Compiling with Ubuntu with Python provided by apt

pf4d

I am attempting to compile on Ubuntu 16.04.3 using Python and numpy installed via package manager. Here is the steps I take to install:

function install_issm()


{
  sudo apt-get install libtool cmake autotools-dev python python-numpy;
  svn --username anon --password anon checkout http://issm.ess.uci.edu/svn/issm/issm/trunk ./issm;
  cd issm/externalpackages/m1qn3;
  ./install.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../mpich/;
  ./install-3.0-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../petsc/;
  ./install-3.6-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../triangle/;
  ./install-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd $ISSM_DIR;
  autoreconf -ivf;
  ./configure \
    --prefix="$ISSM_DIR" \
    --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
    --with-python-dir="/usr" \
    --with-python-numpy-dir="/usr/lib/python2.7/dist-packages/numpy" \
    --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include"  \
    --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \
    --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --with-numthreads=2;
  make -j4;
  make install;

}

During the compilation of PETSc, I get the warning:


=============================================================================== 
***** WARNING: MPI_DIR (set to /home/pf4d/software/issm/externalpackages/mpich/install) found in environment variables - ignoring
use ./configure MPI_DIR=$MPI_DIR if you really want to use that value ******
===============================================================================

ISSM configures without error, but at compile time I get the error:

/usr/bin/ld: cannot find -lpmpich


collect2: error: ld returned 1 exit status

Makefile: recipe for target 'libISSMCore.la' failed

Any ideas?

mathieumorlighem

Hi Evan,

you are pretty lucky if this works out of the box! can you tell us what you get when you do:

ls $ISSM_DIR/externalpackages/mpich/install/lib/

Thanks

Mathieu

dlcheng

Hi Evan,

I have a similar setup - I removed the -lpmpich library flag in the mpi directive. --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lpmpich -lmpich -lmpl" \ to --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl" \ I'm not sure if this change is specific to Ubuntu Linux, or is just a typo, but let us know if you have any other problems.

Regards,

Daniel

pf4d

Mathieu:

$ ls $ISSM_DIR/externalpackages/mpich/install/lib/


libfmpich.a          libmpichcxx.so         libmpich.la         libmpl.so.1.0.0
libfmpich.la         libmpichcxx.so.10      libmpich.so         libopa.a
libfmpich.so         libmpichcxx.so.10.0.4  libmpich.so.10      libopa.la
libfmpich.so.10      libmpichf90.a          libmpich.so.10.0.4  libopa.so
libfmpich.so.10.0.4  libmpichf90.la         libmpl.a            libopa.so.1
libmpich.a           libmpichf90.so         libmpl.la           libopa.so.1.0.0
libmpichcxx.a        libmpichf90.so.10      libmpl.so           pkgconfig

libmpichcxx.la libmpichf90.so.10.0.4 libmpl.so.1

pf4d

Daniel,

Using your method, I now have the error:

CXXLD issm.exe


/usr/bin/ld: ./.libs/libISSMCore.so: undefined reference to symbol '_gfortran_transfer_real_write@@GFORTRAN_1.4'
//usr/lib/x86_64-linux-gnu/libgfortran.so.3: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile: recipe for target 'issm.exe' failed
make: ***  Error 1

pf4d

OK! So I added the line

--with-fortran-lib="-L/usr/lib/x86_64-linux-gnu/ -lgfortran" \

to the configure script, and have compiled without error. For reference, the final install function for Ubuntu 16.04.3 is printed below.

One final question: I do not use Matlab, and would like to start using the Python interpreter. I see that you have a script "mToPy.py" that may possibly convert arbitrary issm matlab scripts to python. Does this work?

Also, I found some scripts that appear to have been converted in "/trunk/test/Par"; however, they import some functions defined in scripts located in "/trunk/src/py3" that have not been added to pythonpath during installation. Do you have any additional scripts or a suggested method for finishing the python installation?

I will be working with Greenland's 79 N Glacier, so perhaps the "79North.py" script is where I should begin?

Thanks for you fast responses,

Evan

function install_issm()


{
  sudo apt-get install libtool cmake autotools-dev python python-numpy;
  svn --username anon --password anon checkout http://issm.ess.uci.edu/svn/issm/issm/trunk ./issm;
  cd issm/externalpackages/m1qn3;
  ./install.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../mpich/;
  ./install-3.0-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../petsc/;
  ./install-3.6-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd ../triangle/;
  ./install-linux64.sh;
  source $ISSM_DIR/etc/environment.sh;
  cd $ISSM_DIR;
  autoreconf -ivf;
  ./configure \
    --prefix="$ISSM_DIR" \
    --with-python-dir="/usr" \
    --with-fortran-lib="-L/usr/lib/x86_64-linux-gnu/ -lgfortran" \
    --with-python-numpy-dir="/usr/lib/python2.7/dist-packages/numpy" \
    --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
    --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include"  \
    --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich -lmpl" \
    --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
    --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install/" \
    --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
    --with-numthreads=2;
  make -j4;
  make install;
}

mathieumorlighem

Hi Evan,

ok I am glad it worked. Regarding python: MATLAB is the only interface that has all capabilities and is fully supported. Python is still under development, it does not have all the features that the MATLAB interface has (like dakota, plotmodel, etc) and is in the process of being rewritten. Personally, I highly recommend to use MATLAB, but you are free to use the python interface. If you do choose python, don't expect much support from us.

mToPy.py is an old script I don't recommend using it. What's in test/Par is for the nightly runs only (regression tests), so you would not get a good model for 79North as it is based on old datasets. You might want to start from the Jakobshavn tutorial and change the domain to 79North.

Good luck!

Mathieu