Building the Dakota package (ISSM v4.18)

Kevin

Hi everyone,

I have been trying to install the Dakota package (on MacOS Catalina) with the latest version of ISSM (v4.18) using the installation script install-6.2-macosx64-catalina.sh. Cmake seems unable to find the different compilers given by the configure options. It looks like these compilers should be in the external package mpich (-D CMAKE_C_COMPILER=$HOME/externalpackages/mpich/install/bin/mpicc, ...), which is not required anymore to install ISSM. Should I install the external package mpich or provide others paths for the compilers (maybe in the petsc package)?

PS: I also identified two small issues in the compilation script. 1) It looks like the command line to download dakota is preceded by a comment symbol (dakota-6.2-public-src.tar.gz cannot be downloaded then). 2) I assume the HOME directory should be replaced ISSM_DIR.

Thanks,
Kevin

justinquinn

Hi Kevin,
You are right: that script does not look like it will work out of the box. Could you please try the install-6.2-mac.sh script instead?

Kevin

Hi Justin,
Thanks for the reply. I have just tried with the install-6.2-mac.sh script and it is working out perfectly fine now (I just needed to also install gsl). However, the dakota library now causes matlab to crash (see error message below). Actually, this is not the first time I got this issue (even without dakota so this is probably not related to this library specifically). Do you have any idea how I can fix it?

Class JavaLaunchHelper is implemented in both /Applications/MATLAB_R2017b.app/sys/java/jre/maci64/jre/bin/java (0x10704d4c0) and /Applications/MATLAB_R2017b.app/sys/java/jre/maci64/jre/lib/jli/libjli.dylib (0x15fbd9480). One of the two will be used. Which one is undefined.

Thanks

justinquinn

Kevin Hi Kevin, sorry for the late reply. I haven't seen that one before. I might suggest updating to a more recent version of MATLAB.

Note the following tried and true configuration for ISSM with Dakota and soild earth capabilities on macOS:

Configuration (passed to ${ISSM_DIR}/configure; adjust paths to Python, NumPy, and libgfortran):

--prefix=${ISSM_DIR} \
--disable-static \
--enable-development \
--enable-debugging \
--with-numthreads=4 \
--with-matlab-dir=${MATLAB_PATH} \
--with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \
--with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy \
--with-fortran-lib="-L/usr/local/Cellar/gcc/10.2.0/lib/gcc/10 -lgfortran" \
--with-mpi-include=${ISSM_DIR}/externalpackages/petsc/install/include \
--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
--with-blas-lapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-metis-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-parmetis-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-scalapack-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-mumps-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-hdf5-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-petsc-dir=${ISSM_DIR}/externalpackages/petsc/install \
--with-gsl-dir=${ISSM_DIR}/externalpackages/gsl/install \
--with-boost-dir=${ISSM_DIR}/externalpackages/boost/install \
--with-dakota-dir=${ISSM_DIR}/externalpackages/dakota/install \
--with-triangle-dir=${ISSM_DIR}/externalpackages/triangle/install \
--with-chaco-dir=${ISSM_DIR}/externalpackages/chaco/install \
--with-m1qn3-dir=${ISSM_DIR}/externalpackages/m1qn3/install \
--with-semic-dir=${ISSM_DIR}/externalpackages/semic/install

External package installation scripts:

autotools	install-mac.sh
cmake		install.sh
petsc		install-3.12-mac.sh
gsl			install.sh
boost		install-1.7-mac.sh
dakota		install-6.2-mac.sh
curl		        install-7-mac.sh
netcdf		install-4.7-parallel.sh
proj		        install-6.2.sh
gdal		install-3-python.sh
gshhg		install.sh
gmt			install-6-mac.sh
gmsh		install-4.sh
triangle	        install-mac.sh
chaco		install.sh
m1qn3		install.sh
semic		install.sh

Kevin

justinquinn Hi Justin, no worries. Indeed, it might only be an internal problem related to my matlab version. I am going to try to reconfigure with the configuration script you suggested and see how it works. Thanks.

justinquinn

Kevin Ok, cool. Let us know how it goes and if you run into any further issues.

justinquinn

Kevin Following our conversation today, looks like you need to update to R2019b or later to be able to run MATLAB on Catalina.

Source: https://www.mathworks.com/matlabcentral/answers/489700-is-matlab-compatible-with-macos-catalina#answer_400285