It seems like your Amber installation is broken (at least the python
components) for some reason. This could happen if you've recently
changed your environment somehow. I recommend reconfiguring and
recompling Amber.
-Dan
On Wed, Mar 9, 2016 at 9:57 AM, Wesley Alves <wesley.diatom.gmail.com> wrote:
> Hi Daniel,
> I run each test forward each component installation, and any test dont work.
>
> I just tried run the specific script, such test_amber_serial.sh an others,
> nothing work too.
>
> The complete error message for serial test:
>
>
>>labime.prion:~/amber14/test> ./test_amber_serial.sh
>
>>Warning: DO_PARALLEL is set to "mpirun -np 2".
> This environment variable is being unset for serial testing.
>
>>Traceback (most recent call last):
>> File "<stdin>", line 18, in <module>
> File
> "/home/labime/amber14/lib/python2.7/site-packages/chemistry/__init__.py",
> line 14, in <module>
> from chemistry import amber, charmm, tinker
>> File
> "/home/labime/amber14/lib/python2.7/site-packages/chemistry/amber/__init__.py",
> line 13, >in <module>
>> from chemistry.amber.netcdffiles import use, NetCDFTraj,
> NetCDFRestart, HAS_NETCDF
> File
> "/home/labime/amber14/lib/python2.7/site-packages/chemistry/amber/netcdffiles.py",
> line 75, in <module>
> from scipy.io.netcdf import netcdf_file as spNetCDFFile
> File "/usr/lib64/python2.7/site-packages/scipy/io/__init__.py", line 97,
> in <module>
> from .matlab import loadmat, savemat, whosmat, byteordercodes
> File "/usr/lib64/python2.7/site-packages/scipy/io/matlab/__init__.py",
> line 13, in <module>
> from .mio import loadmat, savemat, whosmat
> File "/usr/lib64/python2.7/site-packages/scipy/io/matlab/mio.py", line
> 12, in <module>
> from .miobase import get_matfile_version, docfiller
> File "/usr/lib64/python2.7/site-packages/scipy/io/matlab/miobase.py",
> line 22, in <module>
> from scipy.misc import doccer
> File "/usr/lib64/python2.7/site-packages/scipy/misc/__init__.py", line
> 51, in <module>
> from scipy.special import comb, factorial, factorial2, factorialk
> File "/usr/lib64/python2.7/site-packages/scipy/special/__init__.py", line
> 627, in <module>
> from ._ufuncs import *
> File "__init__.pxd", line 155, in init scipy.special._ufuncs
> (scipy/special/_ufuncs.c:26236)
> ValueError: numpy.dtype has the wrong size, try recompiling
>
> --
> Wesley Júnio Alves da Conceição
> Undergraduate Biophysics Student
> Laboratory for Molecular Modelling and Dynamics - Carlos Chagas Filho
> Biophysics Institute
> Laboratory for Structural Molecular Biology - Pharmacy Faculty
> Federal University of Rio de Janeiro
> Rio de Janeiro - RJ
> Brazil
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 09 2016 - 11:00:04 PST
