Ufs hera update

var/spack/repos/builtin/packages/bacio/package.py

@@ -7,7 +7,7 @@
 
 
 class Bacio(CMakePackage):
-    """The bacio ibrary performs binary I/O for the NCEP models, processing
+    """The bacio library performs binary I/O for the NCEP models, processing
     unformatted byte-addressable data records, and transforming the little
     endian files and big endian files."""
 
@@ -39,3 +39,6 @@ def cmake_args(self):
         args = [self.define_from_variant("CMAKE_POSITION_INDEPENDENT_CODE", "pic")]
 
         return args
+
+    def patch(self):
+        filter_file('2\.4\.0',str(self.spec.version),"VERSION",when="bacio@2.4.1")

var/spack/repos/builtin/packages/esmf/package.py

@@ -4,6 +4,7 @@
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
+import subprocess
 
 from spack.package import *
 
@@ -88,6 +89,7 @@ class Esmf(MakefilePackage):
         when="@8.3.0b09",
     )
     variant("debug", default=False, description="Make a debuggable version of the library")
+    variant("shared", default=True, description="Build shared library")
 
     # Required dependencies
     depends_on("zlib")
@@ -310,6 +312,11 @@ def edit(self, spec, prefix):
             # NetCDF format.
             os.environ["ESMF_NETCDF"] = "nc-config"
             os.environ["ESMF_NFCONFIG"] = "nf-config"
+            if spec["netcdf-c"].satisfies("~shared"):
+                nc_pc_cmd = ["nc-config","--static","--libs"]
+                nc_flags = \
+                  subprocess.check_output(nc_pc_cmd, encoding="utf8").strip()
+                os.environ["ESMF_NETCDF_LIBS"] = nc_flags
 
         ###################
         # Parallel-NetCDF #
@@ -356,6 +363,9 @@ def edit(self, spec, prefix):
             # ESMF_XERCES_INCLUDE
             # ESMF_XERCES_LIBPATH
 
+        if "~shared" in spec:
+            os.environ["ESMF_SHARED_LIB_BUILD"] = "OFF"
+
     @run_after("install")
     def install_findesmf(self):
         install_tree("cmake", self.prefix.cmake)

var/spack/repos/builtin/packages/hdf5/package.py

@@ -573,6 +573,12 @@ def fix_package_config(self):
             backup=False,
         )
 
+        # HDF5 build incorrectly assign -l to zlib file path
+        filter_file(
+            "-l(/[^\s]+/libz\.a)", r"\1 -lz",
+            *pc_files, when="~shared"
+        )
+
         # Create non-versioned symlinks to the versioned pkg-config files:
         with working_dir(self.prefix.lib.pkgconfig):
             for f in pc_files:

var/spack/repos/builtin/packages/libpng/package.py

@@ -26,6 +26,8 @@ class Libpng(AutotoolsPackage):
 
     depends_on("zlib@1.0.4:")  # 1.2.5 or later recommended
 
+    variant("shared", default=True)
+
     def configure_args(self):
         args = [
             # not honored, see
@@ -34,6 +36,7 @@ def configure_args(self):
             f"CPPFLAGS={self.spec['zlib'].headers.include_flags}",
             f"LDFLAGS={self.spec['zlib'].libs.search_flags}",
         ]
+        if "~shared" in self.spec: args += ["--enable-static","--disable-shared"]
         return args
 
     def check(self):

var/spack/repos/builtin/packages/nccmp/package.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 from spack.package import *
+import subprocess
 
 
 class Nccmp(CMakePackage):
@@ -17,6 +18,7 @@ class Nccmp(CMakePackage):
 
     depends_on("cmake@3.12:", type="build")
     depends_on("netcdf-c", type=("build", "run"))
+    depends_on("mpi", when="^netcdf-c+mpi~shared")
 
     def cmake_args(self):
         args = []
@@ -28,4 +30,18 @@ def cmake_args(self):
         if cflags:
             args.append(self.define("CMAKE_C_FLAGS", " ".join(cflags)))
 
+        nc = self.spec["netcdf-c"]
+        if "~shared" in nc:
+            nc_pc_cmd = ["nc-config","--static","--libs"]
+            nc_flags = \
+              subprocess.check_output(nc_pc_cmd, encoding="utf8").strip()
+            args.append(self.define("CMAKE_EXE_LINKER_FLAGS", nc_flags))
+            if "+mpi" in nc:
+                args.append(
+                  self.define(
+                    "CMAKE_C_COMPILER",
+                    self.spec["mpi"].mpicc
+                  )
+                )
+
         return args

var/spack/repos/builtin/packages/netcdf-fortran/package.py

@@ -6,6 +6,7 @@
 import glob
 import os
 from shutil import Error, copyfile
+import subprocess
 
 from spack.package import *
 
@@ -36,6 +37,7 @@ class NetcdfFortran(AutotoolsPackage):
     depends_on("netcdf-c")
     depends_on("netcdf-c@4.7.4:", when="@4.5.3:")  # nc_def_var_szip required
     depends_on("doxygen", when="+doc", type="build")
+    depends_on("mpi", when="^hdf5~shared+mpi")
 
     # The default libtool.m4 is too old to handle NAG compiler properly:
     # https://github.com/Unidata/netcdf-fortran/issues/94
@@ -134,6 +136,26 @@ def configure_args(self):
                 # configuration failure, we set the following cache variable:
                 config_args.append("ac_cv_func_MPI_File_open=yes")
 
+        if "~shared" in netcdf_c_spec:
+            netcdf_libs_cmd = ["pkg-config","netcdf","--libs"]
+            netcdf_libs = subprocess.check_output(netcdf_libs_cmd, encoding="utf-8").strip()
+            config_args.append("LIBS=" + netcdf_libs)
+
+            netcdf_ldflags_cmd = ["pkg-config","netcdf","--libs-only-L"]
+            netcdf_ldflags = \
+              subprocess.check_output(netcdf_ldflags_cmd, encoding="utf8").strip()
+            config_args.append("LDFLAGS=" + netcdf_ldflags)
+
+            netcdf_cflags_cmd = ["pkg-config","netcdf","--cflags"]
+            netcdf_cflags = \
+              subprocess.check_output(netcdf_cflags_cmd, encoding="utf8").strip()
+            config_args.append("CPPFLAGS=" + netcdf_cflags)
+
+        if "~shared" in self.spec:
+            config_args.append("CC=%s" % self.spec["mpi"].mpicc)
+            config_args.append("FC=%s" % self.spec["mpi"].mpifc)
+            config_args.append("F77=%s" % self.spec["mpi"].mpif77)
+
         return config_args
 
     @run_after("configure")

var/spack/repos/jcsda-emc/packages/mapl/package.py

@@ -3,6 +3,8 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import subprocess
+
 from spack.package import *
 
 
@@ -62,12 +64,14 @@ class Mapl(CMakePackage):
     variant("shared", default=True)
     variant("debug", default=False, description="Make a debuggable version of the library")
     variant("extdata2g", default=False, description="Use ExtData2G")
+    variant("pnetcdf", default=True, description="Use parallel netCDF")
 
     depends_on("cmake@3.17:")
     depends_on("mpi")
     depends_on("hdf5")
     depends_on("netcdf-c")
     depends_on("netcdf-fortran")
+    depends_on("parallel-netcdf", when="+pnetcdf")
     depends_on("esmf@8.3:", when="@2.22:")
     depends_on("esmf", when="@:2.12.99")
     depends_on("esmf~debug", when="~debug")
@@ -107,3 +111,11 @@ def cmake_args(self):
             args.append(self.define("CMAKE_Fortran_FLAGS", " ".join(fflags)))
 
         return args
+
+    def patch(self):
+        if "~shared" in self.spec["netcdf-c"]:
+            nc_pc_cmd = ["nc-config","--static","--libs"]
+            nc_flags = \
+              subprocess.check_output(nc_pc_cmd, encoding="utf8").strip()
+            filter_file("(target_link_libraries[^)]+PUBLIC )", \
+              r'\1 %s '%nc_flags, "pfio/CMakeLists.txt")