Problems when installing ISSM

justinquinn

Ah, try export ISSM_DIR=/e/ISSM in your .bashrc, start a new terminal, then try the PETSc installation again.

wudipao88

Thank you for your guidance. After changing the path in .bashrc, the installation of petsc is smoother than before. However, the installation is still not completely successful. Here is the installation feedback:

===============================================================================

Configuring PETSc to compile on your system

/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/base.py:221: SyntaxWarning: invalid escape sequence '\ '
prog = prog.replace('\ ',' ').replace('(','(').replace(')',')')
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/base.py:221: SyntaxWarning: invalid escape sequence '('
prog = prog.replace('\ ',' ').replace('(','(').replace(')',')')
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/base.py:221: SyntaxWarning: invalid escape sequence ')'
prog = prog.replace('\ ',' ').replace('(','(').replace(')',')')
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/framework.py:205: SyntaxWarning: invalid escape sequence '['
self.help.title = 'Configure Help\n Comma separated lists should be given between [] (use [ ] in tcsh/csh)\n For example: --with-mpi-lib=[/usr/local/lib/libmpich.a,/usr/local/lib/libpmpich.a]\n Options beginning with --known- are to provide values you already know\n Options beginning with --with- indicate that you are requesting something\n For example: --with-clanguage=c++\n <prog> means a program name or a full path to a program\n For example:--with-cmake=/Users/bsmith/bin/cmake\n <bool> means a boolean, use either 0 or 1\n <dir> means a directory\n For example: --with-packages-download-dir=/Users/bsmith/Downloads\n For packages use --with-PACKAGE-dir=<dir> OR\n --with-PACKAGE-include=<dir> --with-PACKAGE-lib=<lib> OR --download-PACKAGE'
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/setCompilers.py:225: SyntaxWarning: invalid escape sequence '\s'
strmatch = re.match('GNU Fortran\s+(.)\s+(\d+).(\d+)',output)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/setCompilers.py:240: SyntaxWarning: invalid escape sequence '\s'
strmatch = re.match('GNU Fortran\s+(.)\s+(\d+).(\d+)',output)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/setCompilers.py:255: SyntaxWarning: invalid escape sequence '\s'
strmatch = re.match('GNU Fortran\s+(.)\s+(\d+).(\d+)',output)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/setCompilers.py:270: SyntaxWarning: invalid escape sequence '\s'
strmatch = re.match('GNU Fortran\s+(.)\s+(\d+).(\d+)',output)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/types.py:242: SyntaxWarning: invalid escape sequence '\s'
MaxPathLength = re.compile('\nchar petsc_max_path_len\s?[\s?] = '+HASHLINESPACE+'\"([0-9]+)\"'+HASHLINESPACE+';').search(buf).group(1)
/e/ISSM/externalpackages/petsc/src/config/PETSc/options/petscclone.py:40: SyntaxWarning: invalid escape sequence '*'
self.addDefine('VERSION_BRANCH_GIT','"'+re.compile('* (.*)').search(o4).group(1)+'"')
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/MPI.py:213: SyntaxWarning: invalid escape sequence '\ '
self.mpiexec = self.mpiexec.replace(' ', '\ ').replace('(', '$').replace(')', '$').replace('\ -',' -')
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/MPI.py:569: SyntaxWarning: invalid escape sequence '.'
mpich_numversion = re.compile('\nconst char mpich_ver ='+HASHLINESPACE+'"([.0-9]+)"'+HASHLINESPACE+';').search(buf).group(1)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/MPI.py:621: SyntaxWarning: invalid escape sequence '['
msmpi_version = re.compile('\nchar msmpi_hex[] = '+HASHLINESPACE+'\"([a-zA-Z0-9_])\"'+HASHLINESPACE+';').search(buf).group(1)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/openblas.py:68: SyntaxWarning: invalid escape sequence '\s'
ver = re.match("\sOpenBLAS\s([0-9.]+)\s",ver).group(1)
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/SuiteSparse.py:64: SyntaxWarning: invalid escape sequence '\$'
ldflags+=" -L\$(INSTALL_LIB)"
/e/ISSM/externalpackages/petsc/src/config/BuildSystem/config/packages/sowing.py:57: SyntaxWarning: invalid escape sequence '('
ver = re.compile('bfort (sowing) release ([0-9]+).([0-9]+).([0-9]+)').match(output)
=============================================================================== ***** WARNING: Using default optimization C flags -g -O You might consider manually setting optimal optimization flags for your system with COPTFLAGS="optimization flags" see config/examples/arch--opt.py for examples =============================================================================== =============================================================================== ***** WARNING: Using default C++ optimization flags -g -O You might consider manually setting optimal optimization flags for your system with CXXOPTFLAGS="optimization flags" see config/examples/arch--opt.py for examples =============================================================================== =============================================================================== ***** WARNING: Using default FORTRAN optimization flags -g -O You might consider manually setting optimal optimization flags for your system with FOPTFLAGS="optimization flags" see config/examples/arch--opt.py for examples =============================================================================== TESTING: configureLibrary from config.packages.metis(config/BuildSystem/config/packages/metis.py:49) /e/ISSM/externalpackages/petsc/src/config/BuildSystem/retrieval.py:226: SyntaxWarning: invalid escape sequence '\;'
config.base.Configure.executeShellCommand('cd '+root+'; chmod -R a+r '+dirname+';find '+dirname + ' -type d -name "*" -exec chmod a+rx {} \;', log = self.log)
=============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-metis.git for METIS =============================================================================== =============================================================================== Configuring METIS with cmake; this may take several minutes =============================================================================== =============================================================================== Compiling and installing METIS; this may take several minutes =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-parmetis.git for PARMETIS =============================================================================== =============================================================================== Configuring PARMETIS with cmake; this may take several minutes =============================================================================== =============================================================================== Compiling and installing PARMETIS; this may take several minutes =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-fblaslapack for FBLASLAPACK =============================================================================== =============================================================================== Compiling FBLASLAPACK; this may take several minutes =============================================================================== =============================================================================== Trying to download git://https://bitbucket.org/petsc/pkg-scalapack for SCALAPACK =============================================================================== =============================================================================== Compiling and installing Scalapack; this may take several minutes =============================================================================== *******************************************************************************

UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):

Error running make on SCALAPACK

makefile:15: arch-mswin-c-opt/lib/petsc/conf/petscvariables: No such file or directory
make[1]: *** No rule to make target 'arch-mswin-c-opt/lib/petsc/conf/petscvariables'. Stop.
gmakefile:5: arch-mswin-c-opt/lib/petsc/conf/petscvariables: No such file or directory
make: *** [GNUmakefile:17: arch-mswin-c-opt/lib/petsc/conf/petscvariables] Error 2
makefile:15: arch-mswin-c-opt/lib/petsc/conf/petscvariables: No such file or directory
make[1]: *** No rule to make target 'arch-mswin-c-opt/lib/petsc/conf/petscvariables'. Stop.
gmakefile:5: arch-mswin-c-opt/lib/petsc/conf/petscvariables: No such file or directory
make: *** [GNUmakefile:17: arch-mswin-c-opt/lib/petsc/conf/petscvariables] Error 2

justinquinn

wudipao88

There's something still off in your setup. On our end, for example, the output is like,

===============================================================================
             Configuring PETSc to compile on your system
===============================================================================
===============================================================================
      ***** WARNING: Using default optimization C flags -g -O
      You might consider manually setting optimal optimization flags for your system with
      COPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples
===============================================================================
===============================================================================
      ***** WARNING: Using default C++ optimization flags -g -O
      You might consider manually setting optimal optimization flags for your system with
      CXXOPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples
===============================================================================
===============================================================================
      ***** WARNING: Using default FORTRAN optimization flags -g -O
      You might consider manually setting optimal optimization flags for your system with
      FOPTFLAGS="optimization flags" see config/examples/arch-*-opt.py for examples
===============================================================================
===============================================================================
      Trying to download git://https://bitbucket.org/petsc/pkg-metis.git for METIS
===============================================================================
===============================================================================
      Configuring METIS with cmake; this may take several minutes
===============================================================================
[...]

without all the warnings about invalid escape sequences.

When you start up your terminal, does the prompt look like <USER>@<HOSTNAME> MINGW64 ~?

wudipao88

Yes, <USER>@<HOSTNAME> MINGW64 ~ is appeared when I start up MSYS2 MINGW64. Here is what I added to the .bashrc, is there any problem else?

## MATLAB # MATLAB_VER="R2024a" # Allows for easy resetting of MATLAB version added to path export MATLAB_PATH=$(cygpath -u $(cygpath -ms "/e/Program Files/MATLAB/${MATLAB_VER}")) export PATH="${MATLAB_PATH}/bin:${PATH}"

## ISSM # export ISSM_DIR=/e/ISSM export ISSM_DIR_WIN=$(cygpath -ms "${ISSM_DIR}") # Needed by MATLAB

Thanks !

justinquinn

wudipao88 Yeah, that all looks good. Do you have the ability to write to the C drive? If so, try checking out another copy of the repo there and see if compiling PETSc works. You will have to update ISSM_DIR in your .bashrc to the new location of course. I wonder if MSYS2 is having an issue with drives other than the default for some reason?

wudipao88

justinquinn I put the ISSM on the C drive and tried to install the external packages again, but when installing petsc there was still an error message of "invalid escape sequences", I really don't know what caused this installation error.😂

wudipao88

justinquinn I did not install Anaconda, is this related to my installation error?

justinquinn

wudipao88 Well that stinks. It was worth a try anyhow.

justinquinn

wudipao88 I'm going to try to do a fresh install of MSYS2 on a Windows VM to see if I can reproduce the error. Are you on Windows 10 or 11?

justinquinn

wudipao88 No, Anaconda is not required and can, in fact, cause a lot of issues with configuration/compiling.

wudipao88

justinquinn My operating system is Windows 10. Thanks a lot !

justinquinn

wudipao88 Good (bad?) news: I was able to recreate your issue with installing PETSc on Windows under MSYS2. Now I just have to sort out why it's happening there and not on the other machines. Will update you as soon as I have an answer.

justinquinn

wudipao88 Okay, so it may be an easy fix after all: looks like they removed gfortran from the base-devel package set in Pacman for MSYS2. You can install it with,

pacman -S mingw-w64-x86_64-gcc-fortran

You can effectively ignore the SyntaxWarning's from Python. This was introduced in Python 3.12. Let me know if this works for you.

justinquinn

wudipao88 Actually, I have the same issue now that you had with Scalapack under PETSc. Investigating further.

justinquinn

wudipao88

Alright, I have a solution for you! Note that this was all due to changes with the versions of GCC and Python that are current for pacman.

1) Run pacman -S python-setuptools mingw-w64-x86_64-gcc-fortran (I think you may have already installed gfortran)
2) Run git pull in $ISSM_DIR
3) Run the PETSc installation again

I think your issue with the patch in Triangle may be due to the fact that you had already run the installation. If you rm -rf $ISSM_DIR/externalpackages/triangle/install and run the install script again, it should work.

Output of the m1qn3 installation looks fine to me.

Let me know if this works for you and Happy New Year!

justinquinn

wudipao88

Looks like there may be one last thing for me to work out as it seems like MATLAB is not picking up ISSM's libraries now. I'll update you here when I've sorted it.

justinquinn

wudipao88 Okay, that turned out to be an easy fix too: simply update the path to libgfortran in the configuration,

--with-fortran-lib="-L/c/msys64/mingw64/lib -lgfortran"

I've updated the documentation on the website to reflect all of the above. You should be good to go now, but let us know if you have any further issues. Thanks for your patience and for bringing this to our attention.

wudipao88

justinquinn Thank you very much for your efforts! I re-downloaded your updated ISSM source code from Github and re-tried the installation. Below is my feedback on installing petsc, which I think was successfully installed except for the SyntaxWarning which can be ignored.

......
=========================================
Now to install the libraries do:
make PETSC_DIR=/c/ISSM/externalpackages/petsc/src PETSC_ARCH=arch-mswin-c-opt install
=========================================
*** Using PETSC_DIR=/c/ISSM/externalpackages/petsc/src PETSC_ARCH=arch-mswin-c-opt ***
*** Installing PETSc at prefix location: /c/ISSM/externalpackages/petsc/install  ***
====================================
Install complete.
Now to check if the libraries are working do (in current directory):
make PETSC_DIR=/c/ISSM/externalpackages/petsc/install PETSC_ARCH="" check
====================================
/usr/bin/make  --no-print-directory -f makefile PETSC_ARCH=arch-mswin-c-opt PETSC_DIR=/c/ISSM/externalpackages/petsc/src mpi4py-install petsc4py-install libmesh-install mfem-install slepc-install hpddm-install amrex-install bamg-install
make[2]: Nothing to be done for 'mpi4py-install'.
make[2]: Nothing to be done for 'petsc4py-install'.
make[2]: Nothing to be done for 'libmesh-install'.
make[2]: Nothing to be done for 'mfem-install'.
make[2]: Nothing to be done for 'slepc-install'.
make[2]: Nothing to be done for 'hpddm-install'.
make[2]: Nothing to be done for 'amrex-install'.
make[2]: Nothing to be done for 'bamg-install'.

The feedback after installing triangle is as follows:

Archive:  triangle.zip
  inflating: src/A.poly
  inflating: src/README
  inflating: src/makefile
  inflating: src/showme.c
  inflating: src/triangle.c
  inflating: src/triangle.h
  inflating: src/tricall.c
patching file src/triangle.c
patching file src/triangle.h
patching file src/triangle.h
Hunk #1 succeeded at 253 (offset -6 lines).
gcc  -DNO_TIMER -fpic -DTRILIBRARY -shared -o libtriangle.dll triangle.c
triangle.c: In function 'printtriangle':
triangle.c:3681:50: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3681 |   printf("triangle x%lx with orientation %d:\n", (unsigned long) t->tri,
      |                                                  ^
triangle.c:3687:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3687 |     printf("    [0] = x%lx  %d\n", (unsigned long) printtri.tri,
      |                                    ^
triangle.c:3694:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3694 |     printf("    [1] = x%lx  %d\n", (unsigned long) printtri.tri,
      |                                    ^
triangle.c:3701:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3701 |     printf("    [2] = x%lx  %d\n", (unsigned long) printtri.tri,
      |                                    ^
triangle.c:3710:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3710 |            (t->orient + 1) % 3 + 3, (unsigned long) printvertex,
      |                                     ^
triangle.c:3717:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3717 |            (t->orient + 2) % 3 + 3, (unsigned long) printvertex,
      |                                     ^
triangle.c:3724:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3724 |            t->orient + 3, (unsigned long) printvertex,
      |                           ^
triangle.c:3730:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3730 |       printf("    [6] = x%lx  %d\n", (unsigned long) printsh.ss,
      |                                      ^
triangle.c:3735:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3735 |       printf("    [7] = x%lx  %d\n", (unsigned long) printsh.ss,
      |                                      ^
triangle.c:3740:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3740 |       printf("    [8] = x%lx  %d\n", (unsigned long) printsh.ss,
      |                                      ^
triangle.c: In function 'printsubseg':
triangle.c:3776:10: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3776 |          (unsigned long) s->ss, s->ssorient, mark(*s));
      |          ^
triangle.c:3781:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3781 |     printf("    [0] = x%lx  %d\n", (unsigned long) printsh.ss,
      |                                    ^
triangle.c:3788:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3788 |     printf("    [1] = x%lx  %d\n", (unsigned long) printsh.ss,
      |                                    ^
triangle.c:3797:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3797 |            2 + s->ssorient, (unsigned long) printvertex,
      |                             ^
triangle.c:3804:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3804 |            3 - s->ssorient, (unsigned long) printvertex,
      |                             ^
triangle.c:3811:36: warning: cast from p

I don't know if this feedback means the success or failure of the installation, please interpret it.

justinquinn

wudipao88 Hi, yes both look good. Go ahead and try the ISSM configuration and compile.

wudipao88

justinquinn OK. I tried configuration and ran the following configuration code:

./configure \
	--prefix=${ISSM_DIR} \
	--with-numthreads=4 \
	--with-vendor="win-msys2" \
	--with-matlab-dir=${MATLAB_PATH} \
	--with-mpi-include="${MSMPI_ROOT}/include" \
	--with-mpi-libdir="${MSMPI_ROOT}/lib" \
	--with-mpi-libflags="-lmsmpi" \
	--with-fortran-lib="-L/c/msys64/mingw64/lib -lgfortran" \
	--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="${ISSM_DIR}/externalpackages/triangle/install" \
	--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install"

The feedback given is as follows:

configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: Files/MATLAB/R2024a
configure: WARNING: unrecognized options: --with-vendor
configure: loading site script /etc/config.site
configure: ============================================================================
configure: =      Ice-sheet and Sea-level System Model (ISSM) 4.24 configuration      =
configure: ============================================================================
checking build system type... Invalid configuration 'Files/MATLAB/R2024a': machine 'Files/MATLAB/R2024a-unknown' not recognized
configure: error: /bin/sh ././aux-config/config.sub Files/MATLAB/R2024a failed
./configure: line 40: sort: No such file or directory
./configure: line 37: sed: No such file or directory

justinquinn

wudipao88 Looks like you might need double quotes around the path that MATLAB_PATH is set to? We define it like this,

MATLAB_PATH=$(cygpath -u $(cygpath -ms "/c/Program Files/MATLAB/R2023b"))

If it's in your ./bash_profile/.bashrc (or anywhere else, really) you will need to export it. It looks like it's being picked up, but that the spaces in the path are not being escaped.