[ase-users] Unable to read the created .nc file
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Fri Mar 25 17:33:56 CET 2011
Hi,
Jakob Blomqvist wrote:
> This might be silly question but how do I try out locally installed
> trunk through Torque? I have set PATH and PYTHONPATH to first point to
> trunk version and when I try to print version using a test script like
> from ase.version import version; print version:
> $ python test.py
> i get
> "3.5.0"
>
> but if i send my script through qsub I get
> "3.4.1"
>
the point is that you need to set the variables in the right place.
See example
https://wiki.fysik.dtu.dk/niflheim/Installed_software#modules-in-batch-jobs
The safest way is to remove any settings from you login scrips
(~/.bashrc, ~/.cshrc, ...)
and set the variables per job, as in the mentioned example.
>
> Another issue is that when I try to run a simple bulk script below using
> $ python albulk.py
> i get
> expected output
>
> but with
> $mpirun -np 2 albulk.py
it's the dacapo.run script that should call mpiexec.
See example here:
https://trac.fysik.dtu.dk/projects/ase/browser/trunk/ase/calculators/jacapo/tools/dacapo.run
- i think this one should work with torque.
>
> I get
> ################
> Traceback (most recent call last):
> File "albulk.py", line 18, in <module>
> atoms=bulk)
> File "/home/jakob/ase/ase/calculators/jacapo/jacapo.py", line 302,
> in __init__
> self.set(**kwargs) #if nothing changes, nothing will be done
> File "/home/jakob/ase/ase/calculators/jacapo/jacapo.py", line 336,
> in set
> notchanged = not eval('%s(self,kwargs[key])' % changef)
> File "<string>", line 1, in <module>
> File "/home/jakob/ase/ase/calculators/jacapo/changed.py", line 40,
> in kpts_changed
> grid = calc.get_kpts()
> File "/home/jakob/ase/ase/calculators/jacapo/jacapo.py", line 2154,
> in get_kpts
> nc = netCDF(self.nc, 'r')
> File "/usr/lib/python2.6/dist-packages/Scientific/IO/NetCDF.py",
> line 177, in NetCDFFile
> return apply(_NetCDFFile, args)
> IOError: netcdf: NetCDF: Unknown file format
> [-0.142687 -0.142687 -0.142687 0.00839633 0.00839633 0.00839633]
>
> ################
> So, it still seems to get the correct result in the end, however I
> wonder if it even ran it in parallel?
> What is the easiest way to check if a dacapo/jacapo job has run
> properly in parallel? I can't see anything in output-txt file.
on the top of the txt file you can see on how many nodes it runs: it
lists all the hostnames.
Marcin
>
> albulk.py:
> *************************
> #!/usr/bin/env python
> from ase import Atom, Atoms
> from ase.calculators.jacapo import *
>
>
> a = 3.8 # approximate lattice constant
> b = a / 2.
> bulk = Atoms([Atom('Al',(0.0,0.0,0.0))],
> cell=[(0,b,b),
> (b,0,b),
> (b,b,0)])
>
> calc = Jacapo('2.2.1-Al.nc',
> pw=350,
> kpts=(4,4,4),
> calculate_stress=True,
> atoms=bulk)
>
> print bulk.get_stress()
> ***************************
>
>
>
>
>
>
> Dr. Jakob Blomquist
> IMP, School of Technology
> Malmo University
> SWEDEN
> +46(0)40 6657626
> jakob.blomqvist at mah.se
>
> >>> Marcin Dulak <Marcin.Dulak at fysik.dtu.dk> 03/25/11 10:59 AM >>>
> Hi,
>
> the jacapo handling of restart has been fixed in the development version
> of ase: https://wiki.fysik.dtu.dk/ase/download.html#id8
> Please use the ase trunk.
>
> Best regards,
>
> Marcin
>
> c cook wrote:
> > Hello again,
> >
> > I started to do some simple testing:
> >
> >
> http://beowulf.cheme.cmu.edu/jacapo/2-bulk/2.2-unitcell-optimization/2.2.0-unit-cell-optimization.html#simple-total-energy-calculation
> >
> >
> > the first step to calculate the energy seen below worked
> > #!/usr/bin/env python
> > from ase import *
> > from ase.calculators.jacapo import *
> >
> >
> > a = 3.8 # approximate lattice constant
> > b = a / 2.
> > bulk = Atoms([Atom('Al',(0.0,0.0,0.0))],
> > cell=[(0,b,b),
> > (b,0,b),
> > (b,b,0)])
> >
> > calc = Jacapo('2.2.1-Al.nc <http://2.2.1-Al.nc>',
> > pw=350,
> > kpts=(4,4,4),
> > calculate_stress=True,
> > atoms=bulk)
> >
> > print bulk.get_stress()
> > the 2.2.1-Al.nc <http://2.2.1-Al.nc> and the corresponding .txt file
> > were created,
> >
> > but when I went further to:
> >
> > #!/usr/bin/env python
> > from ase.calculators.jacapo import *
> >
> > bulk = Jacapo.read_atoms('2.2.1-Al.nc <http://2.2.1-Al.nc>')
> >
> > print 'energy: ' ,bulk.get_potential_energy()
> >
> >
> > sxx, syy, szz, syz, sxz, sxy = bulk.get_stress()
> >
> > import numpy as np
> > from ase.units import GPa
> > print 'Stress (GPa) = '
> > print np.array([[sxx, sxy, sxz],
> > [sxy, syy, syz],
> > [sxz, syz, szz]])/GPa
> > I' ve got the following error:
> >
> > File "./bulkAl2.sh", line 4, in <module>
> > bulk = Jacapo.read_atoms('2.2.1-Al.nc <http://2.2.1-Al.nc>')
> > File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 3059,
> > in read_atoms
> > calc = Jacapo(filename)
> > File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 231,
> > in __init__
> > self.set_nc(nc)
> > File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 1135,
> > in set_nc
> > self.update_input_parameters()
> > File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 383,
> > in update_input_parameters
> > self.pars[key] = eval(getf)
> > File "<string>", line 1, in <module>
> > File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 2257,
> > in get_psp
> > raise Exception, 'You can only specify Z or sym!'
> > Exception: You can only specify Z or sym!
> >
> >
> > I've checked in the jacapo.py and the only reference to the error is
> this:
> >
> > *def set_psp(self,*
> > * sym=None,*
> > * z=None,*
> > * psp=None):*
> > * '''*
> > * set the pseudopotential file for a species or an atomic number.*
> > *
> > *
> > * :Parameters:*
> > *
> > *
> > * sym : string*
> > * chemical symbol of the species*
> > *
> > *
> > * z : integer*
> > * the atomic number of the species*
> > *
> > *
> > * psp : string*
> > * filename of the pseudopotential*
> > *
> > *
> > * *
> > * you can only set sym or z.*
> > *
> > *
> > * examples::*
> > * *
> > * set_psp('N',psp='pspfile')*
> > * set_psp(z=6,psp='pspfile')*
> > * '''*
> > * log.debug(str([sym, z, psp]))*
> > * if (sym, z, psp) == (None, None, None):*
> > * return*
> > * *
> > * if (sym is None and z is not None):*
> > * from ase.data import chemical_symbols*
> > * sym = chemical_symbols[z]*
> > * elif (sym is not None and z is None):*
> > * pass*
> > * else:*
> > * raise Exception, 'You can only specify Z or sym!'*
> >
> >
> > But, I am stuck here. The DACAPOPATH is correctly pointing to the psp
> > directory, and anyways, why it didn't complain when he did the energy
> > calculation?
> >
> > And this is happening every time there is a need to read an already
> > created .nc file (I 've tried couple of more examples and I got the
> > same error)
> >
> > What am I doing wrong?
> >
> > Thanks,
> > Csaba
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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
>
> ***********************************
>
> _______________________________________________
> 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
***********************************
More information about the ase-users
mailing list