Merge branch 'master' of github.com:computationalmodelling/fidimag

Author: rpep

.travis.yml

@@ -18,11 +18,11 @@ before_install:
   - export PATH=/home/travis/miniconda/bin:$PATH
 
 install:
-  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov gcc
+  - conda create -q -y -n fidimag-test python=$TRAVIS_PYTHON_VERSION cython matplotlib pytest scipy pytest-cov cmake
   - source activate fidimag-test
   - pip install pyvtk six nbval ipywidgets
   # Download and compile FFTW & Sundials locally
-  - bash bin/install-sundials-2.5.sh
+  - bash bin/install-sundials.sh
   - bash bin/install-fftw.sh
 
 before_script:

bin/install-sundials.sh

@@ -8,14 +8,8 @@ set -e
 SUNDIALS=sundials-2.6.2
 
 # Make sure CMake is installed, since SUNDIALS requires it.
-which cmake > /dev/null
-if [ $? -eq 0 ]
-then
-    echo "Found CMake."
-else
-    echo "CMake required to build SUNDIALS. Installing."
-    sudo apt-get install cmake
-fi
+type cmake >/dev/null 2>&1 || { printf "CMake required to build SUNDIALS. You can install it by typing: \nsudo apt install cmake\n"; exit 1;}
+
 
 HERE_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 FIDIMAG_DIR="$(dirname "$HERE_DIR")"

doc/install.rst

@@ -43,18 +43,18 @@ for example, suppose fidimag is in the directory of ~/work, then::
 
    export PYTHONPATH=~/work/fidimag:$PYTHONPATH
 
-Add the library path to LD_LIBRARY_PATH
----------------------------------------
-
-By default, the libraries are installed in fidimag/local, so in order
-to run fidimag we need to include the libs path in LD_LIBRARY_PATH, so
-please add the following to your .bashrc file::
-
-   export LD_LIBRARY_PATH=/path/to/fidimag/local/lib:$LD_LIBRARY_PATH
-
-for instance::
-
-  export LD_LIBRARY_PATH=~/work/fidimag/local/lib:$LD_LIBRARY_PATH
+.. Add the library path to LD_LIBRARY_PATH
+.. -----------------------------------------
+..
+.. By default, the libraries are installed in fidimag/local, so in order
+.. to run fidimag we need to include the libs path in LD_LIBRARY_PATH, so
+.. please add the following to your .bashrc file::
+..
+..   export LD_LIBRARY_PATH=/path/to/fidimag/local/lib:$LD_LIBRARY_PATH
+..
+.. for instance::
+..
+..  export LD_LIBRARY_PATH=~/work/fidimag/local/lib:$LD_LIBRARY_PATH
 
 
 Adding OOMMF path to the system
@@ -217,7 +217,7 @@ Notes:
   failed without a working X server).
 
 Install on OS X
-=================
+==================
 
 The inbuilt OS X gcc compiler (actually clang) doesn't have OpenMP support. A workaround is to
 
@@ -236,3 +236,38 @@ Also install pytest (``conda install pytest`` if using conda) and
 Then run ``make``.
 
 Set the Pythonpath so that the fidimag source is in the path.
+
+
+Possible Issues on Mac OS 
+=============================
+ImportErrors may arise when loading fidimag if the version of sundials is 2.6, ::
+
+    ImportError: dlopen(/Users/ww1g11/Softwares/fidimag/fidimag/extensions/clib.so, 2): Library not loaded: libsundials_cvodes.2.dylib
+    Referenced from: /Users/ww1g11/Softwares/fidimag/fidimag/extensions/clib.so
+    Reason: image not found
+
+this is because the sundials library (libsundials_cvodes.2.dylib) in clib.so doesn't have a full path, 
+which can be seen by using ``otool -L fidimag/extensions/clib.so``, ::
+
+  fidimag/extensions/clib.so:
+    /Users/ww1g11/Softwares/fidimag/local/lib/libfftw3_omp.3.dylib (compatibility version 8.0.0, current version 8.4.0)
+    /opt/local/lib/libfftw3.3.dylib (compatibility version 8.0.0, current version 8.4.0)
+    libsundials_cvodes.2.dylib (compatibility version 2.0.0, current version 2.0.0)
+    libsundials_nvecserial.0.dylib (compatibility version 0.0.0, current version 0.0.2)
+    libsundials_nvecopenmp.0.dylib (compatibility version 0.0.0, current version 0.0.2)
+    /opt/local/lib/libgcc/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
+    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
+    /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
+
+A solution is to change these path manually with ``install_name_tool``, so we have provided a python script (``fix_load_path_mac.py``) to do this.
+After run the script, the library path is fixed, for example, the output of the cmd ``otool -L fidimag/extensions/clib.so`` gives ::
+
+  fidimag/extensions/neb_clib.so:
+    /Users/ww1g11/Softwares/fidimag/local/lib/libfftw3_omp.3.dylib (compatibility version 8.0.0, current version 8.4.0)
+    /opt/local/lib/libfftw3.3.dylib (compatibility version 8.0.0, current version 8.4.0)
+    /Users/ww1g11/Softwares/fidimag/local/lib/libsundials_cvodes.2.dylib (compatibility version 2.0.0, current version 2.0.0)
+    /Users/ww1g11/Softwares/fidimag/local/lib/libsundials_nvecserial.0.dylib (compatibility version 0.0.0, current version 0.0.2)
+    /Users/ww1g11/Softwares/fidimag/local/lib/libsundials_nvecopenmp.0.dylib (compatibility version 0.0.0, current version 0.0.2)
+    /opt/local/lib/libgcc/libgomp.1.dylib (compatibility version 2.0.0, current version 2.0.0)
+    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
+    /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)

fidimag/common/integrators.py

@@ -3,7 +3,7 @@
 
 """
 from scipy.integrate import ode
-from fidimag.extensions.cvode import CvodeSolver as SundialsIntegrator
+from fidimag.extensions.cvode import CvodeSolver, CvodeSolver_OpenMP
 
 EPSILON = 1e-16
 

fidimag/common/sundials/cvode.pxd

@@ -9,18 +9,33 @@ cdef extern from "sundials/sundials_nvector.h":
 
     ctypedef _generic_N_Vector *N_Vector
     N_Vector N_VNew_Serial(long int vec_length)
+    N_Vector N_VNew_OpenMP(long int vec_length)
     void N_VDestroy_Serial(N_Vector v)
+    void N_VDestroy_OpenMP(N_Vector v)
     void N_VPrint_Serial(N_Vector v)
+    void N_VPrint_OpenMP(N_Vector v)
 
 cdef extern from "nvector/nvector_serial.h":
-    cdef N_Vector N_VMake_Serial(long int vec_length, realtype *v_data)
-    
+    cdef N_Vector N_VMake_Serial(long int vec_length, realtype *v_data)    
     cdef struct _N_VectorContent_Serial:
         long int length
         realtype *data
+        booleantype own_data
 
     ctypedef _N_VectorContent_Serial *N_VectorContent_Serial
 
+
+cdef extern from "nvector/nvector_openmp.h":
+    cdef N_Vector N_VMake_OpenMP(long int vec_length, realtype *v_data, int num_threads)
+    
+    cdef struct _N_VectorContent_OpenMP:
+        long int length
+        realtype *data
+        booleantype own_data
+        int num_threads
+        
+    ctypedef _N_VectorContent_OpenMP *N_VectorContent_OpenMP
+
 
 
 cdef extern from "cvode/cvode.h":