importing octant.csa

[fagundesmo]

Dear Dr. Hetland,

I am new octant user and I've just installed octant successfully. However, I have been facing a problem when importing octant.csa, it keeps me showing this error:

OSError Traceback (most recent call last)
in ()
----> 1 import octant.csa

/usr/local/lib/python2.7/dist-packages/octant/csa.py in ()
7 import octant
8
----> 9 class CSA(object):
10 '''cubic spline approximation for re-gridding 2D data sets
11

/usr/local/lib/python2.7/dist-packages/octant/csa.py in CSA()
59 '''
60
---> 61 _csa = np.ctypeslib.load_library('_csa', '/usr/local/lib/python2.7/dis-packages/octant')
62
63

/usr/lib/python2.7/dist-packages/numpy/ctypeslib.pyc in load_library(libname, loader_path)
134 raise
135 ## if no successful return in the libname_ext loop:
--> 136 raise OSError("no file with expected extension")
137
138 ctypes_load_library = deprecate(load_library, 'ctypes_load_library',

OSError: no file with expected extension

Even though, all libs have been installed in their default path (/usr/local/) and csa's path had been changed before I compiled octant. Would you have any idea what it's going on?

Cheers,

Matheus

[garciaga]

I just ran into the same problem. I know this is an old issue but I will write my workaround here for future reference.

To fix it I had to download csa from sakov's github and install it. This generates a libcsa.so which I copied to:

/path/to/my/python/installation/lib/python2.7/site-packages/octant/

as _csa.so

For example in the terminal
cp /path/to/csa/lib/libcsa.so /path/site-packages/octant/_csa.so

It seems to be working so far, I'll report back if I run into issues.

Cheers,

Gabriel

[fagundesmo]

Hi Gabriel,

let me see if I can help you. I have some notes on how I installed it in
portuguese that I did while I was trying to install. However, I installed
it under Ubuntu using gfortran (I'm not sure what your operational system
is). Considering, you're running the installation in the same conditions
that I installed.

svn checkout http://gridgen-c.googlecode.com/svn/gridgen gridgen
svn checkout http://gridutils-c.googlecode.com/svn/ gridutils
svn checkout http://csa-c.googlecode.com/svn/ csa
svn checkout http://nn-c.googlecode.com/svn/ nn

cd nn/nn/
export FC=gfortran
export F77=gfortran
export CC=gcc
export CXX=g++
./configure --prefix=/home/mf/libsmodels
make
make install

cd ../../csa/csa/
export FC=gfortran
export F77=gfortran
export CC=gcc
export CXX=g++
./configure --prefix=/home/mf/libsmodels
make
make install

Na pasta csa terá um arquivo chamado csa.o, faça:
cp csa.o ../../../../../../libsmodels/lib/

cd ../../gridutils/gridutils/
export FC=gfortran
export F77=gfortran
export CC=gcc
export CXX=g++
./configure --prefix=/home/mf/libsmodels
CPPFLAGS=-I/home/mf/libsmodels/include LDFLAGS=-L/home/mf/libsmodels/lib
make
make install

cd ../../gridgen/
export FC=gfortran
export F77=gfortran
export CC=gcc
export CXX=g++
./configure -prefix=/home/mf/libsmodels
CPPFLAGS=-I/home/mf/libsmodels/include LDFLAGS=-L/home/mf/libsmodels/lib

gedit makefile &

Replace in the makefile with the settings below:
gedit makefile &
CFLAGS = -g -O2 -Wall -I/home/mf/libsmodels/include
LDFLAGS = -L/home/mf/libsmodels/lib
LIBS = -lgu -lm -L/home/mf/libsmodels/lib

Close and sabe e keep following the commands below

make
make lib
make shlib
make install

cd ../../../octant/
cd octant/

Modify in grid.py as showed below in the line ~898 (double check it)

gedit grid.py &

    self._libgridgen = np.ctypeslib.load_library('libgridgen.so',

'/home/mf/libsmodels/lib')
#print octant.path[0]
#self._libgridgen = np.ctypeslib.load_library('_gridgen',
octant.path[0])

save and close it. Afterwards, do one last modification:

cd ../
python setup.py build --fcompiler=gfortran

now in the dir ~/octant/octant/ open the file csa.py and modify with the
same below:

_csa = np.ctypeslib.load_library('csa.o',

'/home/mf/libsmodels/libs(substitute
with your path)')

Save and close it, go back to the dir

cd ../
python setup.py install --prefix=/home/mf/pythonmodels/octant

Adding the paths on .bashrc
export PYTHONPATH=$PYTHONPATH:/home/mf/pythonmodels/octant
export PYTHONPATH=$PYTHONPATH:/home/mf/pythonmodels/octant/include
export
PYTHONPATH=$PYTHONPATH:/home/mf/pythonmodels/octant/lib/python2.7/site-packages
export PYTHONPATH=$PYTHONPATH:/home/mf/pythonmodels/octant/lib

Sorry for my mistakes in english, I hope that can help you set everything
correct.

Cheers,

Matheus

•                                                        Matheus
  

  Fagundes, aluno de graduação*

•                              Laboratório de Hidrodinâmica Costeira,
  

  Estuarina e de Águas Interiores - LHICEAI*

•                                                    Departamento de
  

  Oceanografia e Limnologia - DEOLI*

•                                                      Centro de
  

  Ciências Biológicas e da Saúde - CCBS**
  Universidade Federal do Maranhão - UFMA*

On Wed, May 4, 2016 at 5:13 PM, Gabriel García Medina <
notifications@github.com> wrote:

I just ran into the same problem. I know this is an old issue but I will
write my workaround here for future reference.

To fix it I had to download csa from sakov's github and install it. This
generates a libcsa.so which I copied to:

/path/to/my/python/installation/lib/python2.7/site-packages/octant/

as _csa.so

For example in the terminal
cp /path/to/csa/lib/libcsa.so /path/site-packages/octant/_csa.so

It seems to be working so far, I'll report back if I run into issues.

Cheers,

Gabriel

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub
#4 (comment)

[drf5n]

The googlecode links listed above seem broken, but you can do a recent version of csa-c with:

git clone https://github.com/sakov/csa-c.git
pushd csa-c/csa
./configure --prefix=$CONDA_PREFIX # or whereever
make clean install
popd