enable building of spack issm installation with wrappers

packages/access-triangle/package.py

@@ -0,0 +1,84 @@
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+# ----------------------------------------------------------------------------
+#
+#     spack install access-triangle-git
+#
+# You can edit this file again by typing:
+#
+#     spack edit access-triangle-git
+#
+# ----------------------------------------------------------------------------
+
+from spack.package import *
+import glob
+import os
+
+
+class AccessTriangle(MakefilePackage):
+    """Spack package for the ISSM Triangle library."""
+
+    homepage = "https://github.com/ACCESS-NRI/issm-triangle"
+    git = 'https://github.com/ACCESS-NRI/issm-triangle.git'
+
+    version('main')
+
+    # # If on some systems 'gmake' is truly required, keep it. Otherwise, 'make'
+    # # is often sufficient because Spack sets MAKE appropriately.
+    depends_on('gmake',  type='build')
+    depends_on('libx11', type='link')
+
+    def url_for_version(self, version):
+        return "https://github.com/ACCESS-NRI/issm-triangle/archive/refs/heads/{0}.tar.gz".format(version)
+
+    def edit(self, spec, prefix):
+        """
+        Below, we just copy in the 'configs'
+        so that the build can find them in `self.build_directory`.
+        """
+        src_dir = join_path(self.stage.source_path, "src")
+        mkdirp(src_dir)
+
+        # Copy necessary files to src directory
+        install('configs/makefile', src_dir)
+        install('configs/linux/configure.make', src_dir)
+        install('triangle.c', src_dir)
+        install('triangle.h', src_dir)
+
+    def build(self, spec, prefix):
+        """
+        This is where we actually call `make shared`.
+        Using MakefilePackage, you *could* rely on build_targets,
+        but we'll be explicit here so you can see it clearly.
+        """
+        with working_dir(join_path(self.stage.source_path, "src")):
+            make('shared')
+
+        #raise an exception
+
+    def install(self, spec, prefix):
+        """
+        Copy the resulting library and headers into the Spack prefix.
+        """
+        src = join_path(self.stage.source_path, "src")
+
+        # Create prefix directories
+        mkdirp(prefix.include)
+        mkdirp(prefix.lib)
+
+        with working_dir(src):
+            # Make sure we see what's actually there, for debugging:
+            ls_output = Executable('ls')('-l', '.', output=str, error=str)
+            print("Files in build directory:\n", ls_output)
+
+            install('triangle.h', prefix.include)
+
+            for libfile in glob.glob("libtriangle.*"):
+                install(libfile, prefix.lib)
+
+
+
+
+

packages/issm/package.py

@@ -1,57 +1,137 @@
-# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
-# Spack Project Developers. See the top-level COPYRIGHT file for details.
+# Copyright 2013-2023 Lawrence Livermore National Security, 
+# LLC and other Spack Project Developers. See the top-level COPYRIGHT 
+# file for details.
 #
 # Copyright 2023 Angus Gibson
+# Modified by Justin Kin Jun Hew, 2025
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack.package import *
+import os 
+import subprocess
 
 
 class Issm(AutotoolsPackage):
     """Ice-sheet and Sea-Level System Model"""
 
     homepage = "https://issm.jpl.nasa.gov/"
-    git = "https://github.com/ISSMteam/ISSM.git"
+    git      = "https://github.com/ACCESS-NRI/ISSM.git"
 
-    version("develop")
-    version("4.24", sha256="0487bd025f37be4a39dfd48b047de6a6423e310dfe5281dbd9a52aa35b26151a")
+    #version("4.24", sha256="c71d870e63f0ce3ae938d6a669e80dc2cecef827084db31a4b2cfc3a26a44820")
+
+    version("main", branch="main", git="https://github.com/ACCESS-NRI/ISSM.git")
+    version("access-development", branch="access-development", git="https://github.com/ACCESS-NRI/ISSM.git")
 
+    #
+    # Variants
+    #
+    variant("wrappers", default=False,
+            description="Enable building with MPI wrappers")
+
+    # If you want to make external Fortran linking optional or specialized,
+    # you can create a separate variant for it, but typically you might
+    # rely on Spack's compiler wrappers for Fortran libraries.
+
+    #
+    # Build dependencies
+    #
     depends_on("autoconf", type="build")
     depends_on("automake", type="build")
-    depends_on("libtool", type="build")
-    depends_on("m4", type="build")
-
+    depends_on("libtool",  type="build")
+    depends_on("m4",       type="build")
+
+    # Required libraries
+    #
     depends_on("mpi")
     depends_on("petsc+metis+mumps+scalapack")
     depends_on("m1qn3")
 
+    #
+    # Optional libraries
+    #
+    depends_on('access-triangle', when='+wrappers')
+    depends_on("parmetis",  when="+wrappers")
+    # depends_on("python@3.9.0:3.9", when="+wrappers", type=("build", "run"))
+    # depends_on("py-numpy",         when="+wrappers", type=("build", "run"))
+
     def url_for_version(self, version):
-        return "https://github.com/ISSMteam/ISSM/tarball/v{0}".format(version)
+        # Example of how you might form a URL for a particular version:
+        #branch = "access-development"
+        return "https://github.com/ACCESS-NRI/ISSM/archive/refs/heads/{0}.tar.gz".format(version)
 
     def autoreconf(self, spec, prefix):
+        # If the repo has an Autotools build system, run autoreconf:
         autoreconf("--install", "--verbose", "--force")
+
+    def setup_run_environment(self, env):
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
 
     def configure_args(self):
+        """Populate configure arguments, including optional flags to mimic 
+        your manual `./configure` invocation on Gadi."""
         args = [
-          "--with-wrappers=no",
-          "--enable-debugging",
-          "--enable-development",
-          "--enable-shared",
-          "--without-kriging",
+            "--enable-debugging",
+            "--enable-development",
+            "--enable-shared",
+            "--without-kriging",
         ]
-        args.append("--with-petsc-dir={0}".format(self.spec["petsc"].prefix))
-        args.append("--with-metis-dir={0}".format(self.spec["metis"].prefix))
-        args.append("--with-mumps-dir={0}".format(self.spec["mumps"].prefix))
-        args.append("--with-m1qn3-dir={0}".format(self.spec["m1qn3"].prefix.lib))
 
-        # Even though we set the MPI compilers manually, the build system
-        # wants us to explicitly request an MPI-enabled build by telling
-        # it the MPI include directory.
+        #
+        # Wrappers
+        #
+        if "+wrappers" in self.spec:
+            args.append("--with-wrappers=yes")
+        else:
+            args.append("--with-wrappers=no")
+
+        #
+        # MPI: Even if we use Spack's MPI wrappers, the build system may 
+        # want explicit mention of MPI includes and compilers:
+        #
         args.append("--with-mpi-include={0}".format(self.spec["mpi"].prefix.include))
         args.append("CC=" + self.spec["mpi"].mpicc)
         args.append("CXX=" + self.spec["mpi"].mpicxx)
         args.append("FC=" + self.spec["mpi"].mpifc)
         args.append("F77=" + self.spec["mpi"].mpif77)
 
+        #
+        # PETSc, MUMPS, METIS, SCALAPACK, etc.
+        # (Spack typically puts these in the compiler/link environment,
+        #  but if the ISSM configure script looks for explicit --with-* 
+        #  flags, we pass them.)
+        #
+        args.append("--with-petsc-dir={0}".format(self.spec["petsc"].prefix))
+        args.append("--with-metis-dir={0}".format(self.spec["metis"].prefix))
+        args.append("--with-mumps-dir={0}".format(self.spec["mumps"].prefix))
+        # If you rely on sca/lapack from PETSc, these lines might 
+        # not be strictly necessary. If ISSM's configure script 
+        # checks them individually, add them:
+        args.append("--with-scalapack-dir={0}".format(self.spec["scalapack"].prefix))
+        args.append("--with-parmetis-dir={0}".format(self.spec["parmetis"].prefix))
+        args.append("--with-triangle-dir={0}".format(self.spec["access-triangle"].prefix))
+
+        #
+        # M1QN3
+        #
+        # Some codes want the actual library subdir for m1qn3, 
+        # e.g. "prefix.lib" or "prefix" depending on the configure logic:
+        #
+        args.append("--with-m1qn3-dir={0}".format(self.spec["m1qn3"].prefix.lib))
+        args.append("--with-python-version=3.9")
+        args.append("--with-python-dir=/apps/python3/3.9.2")
+
+
+        numpy_site_packages = "/apps/python3/3.9.2/lib/python3.9/site-packages/numpy-1.20.0-py3.9-linux-x86_64.egg/numpy"
+        numpy_core_dir = "/apps/python3/3.9.2/lib/python3.9/site-packages/numpy-1.20.0-py3.9-linux-x86_64.egg/numpy"
+        args.append("--with-python-numpy-dir={0}".format(numpy_core_dir))
+
         return args
+
+    def install(self, spec, prefix):
+        # Run the normal Autotools install logic
+        super().install(spec, prefix)
+
+        # Copy the entire source tree into an additional directory
+        install_tree(self.stage.source_path, prefix.src)
+