svn.fysik.dtu.dk/projects/ase/tags/
>
> sudo bash -c'echo "debhttp://widehat.opensuse.org/repositories/home:/dtufys/xUbuntu_12.04 /" > /etc/apt/sources.list.d/home_dtufys.sources.list'
> wgethttp://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 <http://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
> <mailto: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
> 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
>
>
>
>
>
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
--
***********************************
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk
***********************************
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