...Hi
I have used
managed to solve *AmberTools15* reinstalling as follows:
First installed libraries missing:
http://www.scipy.org/install.html
this is to install libraries in python case missing
*sudo apt-get install python-numpy python-scipy python-matplotlib ipython
ipython-notebook python-pandas python-SymPy python-nose*
do this before installing
tar jxvf Amber15.tar.bz2
export AMBERHOME=`pwd`
*./configure --with-python /usr/bin/python2.7*
source amber.sh
make install
make test
The following command to install in parallel (requires first install mpi
with the same compiler gnu)
*./configure --with-python /usr/bin/python2.7 -mpi gnu*
make install
then it was just to set the bash file contents amber.sh
In my case:
export AMBERHOME="/home/marcelo/PROGRAMS/AMBER-NEW/amber14"
export PATH="${AMBERHOME}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages"
else
export
PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
if [ -z "${LD_LIBRARY_PATH}" ]; then
export LD_LIBRARY_PATH="${AMBERHOME}/lib"
else
export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
fi
Att.,
Marcelo A. Chagas
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
*
http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2016-03-16 14:48 GMT-03:00 Wesley Alves <wesley.diatom.gmail.com>:
> Hi dears,
> I dont know whats happening in my amber tests.
> someone can help me ?
> Wesley
>
>
> make[1]: Entering directory '/home/labime/amber14/AmberTools/test'
> ./test_at_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
> Makefile:6: recipe for target 'test' failed
> make[1]: *** [test] Error 1
> make[1]: Leaving directory '/home/labime/amber14/AmberTools/test'
> Makefile:43: recipe for target 'test.serial' failed
> make: *** [test.serial] Error 2
>
>
> --
> 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
>
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Received on Wed Mar 16 2016 - 11:30:03 PDT
