Hi,
I am looking to compile ISSM from source on Linux (Ubuntu 20.04, virtual machine) and have been running into a few snags. I have installed all the packages and make install
, however there seem to be some errors in the installation and ISSM does not work. My objective is to get the 'solid earth capabilities' version running.
When I try and run md = model(), matlab throws error :
Invalid MEX file /home/maxvwdv/Documents/ISSM/trunk/lib/IssmConfig_matlab.mexa64 : libtriangle.so : cannot open shared object file : No such file or directory.
I am a little uncertain whether the issue is with how I configured/installed ISSM, or something else.
I installed the following packages:
autotools
cmake
petsc
triangle
chaco
m1qn3
semic
boost
curl
netcdf
proj
gdal
gshhg
gmt
gmsh
nose
(python with numpy)
math77
I was having issues with the /scripts/DownloadExternalPackages.sh loading empty files (e.g. creates 0 byte tar.gz instead of downloading the needed file), so I replaced it in most installation files with wget 'link' --no-check-certificate
which seemed to work.
I then configured with the following script:
./configure \
--prefix=$ISSM_DIR \
--with-matlab-dir="/usr/local/MATLAB/R2020a" \
--with-cmake-dir="$ISSM_DIR/externalpackages/cmake/install" \
--with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
--with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include" \
--with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib/ -lmpi -lmpicxx -lmpifort" \
--with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
--with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
--with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
--with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
--with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
--with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \
--with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
--with-semic-dir="$ISSM_DIR/externalpackages/semic/install" \
--with-boost-dir="$ISSM_DIR/externalpackages/boost/install" \
--with-netcdf-dir="$ISSM_DIR/externalpackages/netcdf/install" \
--with-proj-dir="$ISSM_DIR/externalpackages/proj/install" \
--with-gdal-dir="$ISSM_DIR/externalpackages/gdal/install" \
--with-gshhg-dir="$ISSM_DIR/externalpackages/gshhg/install" \
--with-gmt-dir="$ISSM_DIR/externalpackages/gmt/install" \
--with-gmsh-dir="$ISSM_DIR/externalpackages/gmsh/install" \
--with-math77-dir="$ISSM_DIR/externalpackages/math77/install" \
--with-numthreads=2
I first had a line in configure.sh with --with python-dir=/usr \
, however was getting an error (fatal error: arrayobject.h: No such file or directory). I checked that the 'arrayobject.h' file was present in the expected location, but could not get the script to recognize it, so removed the python line from the configure script.
After removing the python line, configuration ran without errors, as did make
and make install
. I am not sure if that is what is causing other issues with ISSM post-installation, of if there may be another cause. Does anyone have any leads to track down the problem?