nwchem: add master (#48919)

* Add possibility to build nwchem from master branch

* add oneapi@2025: patch for @7.2.3

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>

lib/spack/docs/build_settings.rst

@@ -34,7 +34,6 @@ an object, with the following keys:
 
 1. ``roots``: if ``true`` root specs are reused, if ``false`` only dependencies of root specs are reused
 2. ``from``: list of sources from which reused specs are taken
-3. ``namespaces``: list of namespaces from which to reuse specs, or the string ``"any"``.
 
 Each source in ``from`` is itself an object:
 
@@ -57,7 +56,6 @@ For instance, the following configuration:
    concretizer:
      reuse:
        roots: true
-       namespaces: [builtin]
        from:
        - type: local
          include:
@@ -65,8 +63,7 @@ For instance, the following configuration:
          - "%clang"
 
 tells the concretizer to reuse all specs compiled with either ``gcc`` or ``clang``, that are installed
-in the local store. Any spec from remote buildcaches is disregarded. Any spec from a namespace other than
+in the local store. Any spec from remote buildcaches is disregarded.
-Spack's builtin repo is disregarded.
 
 To reduce the boilerplate in configuration files, default values for the ``include`` and
 ``exclude`` options can be pushed up one level:

lib/spack/spack/package_base.py

@@ -2284,14 +2284,6 @@ def rpath_args(self):
 build_system_flags = PackageBase.build_system_flags
 
 
-def use_cray_compiler_names():
-    """Compiler names for builds that rely on cray compiler names."""
-    os.environ["CC"] = "cc"
-    os.environ["CXX"] = "CC"
-    os.environ["FC"] = "ftn"
-    os.environ["F77"] = "ftn"
-
-
 def possible_dependencies(
     *pkg_or_spec: Union[str, spack.spec.Spec, typing.Type[PackageBase]],
     transitive: bool = True,

lib/spack/spack/schema/concretizer.py

@@ -25,12 +25,6 @@
                             "roots": {"type": "boolean"},
                             "include": LIST_OF_SPECS,
                             "exclude": LIST_OF_SPECS,
-                            "namespaces": {
-                                "oneOf": [
-                                    {"type": "string", "enum": ["any"]},
-                                    {"type": "array", "items": {"type": "string"}},
-                                ]
-                            },
                             "from": {
                                 "type": "array",
                                 "items": {

lib/spack/spack/solver/asp.py

@@ -3986,7 +3986,6 @@ def __init__(self, configuration: spack.config.Configuration) -> None:
         self.configuration = configuration
         self.store = spack.store.create(configuration)
         self.reuse_strategy = ReuseStrategy.ROOTS
-        self.reuse_namespaces = "any"
 
         reuse_yaml = self.configuration.get("concretizer:reuse", False)
         self.reuse_sources = []
@@ -4017,7 +4016,6 @@ def __init__(self, configuration: spack.config.Configuration) -> None:
                 self.reuse_strategy = ReuseStrategy.ROOTS
             else:
                 self.reuse_strategy = ReuseStrategy.DEPENDENCIES
-            self.reuse_namespaces = reuse_yaml.get("namespaces", "any")
             default_include = reuse_yaml.get("include", [])
             default_exclude = reuse_yaml.get("exclude", [])
             default_sources = [{"type": "local"}, {"type": "buildcache"}]
@@ -4085,9 +4083,6 @@ def reusable_specs(self, specs: List[spack.spec.Spec]) -> List[spack.spec.Spec]:
         if self.reuse_strategy == ReuseStrategy.DEPENDENCIES:
             result = [spec for spec in result if not any(root in spec for root in specs)]
 
-        if self.reuse_namespaces != "any":
-            result = [spec for spec in result if spec.namespace in self.reuse_namespaces]
-
         return result
 
 

lib/spack/spack/test/concretization/core.py

@@ -1460,35 +1460,6 @@ def test_no_reuse_when_variant_condition_does_not_hold(self, mutable_database, m
         new2 = spack.concretize.concretize_one("conditional-variant-pkg +two_whens")
         assert new2.satisfies("@2 +two_whens +version_based")
 
-    def test_reuse_by_namespace(self, mutable_database, mock_packages):
-        spack.config.set("concretizer:reuse", True)
-        # Set spack to prefer an older version when doing new builds, but prioritize reuse higher
-        spack.config.set("packages:libelf", {"version": ["0.8.10"]})
-
-        # Expected behavior is to reuse the libelf@0.8.13 from mutable database
-        # despite configured preference for older version
-        reuse = spack.concretize.concretize_one("libelf")
-        assert reuse.installed
-        assert reuse.satisfies("@0.8.13")
-
-        # Reuse is turned off, so preference will be respected
-        spack.config.set("concretizer:reuse", {"namespaces": []})
-        noreuse = spack.concretize.concretize_one("libelf")
-        assert not noreuse.installed
-        assert noreuse.satisfies("@0.8.10")
-
-        # Expected behavior same as first concretization
-        spack.config.set("concretizer:reuse", {"namespaces": ["builtin.mock"]})
-        noreuse = spack.concretize.concretize_one("libelf")
-        assert noreuse.installed
-        assert noreuse.satisfies("@0.8.13")
-
-        # Expected behavior same as second concretization
-        spack.config.set("concretizer:reuse", {"namespaces": ["foobar"]})
-        noreuse = spack.concretize.concretize_one("libelf")
-        assert not noreuse.installed
-        assert noreuse.satisfies("@0.8.10")
-
     def test_reuse_with_flags(self, mutable_database, mutable_config):
         spack.config.set("concretizer:reuse", True)
         spec = spack.concretize.concretize_one("pkg-a cflags=-g cxxflags=-g")

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

@@ -148,6 +148,14 @@ class Ascent(CMakePackage, CudaPackage):
     # https://github.com/Alpine-DAV/ascent/pull/1123
     patch("ascent-find-raja-pr1123.patch", when="@0.9.0")
 
+    # patch for fix typo in coord_type
+    # https://github.com/Alpine-DAV/ascent/pull/1408
+    patch(
+        "https://github.com/Alpine-DAV/ascent/pull/1408.patch?full_index=1",
+        when="@0.9.3 %oneapi@2025:",
+        sha256="7de7f51e57f3d743c39ad80d8783a4eb482be1def51eb2d3f9259246c661f164",
+    )
+
     ##########################################################################
     # package dependencies
     ###########################################################################
@@ -468,6 +476,9 @@ def hostconfig(self):
         if cflags:
             cfg.write(cmake_cache_entry("CMAKE_C_FLAGS", cflags))
         cxxflags = cppflags + " ".join(spec.compiler_flags["cxxflags"])
+        if spec.satisfies("%oneapi@2025:"):
+            cxxflags += "-Wno-error=missing-template-arg-list-after-template-kw "
+            cxxflags += "-Wno-missing-template-arg-list-after-template-kw"
         if cxxflags:
             cfg.write(cmake_cache_entry("CMAKE_CXX_FLAGS", cxxflags))
         fflags = " ".join(spec.compiler_flags["fflags"])

var/spack/repos/builtin/packages/libgcrypt/o_flag_munging-1.10.patch

@@ -0,0 +1,39 @@
+From 7cea256ef1a6017e722bdfd5b7381fa90580d55a Mon Sep 17 00:00:00 2001
+From: "simit.ghane" <simit.ghane@lge.com>
+Date: Tue, 7 May 2024 14:09:03 +0530
+Subject: [PATCH] fix o_flag_munging
+
+---
+ cipher/Makefile.am | 2 +-
+ random/Makefile.am | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cipher/Makefile.am b/cipher/Makefile.am
+index c3d642b2..04bf25e9 100644
+--- a/cipher/Makefile.am
++++ b/cipher/Makefile.am
+@@ -153,7 +153,7 @@ gost-s-box: gost-s-box.c
+ 
+ 
+ if ENABLE_O_FLAG_MUNGING
+-o_flag_munging = sed -e 's/-O\([2-9sgz][2-9sgz]*\)/-O1/' -e 's/-Ofast/-O1/g'
++o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /g' -e 's/[[:blank:]]-Ofast/ -O1 /g'
+ else
+ o_flag_munging = cat
+ endif
+diff --git a/random/Makefile.am b/random/Makefile.am
+index 0c935a05..a42e4306 100644
+--- a/random/Makefile.am
++++ b/random/Makefile.am
+@@ -56,7 +56,7 @@ jitterentropy-base.c jitterentropy.h jitterentropy-base-user.h
+ 
+ # The rndjent module needs to be compiled without optimization.  */
+ if ENABLE_O_FLAG_MUNGING
+-o_flag_munging = sed -e 's/-O\([1-9sgz][1-9sgz]*\)/-O0/g' -e 's/-Ofast/-O0/g'
++o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /g' -e 's/[[:blank:]]-Ofast/ -O0 /g'
+ else
+ o_flag_munging = cat
+ endif
+-- 
+2.43.0
+

var/spack/repos/builtin/packages/libgcrypt/o_flag_munging-1.11.patch

@@ -0,0 +1,50 @@
+From 9c11f1e12a6ddbd49b5fd38c94e6a004f8da6e29 Mon Sep 17 00:00:00 2001
+From: "simit.ghane" <simit.ghane@lge.com>
+Date: Tue, 11 Jun 2024 07:22:28 +0530
+Subject: [PATCH] random:cipher: handle substitution in sed command
+
+* cipher/Makefile.am (o_flag_munging): Add 'g' flag for first sed
+expression.
+* random/Makefile.am (o_flag_munging): Likewise.
+--
+
+It was there earlier and accidentally removed from
+Makefile.am of cipher and random
+
+Signed-off-by: simit.ghane <simit.ghane@lge.com>
+[jk: add changelog to commit message]
+Signed-off-by: Jussi Kivilinna <jussi.kivilinna@iki.fi>
+---
+ cipher/Makefile.am | 2 +-
+ random/Makefile.am | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cipher/Makefile.am b/cipher/Makefile.am
+index ea9014cc..149c9f21 100644
+--- a/cipher/Makefile.am
++++ b/cipher/Makefile.am
+@@ -169,7 +169,7 @@ gost-s-box$(EXEEXT_FOR_BUILD): gost-s-box.c
+ 
+ 
+ if ENABLE_O_FLAG_MUNGING
+-o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /' -e 's/[[:blank:]]-Ofast/ -O1 /g'
++o_flag_munging = sed -e 's/[[:blank:]]-O\([2-9sgz][2-9sgz]*\)/ -O1 /g' -e 's/[[:blank:]]-Ofast/ -O1 /g'
+ else
+ o_flag_munging = cat
+ endif
+diff --git a/random/Makefile.am b/random/Makefile.am
+index c7100ef8..a42e4306 100644
+--- a/random/Makefile.am
++++ b/random/Makefile.am
+@@ -56,7 +56,7 @@ jitterentropy-base.c jitterentropy.h jitterentropy-base-user.h
+ 
+ # The rndjent module needs to be compiled without optimization.  */
+ if ENABLE_O_FLAG_MUNGING
+-o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /' -e 's/[[:blank:]]-Ofast/ -O0 /g'
++o_flag_munging = sed -e 's/[[:blank:]]-O\([1-9sgz][1-9sgz]*\)/ -O0 /g' -e 's/[[:blank:]]-Ofast/ -O0 /g'
+ else
+ o_flag_munging = cat
+ endif
+-- 
+2.43.0
+

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

@@ -17,26 +17,26 @@ class Libgcrypt(AutotoolsPackage):
 
     version("1.11.0", sha256="09120c9867ce7f2081d6aaa1775386b98c2f2f246135761aae47d81f58685b9c")
     version("1.10.3", sha256="8b0870897ac5ac67ded568dcfadf45969cfa8a6beb0fd60af2a9eadc2a3272aa")
-    version("1.10.2", sha256="3b9c02a004b68c256add99701de00b383accccf37177e0d6c58289664cce0c03")
-    version("1.10.1", sha256="ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de")
-    version("1.10.0", sha256="6a00f5c05caa4c4acc120c46b63857da0d4ff61dc4b4b03933fa8d46013fae81")
 
-    # End of life: 2024-03-31
     with default_args(deprecated=True):
-        version("1.9.4", sha256="ea849c83a72454e3ed4267697e8ca03390aee972ab421e7df69dfe42b65caaf7")
+        version(
-        version("1.9.3", sha256="97ebe4f94e2f7e35b752194ce15a0f3c66324e0ff6af26659bbfb5ff2ec328fd")
+            "1.10.2", sha256="3b9c02a004b68c256add99701de00b383accccf37177e0d6c58289664cce0c03"
-        version("1.9.2", sha256="b2c10d091513b271e47177274607b1ffba3d95b188bbfa8797f948aec9053c5a")
+        )
-        version("1.9.1", sha256="c5a67a8b9b2bd370fb415ed1ee31c7172e5683076493cf4a3678a0fbdf0265d9")
+        version(
+            "1.10.1", sha256="ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de"
+        )
+        version(
+            "1.10.0", sha256="6a00f5c05caa4c4acc120c46b63857da0d4ff61dc4b4b03933fa8d46013fae81"
+        )
+        # End of life: 2024-12-31 (LTS)
+        version("1.8.9", sha256="2bda4790aa5f0895d3407cf7bf6bd7727fd992f25a45a63d92fef10767fa3769")
+        version("1.8.7", sha256="03b70f028299561b7034b8966d7dd77ef16ed139c43440925fe8782561974748")
+        version("1.8.6", sha256="0cba2700617b99fc33864a0c16b1fa7fdf9781d9ed3509f5d767178e5fd7b975")
+        version("1.8.5", sha256="3b4a2a94cb637eff5bdebbcaf46f4d95c4f25206f459809339cdada0eb577ac3")
+        version("1.8.4", sha256="f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227")
+        version("1.8.1", sha256="7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3")
 
-    # End of life: 2024-12-31 (LTS)
+    depends_on("c", type="build")
-    version("1.8.9", sha256="2bda4790aa5f0895d3407cf7bf6bd7727fd992f25a45a63d92fef10767fa3769")
-    version("1.8.7", sha256="03b70f028299561b7034b8966d7dd77ef16ed139c43440925fe8782561974748")
-    version("1.8.6", sha256="0cba2700617b99fc33864a0c16b1fa7fdf9781d9ed3509f5d767178e5fd7b975")
-    version("1.8.5", sha256="3b4a2a94cb637eff5bdebbcaf46f4d95c4f25206f459809339cdada0eb577ac3")
-    version("1.8.4", sha256="f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227")
-    version("1.8.1", sha256="7a2875f8b1ae0301732e878c0cca2c9664ff09ef71408f085c50e332656a78b3")
-
-    depends_on("c", type="build")  # generated
 
     depends_on("libgpg-error@1.25:")
     depends_on("libgpg-error@1.27:", when="@1.9:")
@@ -58,6 +58,9 @@ def flag_handler(self, name, flags):
     # https://git.gnupg.org/cgi-bin/gitweb.cgi?p=libgcrypt.git;a=commit;h=b42116d6067a5233f72e5598032d4b396bb8eaac
     patch("conditional_avx512.patch", when="@1.11.0")
 
+    patch("o_flag_munging-1.10.patch", when="@1.10")
+    patch("o_flag_munging-1.11.patch", when="@1.11")
+
     def check(self):
         # Without this hack, `make check` fails on macOS when SIP is enabled
         # https://bugs.gnupg.org/gnupg/issue2056

var/spack/repos/builtin/packages/nwchem/oneapi2025.patch

@@ -0,0 +1,36 @@
+diff -ruN spack-src/src/config/makefile.h spack-src-patched/src/config/makefile.h
+--- spack-src/src/config/makefile.h	2024-08-28 02:30:22.000000000 +0000
++++ spack-src-patched/src/config/makefile.h	2025-02-07 16:03:07.315882016 +0000
+@@ -2364,15 +2364,14 @@
+ 		    _GOTAVX2 := $(shell cat /proc/cpuinfo | grep fma | tail -n 1 | awk ' /fma/  {print "Y"}')
+ 		    _GOTAVX512F := $(shell cat /proc/cpuinfo | grep avx512f | tail -n 1 | awk ' /avx512f/  {print "Y"}')
+                 endif
+-		_IFCE := $(shell ifort -V  2>&1 |head -1 |awk ' /64/ {print "Y";exit};')
+-		_IFCV7 := $(shell ifort -v  2>&1|grep "Version "|head -n 1|awk ' /7./  {print "Y";exit}')
+-		_IFCV11 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 11) {print "Y";exit}}')
+-		_IFCV12 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 12) {print "Y";exit}}')
+-		_IFCV14 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 14) {print "Y";exit}}')
+-		_IFCV15ORNEWER := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}')
+-	       _IFCV17 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 17) {print "Y";exit}}')
+-	       _IFCV18 := $(shell ifort -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 18) {print "Y";exit}}')
+-
++                _IFCE := $(shell $(FC) -V  2>&1 |head -1 |awk ' /64/ {print "Y";exit};')
++		_IFCV7 := $(shell $(FC) -v  2>&1|grep "Version "|head -n 1|awk ' /7./  {print "Y";exit}')
++		_IFCV11 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 11) {print "Y";exit}}')
++		_IFCV12 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 12) {print "Y";exit}}')
++		_IFCV14 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1|sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 14) {print "Y";exit}}')
++		_IFCV15ORNEWER := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}')
++	        _IFCV17 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 17) {print "Y";exit}}')
++	        _IFCV18 := $(shell $(FC) -logo  2>&1|grep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 18) {print "Y";exit}}')
+ #               Intel EM64T is required
+                 ifneq ($(_IFCE),Y)
+                     defineFCE:
+@@ -2406,7 +2405,7 @@
+ #               CPP=fpp -P
+ #
+                 ifeq ($(_IFCV15ORNEWER), Y)
+-		 IFORTVER := $(shell ifort -v 2>&1|cut -d " " -f 3)
++                 IFORTVER := $(shell $(FC) -v 2>&1|cut -d " " -f 3)
+ #                ifeq ($(IFORTVER),2021.7.0)
+ #                   $(info     )
+ #                   $(info     ifort 2021.7.0 not validated)

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

@@ -13,11 +13,14 @@ class Nwchem(Package):
 
     homepage = "https://nwchemgit.github.io"
     url = "https://github.com/nwchemgit/nwchem/releases/download/v7.2.0-release/nwchem-7.2.0-release.revision-d0d141fd-srconly.2023-03-10.tar.bz2"
+    git = "https://github.com/nwchemgit/nwchem.git"
 
     tags = ["ecp", "ecp-apps"]
 
     maintainers("jeffhammond")
 
+    version("master", branch="master")
+
     version(
         "7.2.3",
         sha256="8cb4ec065215bc0316d8e01f67f1674a572f7d0f565c52e4a327975c04ddb6eb",
@@ -69,6 +72,9 @@ class Nwchem(Package):
         "elpa", default=False, description="Enable optimised diagonalisation routines from ELPA"
     )
 
+    # https://github.com/nwchemgit/nwchem/pull/1034
+    patch("oneapi2025.patch", when="@7.2.3 %oneapi@2025:")
+
     # This patch is for the modification of the build system (e.g. compiler flags) and
     # Fortran syntax to enable the compilation with Fujitsu compilers. The modification
     # will be merged to the next release of NWChem (see https://github.com/nwchemgit/nwchem/issues/347

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

@@ -18,6 +18,7 @@ class Serialbox(CMakePackage):
 
     license("BSD-2-Clause")
 
+    version("2.6.2", sha256="d1b4c79078e3b1d4a45b7b024eb647d21873498ac666e41a5ee8b8e13c95a7ac")
     version("2.6.1", sha256="b795ce576e8c4fd137e48e502b07b136079c595c82c660cfa2e284b0ef873342")
     version("2.6.0", sha256="9199f8637afbd7f2b3c5ba932d1c63e9e14d553a0cafe6c29107df0e04ee9fae")
     version("2.5.4", sha256="f4aee8ef284f58e6847968fe4620e222ac7019d805bbbb26c199e4b6a5094fee")

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

@@ -47,18 +47,16 @@ class Trexio(AutotoolsPackage, CMakePackage):
     depends_on("hdf5@1.8:+hl", when="@:2.3.0 +hdf5")
     depends_on("hdf5@1.8:", when="+hdf5")
 
-    # Append -lhdf5_hl to LIBS when hdf5 variant is activated
-    # or use --without-hdf5 option otherwise.
-
 
 class AutotoolsBuilder(autotools.AutotoolsBuilder):
     def configure_args(self):
         config_args = []
         if "+hdf5" in self.spec:
-            if self.spec("@:2.3.0"):
+            if self.spec.satisfies("@:2.3.0"):
+                # Autotools should take care of adding the necessary flags for HDF5
+                # In older versions, it is not always the case for "hdf5_hl"
+                # Append -lhdf5_hl to LIBS when hdf5 variant is activated
                 config_args.append("LIBS=-lhdf5_hl")
-            else:
-                config.args.append("LIBS=-lhdf5")
         else:
             config_args.append("--without-hdf5")