Mac M1, macports, python, and gfortran (solved)

aaschwanden

Hi:

In case someone else wants to use MacPorts instead of HomeBrew on a Mac, below are a few notes.

I installed ISSM on my M1 Mac with Monterey using MacPorts instead of HomeBrew and installing gfortran from [https://github.com/fxcoudert/gfortran-for-macOS/releases]. After some tweaking, I was able to configure and compile ISSM using:

./configure \
    --prefix="${ISSM_DIR}" \
    --with-python-version=3.10 \
    --with-python-dir="/opt/local/Library/Frameworks/Python.framework/Versions/Current/" \
    --with-python-numpy-dir="/opt/local/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/numpy" \
    --with-fortran-lib="-L/opt/local/lib/gcc12/ -lgfortran" \
    --with-mpi-include="${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-parmetis-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-petsc-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"

You may need to adjust your python version, I'm currently using 3.10.

When I tried to import the python bindings, I got the following error:

ImportError: dlopen(/Users/andy/ISSM/lib/IssmConfig_python.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: /Users/andy/ISSM/lib/IssmConfig_python.so
  Reason: tried: '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)

which is no surprise because gfortran was automatically installed to /usr/local/gfortran: /usr/local/gfortran/lib/libgfortran.5.dylib.

The problem was solved by

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gfortran/lib export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/usr/local/gfortran/lib

(I'm not sure which one did the trick).

aaschwanden

Turns out I was a bit too fast. While the above let's me import the python binding and build a model in python, the same error appears when I try to solve the model:

`$ python jakobshavn.py
Loading SeaRISE data from NetCDF
Anisotropic mesh adaptation
WARNING: mesh present but no geometry found. Reconstructing...

new number of triangles = 3076
Interpolating bedrock topography
Constructing surface elevation
Interpolating velocities
Interpolating temperatures
Interpolating surface mass balance
Construct basal friction parameters
Construct ice rheological properties
/Users/andy/ISSM/examples/Jakobshavn/jakobshavn.py:125: DeprecationWarning: Calling nonzero on 0d arrays is deprecated, as it behaves surprisingly. Use atleast_1d(arr).nonzero() if the old behavior was intended.
pos = (np.array(weakb[0])).nonzero()
Set other boundary conditions
boundary conditions for stressbalance model: spc set as observed velocities
no basalforcings.groundedice_melting_rate specified: values set as zero
no basalforcings.floatingice_melting_rate specified: values set as zero
no balancethickness.thickening_rate specified: values set as zero
checking model consistency
marshalling file Jakobshavn.bin
uploading input file and queuing script
launching solution sequence on remote cluster
dyld[4439]: Library not loaded: @rpath/libgfortran.5.dylib
Referenced from: /Users/andy/ISSM/bin/issm.exe
Reason: tried: '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file)

which happens when I call
import solve md = solve.solve(md, "StressBalance")
which makes me guess that export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gfortran/lib worked for the python bindings but not for the ISSM executable that is called during md = solve().

I'm not familiar with autoconf and export LT_SYS_LIBRARY_PATH=/usr/local/gfortran/lib did not help.

I'm attaching config.log and Makefile.

config.txt

72kB

makefile.txt

32kB

justinquinn

I've been running a new installation on an Intel-based Mac and with the more recent versions of macOS and/or Xcode (Command Line Tools), the usage of rpath has changed somewhat, it seems. What worked for me was to set LIBRARY_PATH in ~/.bash_profile (I did not have to modify LD_LIBRARY_PATH):

export LIBRARY_PATH="/usr/local/Cellar/gcc/12.2.0/lib/gcc/12"

You will have to recompile ISSM, and may have to recompile your external packages if you are still getting the error. Of course, you will also have to modify the above snippet to point to your own (MacPorts) installation of libgfortran. Let us know if this works.