Merge branch 'master' into eschnett/LaMEM-mpitrampoline

* master: (62 commits) iso_codes v4.10.0 (JuliaPackaging#5226) PTSCOTCH: Require MPItrampoline 5, and build with OpenMPI as well (JuliaPackaging#5180) MAGEMin: Require MPItrampoline 5 (JuliaPackaging#5222) LAMMPS: Require MPItrampoline 5 (JuliaPackaging#5221) CrypoMiniSat: Require MPItrampoline 5 (JuliaPackaging#5219) PETSc: Require MPItrampoline 5 (JuliaPackaging#5223) [SBML] missing functions patch (JuliaPackaging#5224) HYPRE: Require MPItrampoline 5 (JuliaPackaging#5220) openPMD_api: Require MPItrampoline 5 (JuliaPackaging#5218) COSMA: Simplify configuring OpenMPI (JuliaPackaging#5217) AMReX: Require MPItrampoline 5 (JuliaPackaging#5215) Register Elfutils executables. (JuliaPackaging#5214) Wizard recipe: DDSCAT-v7.3.3 (JuliaPackaging#5210) ADIOS2: Require MPItrampoline 5 (JuliaPackaging#5212) Bump compat bounds of Python_jll dependencies. (JuliaPackaging#5211) mpi.jl: Require version 5 of MPItrampoline (JuliaPackaging#5209) [web3go] Add new package (JuliaPackaging#5195) add tls config patch for FLINT 2.9.0 (JuliaPackaging#5207) Upgrade enzyme to refs/tags/v0.0.35 (JuliaPackaging#5200) [PROJ] bump version to 9.0.1 (JuliaPackaging#5208) ...
eschnett · Jul 25, 2022 · ec41da2 · ec41da2
2 parents 0c5a0fc + 4f105bc
commit ec41da2
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diff --git a/A/ADIOS2/build_tarballs.jl b/A/ADIOS2/build_tarballs.jl
@@ -6,12 +6,13 @@ const YGGDRASIL_DIR = "../.."
 include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl"))
 
 name = "ADIOS2"
-version = v"2.8.1"
+version = v"2.8.3"
+adios_version = v"2.8.2"
 
 # Collection of sources required to complete build
 sources = [
-    ArchiveSource("https://github.com/ornladios/ADIOS2/archive/refs/tags/v$(version).tar.gz",
-                  "3f515b442bbd52e3189866b121613fe3b59edb8845692ea86fad83d1eba35d93"),
+    ArchiveSource("https://github.com/ornladios/ADIOS2/archive/refs/tags/v$(adios_version).tar.gz",
+                  "9909f6409dc44b2c28c1fda0042dab4b711f25ec3277ef0cb6ffc40f5483910d"),
     DirectorySource("./bundled"),
 ]
 
@@ -35,11 +36,7 @@ if [[ "$target" == *-apple-* ]]; then
         # and wants to use "-framework" as a stand-alone option. This fails
         # gloriously, and cmake concludes that MPI is not available.
         archopts="-DMPI_C_ADDITIONAL_INCLUDE_DIRS='' -DMPI_C_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lpmpi' -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS='' -DMPI_CXX_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lpmpi'"
-    elif grep -q OMPI_MAJOR_VERSION $prefix/include/mpi.h; then
-        archopts="-DMPI_C_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lopen-rte;-lopen-pal;-lm;-lz' -DMPI_CXX_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lopen-rte;-lopen-pal;-lm;-lz'"
     fi
-elif grep -q OMPI_MAJOR_VERSION $prefix/include/mpi.h; then
-    archopts="-DMPI_C_LIBRARIES='-lmpi;-lopen-rte;-lopen-pal;-lm;-lz' -DMPI_CXX_LIBRARIES='-lmpi;-lopen-rte;-lopen-pal;-lm;-lz'"
 elif [[ "$target" == x86_64-w64-mingw32 ]]; then
     # - The MSMPI Fortran bindings are missing a function; see
     #   <https://github.com/microsoft/Microsoft-MPI/issues/7>
@@ -84,9 +81,7 @@ install_license ../Copyright.txt ../LICENSE
 augment_platform_block = """
     using Base.BinaryPlatforms
     $(MPI.augment)
-    function augment_platform!(platform::Platform)
-        augment_mpi!(platform)
-    end
+    augment_platform!(platform::Platform) = augment_mpi!(platform)
 """
 
 # These are the platforms we will build for by default, unless further

diff --git a/A/AMReX/build_tarballs.jl b/A/AMReX/build_tarballs.jl
@@ -7,7 +7,8 @@ include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl"))
 
 name = "AMReX"
 version_string = "22.07"
-version = VersionNumber(version_string)
+# version = VersionNumber(version_string)
+version = v"22.7.1"
 
 # Collection of sources required to complete build
 sources = [
@@ -83,9 +84,9 @@ dependencies = [
 
 platforms, platform_dependencies = MPI.augment_platforms(platforms)
 # Avoid platforms where the MPI implementation isn't supported
-# AMReX's cmake stage fails with OpenMPI on almost all architectures
-platforms = filter(p -> !(p["mpi"] == "openmpi"), platforms)
-# With MPItrampoline, select only those platforms where MPItrampoline is actually built
+# OpenMPI
+platforms = filter(p -> !(p["mpi"] == "openmpi" && arch(p) == "armv6l" && libc(p) == "glibc"), platforms)
+# MPItrampoline
 platforms = filter(p -> !(p["mpi"] == "mpitrampoline" && (Sys.iswindows(p) || libc(p) == "musl")), platforms)
 platforms = filter(p -> !(p["mpi"] == "mpitrampoline" && Sys.isfreebsd(p)), platforms)
 append!(dependencies, platform_dependencies)

diff --git a/B/Blosc2/build_tarballs.jl b/B/Blosc2/build_tarballs.jl
@@ -3,7 +3,7 @@
 using BinaryBuilder, Pkg
 
 name = "Blosc2"
-version = v"2.0.4"
+version = v"2.2.0"
 
 # Collection of sources required to build Blosc2
 sources = [

diff --git a/B/Btop/build_tarballs.jl b/B/Btop/build_tarballs.jl
@@ -0,0 +1,37 @@
+# Note that this script can accept some limited command-line arguments, run
+# `julia build_tarballs.jl --help` to see a usage message.
+using BinaryBuilder
+
+name = "Btop"
+version = v"1.2.8"
+
+# Collection of sources required to complete build
+sources = [
+    ArchiveSource("https://github.com/aristocratos/btop/archive/refs/tags/v$(version).tar.gz",
+                  "7944b06e3181cc1080064adf1e9eb4f466af0b84a127df6697430736756a89ac"),
+]
+
+# Bash recipe for building across all platforms
+script = raw"""
+cd $WORKSPACE/srcdir/btop*/
+# Don't do lto, doesn't seem to work on FreeBSD
+make -j${nproc} OPTFLAGS="-O2 -ftree-loop-vectorize"
+make install PREFIX=${prefix}
+"""
+
+# These are the platforms we will build for by default, unless further
+# platforms are passed in on the command line
+platforms = expand_cxxstring_abis(supported_platforms(; exclude=Sys.iswindows); skip=Returns(false))
+
+# The products that we will ensure are always built
+products = [
+    ExecutableProduct("btop", :btop)
+]
+
+# Dependencies that must be installed before this package can be built
+dependencies = Dependency[
+]
+
+# Build the tarballs, and possibly a `build.jl` as well.
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
+               julia_compat = "1.6", preferred_gcc_version=v"10")
diff --git a/C/COSMA/build_tarballs.jl b/C/COSMA/build_tarballs.jl
@@ -6,7 +6,7 @@ const YGGDRASIL_DIR = "../.."
 include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl"))
 
 name = "COSMA"
-version = v"2.5.1"
+version = v"2.5.2"
 cosma_version = v"2.5.1"
 
 # Collection of sources required to complete build
@@ -44,18 +44,6 @@ else
     OPENMP_CMAKE_FLAGS=
 fi
 
-MPI_CMAKE_FLAGS=
-if grep -q OMPI_MAJOR_VERSION $prefix/include/mpi.h; then
-    if [[ "$target" == *-apple-* ]]; then
-        # MPI_CMAKE_FLAGS="-DMPI_C_ADDITIONAL_INCLUDE_DIRS='' -DMPI_C_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lopen-rte;-lopen-pal;-lm;-lz' -DMPI_C_LIB_NAMES='mpi;open-rte;open-pal' -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS='' -DMPI_CXX_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs;-lmpi;-lopen-rte;-lopen-pal;-lm;-lz' -DMPI_CXX_LIB_NAMES='mpi;open-rte;open-pal' -DMPI_mpi_LIBRARY=$prefix/lib/libmpi.dylib -DMPI_open-rte_LIBRARY=$prefix/lib/libopen-rte.dylib -DMPI_open-pal_LIBRARY=$prefix/lib/libopen-pal.dylib"
-        MPI_CMAKE_FLAGS="-DMPI_C_ADDITIONAL_INCLUDE_DIRS='' -DMPI_C_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs' -DMPI_C_LIB_NAMES='mpi' -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS='' -DMPI_CXX_LIBRARIES='-Wl,-flat_namespace;-Wl,-commons,use_dylibs' -DMPI_CXX_LIB_NAMES='mpi' -DMPI_mpi_LIBRARY=$prefix/lib/libmpi.dylib"
-    # elif [[ "$target" == powerpc64le-* ]]; then
-    else
-        # MPI_CMAKE_FLAGS="-DMPI_C_ADDITIONAL_INCLUDE_DIRS='' -DMPI_C_LIBRARIES='-Wl,--enable-new-dtags;-lmpi;-lopen-rte;-lopen-pal;-lm;-ldl;-lutil,-lrt' -DMPI_C_LIB_NAMES='mpi;open-rte;open-pal' -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS='' -DMPI_CXX_LIBRARIES='-Wl,--enable-new-dtags;-lmpi;-lopen-rte;-lopen-pal;-lm;-ldl;-lutil,-lrt' -DMPI_CXX_LIB_NAMES='mpi;open-rte;open-pal' -DMPI_mpi_LIBRARY=$prefix/lib/libmpi.so -DMPI_open-rte_LIBRARY=$prefix/lib/libopen-rte.so -DMPI_open-pal_LIBRARY=$prefix/lib/libopen-pal.so"
-        MPI_CMAKE_FLAGS="-DMPI_C_ADDITIONAL_INCLUDE_DIRS='' -DMPI_C_LIBRARIES='-Wl,--enable-new-dtags' -DMPI_C_LIB_NAMES='mpi' -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS='' -DMPI_CXX_LIBRARIES='-Wl,--enable-new-dtags' -DMPI_CXX_LIB_NAMES='mpi' -DMPI_mpi_LIBRARY=$prefix/lib/libmpi.so"
-    fi
-fi
-
 mkdir build
 cd build
 
@@ -75,8 +63,7 @@ cmake ../COSMA-* \
     -DMPI_CXX_COMPILER=$bindir/mpicxx \
     -DOPENBLAS_LIBRARIES=$BLAS_LAPACK_LIB \
     -DOPENBLAS_INCLUDE_DIR=$includedir \
-    $OPENMP_CMAKE_FLAGS \
-    $MPI_CMAKE_FLAGS
+    $OPENMP_CMAKE_FLAGS
 
 make -j${nproc}
 make install

diff --git a/C/CSB/build_tarballs.jl b/C/CSB/build_tarballs.jl
@@ -0,0 +1,38 @@
+# Note that this script can accept some limited command-line arguments, run
+# `julia build_tarballs.jl --help` to see a usage message.
+using BinaryBuilder, BinaryBuilderBase, Pkg
+
+name = "CSB"
+version = v"1.0.0"
+
+# Collection of sources required to complete build
+sources = [
+    GitSource("https://github.com/fcdimitr/CSB.git", "ccab7d424fd7e5bfee4ebdb750dfa219228c7a56")
+]
+
+# Bash recipe for building across all platforms
+script = raw"""
+cd $WORKSPACE/srcdir/CSB/
+meson --cross-file=${MESON_TARGET_TOOLCHAIN%.*}_gcc.meson build
+cd build/
+ninja -j${nproc}
+ninja install
+"""
+
+# These are the platforms we will build for by default, unless further
+# platforms are passed in on the command line
+platforms = filter!(p -> proc_family(p) == "intel" && !Sys.iswindows(p), supported_platforms())
+
+
+# The products that we will ensure are always built
+products = [
+    LibraryProduct("libcsb", :libcsb)
+]
+
+# Dependencies that must be installed before this package can be built
+dependencies = [
+    Dependency(PackageSpec(name="cilkrts_jll", uuid="71772805-00bc-5a29-9044-a26d819b7806"))
+]
+
+# Build the tarballs, and possibly a `build.jl` as well.
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6", preferred_gcc_version = v"7.1.0")
diff --git a/C/CryptoMiniSat/build_tarballs.jl b/C/CryptoMiniSat/build_tarballs.jl
@@ -6,7 +6,7 @@ const YGGDRASIL_DIR = "../.."
 include(joinpath(YGGDRASIL_DIR, "platforms", "mpi.jl"))
 
 name = "CryptoMiniSat"
-version = v"5.8.1"
+version = v"5.8.2"
 cryptominisat_version = v"5.8.0"
 
 # Collection of sources required to complete build

diff --git a/D/DDSCAT/build_tarballs.jl b/D/DDSCAT/build_tarballs.jl
@@ -0,0 +1,38 @@
+# Note that this script can accept some limited command-line arguments, run
+# `julia build_tarballs.jl --help` to see a usage message.
+using BinaryBuilder, Pkg
+
+name = "DDSCAT"
+version = v"7.3.3"
+
+# Collection of sources required to complete build
+sources = [
+    ArchiveSource("http://ddscat.wikidot.com/local--files/downloads/ddscat$(version)_220120.tgz", "06f2673a45fcff20b8ed9f37d5bedeb84604d7a9fb10f627096833163769d1e7")
+]
+
+# Bash recipe for building across all platforms
+script = raw"""
+cd $WORKSPACE/srcdir/src
+make ddscat
+mv ddscat "ddscat${exeext}" || true
+install -Dvm 755 "ddscat${exeext}" "${bindir}/ddscat${exeext}"
+install_license /usr/share/licenses/GPL-3.0+
+"""
+
+# These are the platforms we will build for by default, unless further
+# platforms are passed in on the command line
+platforms = expand_gfortran_versions(filter(x->arch(x) != "powerpc64le", supported_platforms()))
+
+
+# The products that we will ensure are always built
+products = [
+    ExecutableProduct("ddscat", :ddscat)
+]
+
+# Dependencies that must be installed before this package can be built
+dependencies = [
+    Dependency(PackageSpec(name="CompilerSupportLibraries_jll", uuid="e66e0078-7015-5450-92f7-15fbd957f2ae")),
+]
+
+# Build the tarballs, and possibly a `build.jl` as well.
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies; julia_compat="1.6")
diff --git a/E/Elfutils/build_tarballs.jl b/E/Elfutils/build_tarballs.jl
@@ -44,13 +44,32 @@ install_license COPYING*
 """
 
 # Only build for Linux
-platforms = filter!(Sys.islinux, supported_platforms())
+platforms = supported_platforms()
+filter!(Sys.islinux, platforms)
+filter!(p -> arch(p) != "armv6l", platforms)
 
 # The products that we will ensure are always built
 products = [
     LibraryProduct("libasm", :libasm),
     LibraryProduct("libdw", :libdw),
     LibraryProduct("libelf", :libelf),
+    ExecutableProduct("eu-addr2line", :eu_addr2line),
+    ExecutableProduct("eu-ar", :eu_ar),
+    ExecutableProduct("eu-elfclassify", :eu_elfclassify),
+    ExecutableProduct("eu-elfcmp", :eu_elfcmp),
+    ExecutableProduct("eu-elfcompress", :eu_elfcompress),
+    ExecutableProduct("eu-elflint", :eu_elflint),
+    ExecutableProduct("eu-findtextrel", :eu_findtextrel),
+    ExecutableProduct("eu-make-debug-archive", :eu_make_debug_archive),
+    ExecutableProduct("eu-nm", :eu_nm),
+    ExecutableProduct("eu-objdump", :eu_objdump),
+    ExecutableProduct("eu-ranlib", :eu_ranlib),
+    ExecutableProduct("eu-readelf", :eu_readelf),
+    ExecutableProduct("eu-size", :eu_size),
+    ExecutableProduct("eu-stack", :eu_stack),
+    ExecutableProduct("eu-strings", :eu_strings),
+    ExecutableProduct("eu-strip", :eu_strip),
+    ExecutableProduct("eu-unstrip", :eu_unstrip),
 ]
 
 # Dependencies that must be installed before this package can be built

diff --git a/E/Enzyme/build_tarballs.jl b/E/Enzyme/build_tarballs.jl
@@ -8,13 +8,13 @@ include(joinpath(YGGDRASIL_DIR, "platforms", "llvm.jl"))
 name = "Enzyme"
 repo = "https://github.com/EnzymeAD/Enzyme.git"
 
-auto_version = "refs/tags/v0.0.33"
+auto_version = "refs/tags/v0.0.35"
 version = VersionNumber(split(auto_version, "/")[end])
 
 llvm_versions = [v"11.0.1", v"12.0.1", v"13.0.1", v"14.0.2"]
 
 # Collection of sources required to build attr
-sources = [GitSource(repo, "441d19707761539e197a352c2bb904107995181b")]
+sources = [GitSource(repo, "4eb8421fdace49a83671e902c0a2c2bccf4f9897")]
 
 # These are the platforms we will build for by default, unless further
 # platforms are passed in on the command line
@@ -38,13 +38,14 @@ NATIVE_CMAKE_FLAGS+=(-DBC_LOAD_FLAGS="-target ${target} --sysroot=/opt/${target}
 
 cmake -B build-native -S enzyme -GNinja "${NATIVE_CMAKE_FLAGS[@]}"
 
-# Only build blasheaders (and eventually tblgen)
-ninja -C build-native -j ${nproc} blasheaders
+# Only build blasheaders and tblgen
+ninja -C build-native -j ${nproc} blasheaders enzyme-tblgen
 
 # 2. Cross-compile
 CMAKE_FLAGS=()
 CMAKE_FLAGS+=(-DENZYME_EXTERNAL_SHARED_LIB=ON)
 CMAKE_FLAGS+=(-DBC_LOAD_HEADER=`pwd`/build-native/BCLoad/gsl/blas_headers.h)
+CMAKE_FLAGS+=(-DEnzyme_TABLEGEN_EXE=`pwd`/build-native/tools/enzyme-tblgen/enzyme-tblgen)
 CMAKE_FLAGS+=(-DENZYME_CLANG=OFF)
 # RelWithDebInfo for decent performance, with debugability
 CMAKE_FLAGS+=(-DCMAKE_BUILD_TYPE=RelWithDebInfo)

diff --git a/F/FLINT/build_tarballs.jl b/F/FLINT/build_tarballs.jl
@@ -26,7 +26,7 @@ using BinaryBuilder, Pkg
 # and possibly other packages.
 name = "FLINT"
 upstream_version = v"2.9.0"
-version_offset = v"0.0.0"
+version_offset = v"0.0.1"
 version = VersionNumber(upstream_version.major * 100 + version_offset.major,
                         upstream_version.minor * 100 + version_offset.minor,
                         upstream_version.patch * 100 + version_offset.patch)
@@ -47,6 +47,10 @@ elif [[ ${target} == *mingw* ]]; then
    extraflags=--reentrant
 fi
 
+for f in ${WORKSPACE}/srcdir/patches/*.patch; do
+  atomic_patch -p1 ${f}
+done
+
 ./configure --prefix=$prefix --disable-static --enable-shared --with-gmp=$prefix --with-mpfr=$prefix --with-blas=$prefix ${extraflags}
 make -j${nproc}
 make install LIBDIR=$(basename ${libdir})

diff --git a/F/FLINT/bundled/patches/fix_tls.patch b/F/FLINT/bundled/patches/fix_tls.patch
@@ -0,0 +1,23 @@
+diff --git a/configure b/configure
+index 3eceecf41..304b1d5a9 100755
+--- a/configure
++++ b/configure
+@@ -687,15 +687,9 @@ if [ "$TLS" = "1" ]; then
+    echo "__thread int x = 42; int main(int argc, char ** argv) { return x != 42; }" > build/test-tls.c
+    $CC build/test-tls.c -o ./build/test-tls > /dev/null 2>&1
+    if [ $? -eq 0 ]; then
+-      build/test-tls > /dev/null 2>&1
+-      if [ $? -eq 0 ]; then
+-         printf "%s\n" "yes"
+-	 echo "yes" >> config.log
+-         CONFIG_TLS="#define FLINT_USES_TLS 1"
+-      else
+-         printf "%s\n" "no"
+-	 echo "no" >> config.log
+-      fi
++      printf "%s\n" "yes"
++      echo "yes" >> config.log
++      CONFIG_TLS="#define FLINT_USES_TLS 1"
+       rm -f build/test-tls{,.c}
+    else
+       rm -f build/test-tls.c
diff --git a/F/FLINT/bundled/patches/remove_endianness_check.patch b/F/FLINT/bundled/patches/remove_endianness_check.patch
diff --git a/G/GDAL/build_tarballs.jl b/G/GDAL/build_tarballs.jl
@@ -4,7 +4,7 @@ using BinaryBuilder, Pkg
 
 name = "GDAL"
 upstream_version = v"3.5.0"
-version_offset = v"0.0.0"
+version_offset = v"0.0.1"
 version = VersionNumber(upstream_version.major * 100 + version_offset.major,
                         upstream_version.minor * 100 + version_offset.minor,
                         upstream_version.patch * 100 + version_offset.patch)
@@ -113,7 +113,7 @@ products = [
 
 # Dependencies that must be installed before this package can be built
 dependencies = [
-    Dependency("GEOS_jll"; compat="~3.10"),
+    Dependency("GEOS_jll"; compat="~3.11"),
     Dependency("PROJ_jll"; compat="~900.0"),
     Dependency("Zlib_jll"),
     Dependency("SQLite_jll"),