Move packages from bsc/ to pkgs/

pkgs/extrae/PTR.patch

@@ -0,0 +1,13 @@
+diff --git a/src/merger/common/bfd_manager.c b/src/merger/common/bfd_manager.c
+index 5f9dacf9..5231e3eb 100644
+--- a/src/merger/common/bfd_manager.c
++++ b/src/merger/common/bfd_manager.c
+@@ -225,7 +225,7 @@ asymbol **BFDmanager_getDefaultSymbols (void)
+  *
+  * @return No return value.
+  */
+-static void BFDmanager_findAddressInSection (bfd * abfd, asection * section, PTR data)
++static void BFDmanager_findAddressInSection (bfd * abfd, asection * section, void * data)
+ {
+ #if HAVE_BFD_GET_SECTION_SIZE || HAVE_BFD_SECTION_SIZE || HAVE_BFD_GET_SECTION_SIZE_BEFORE_RELOC
+ 	bfd_size_type size;

pkgs/extrae/default.nix

@@ -0,0 +1,113 @@
+{ stdenv
+, lib
+, fetchFromGitHub
+, boost
+, libdwarf
+, libelf
+, libxml2
+, libunwind
+, papi
+, binutils-unwrapped
+, libiberty
+, gfortran
+, xml2
+, which
+, libbfd
+, mpi ? null
+, cuda ? null
+, llvmPackages
+, autoreconfHook
+#, python3Packages
+, installShellFiles
+, symlinkJoin
+}:
+
+let
+  libdwarfBundle = symlinkJoin {
+    name = "libdwarfBundle";
+    paths = [ libdwarf.dev libdwarf.lib libdwarf.out ];
+  };
+in
+
+stdenv.mkDerivation rec {
+  pname = "extrae";
+  version = "4.0.1";
+  src = fetchFromGitHub {
+    owner = "bsc-performance-tools";
+    repo = "extrae";
+    rev = "${version}";
+    sha256 = "SlMYxNQXJ0Xg90HmpnotUR3tEPVVBXhk1NtEBJwGBR4=";
+  };
+
+  patches = [
+    # FIXME: Waiting for German to merge this patch. Still not in master, merged
+    # on 2023-03-01 in devel branch (after 3 years), see:
+    # https://github.com/bsc-performance-tools/extrae/pull/45
+    ./use-command.patch
+    # https://github.com/bsc-performance-tools/extrae/issues/71
+    ./PTR.patch
+  ];
+
+  enableParallelBuilding = true;
+  hardeningDisable = [ "all" ];
+
+  nativeBuildInputs = [ installShellFiles ];
+
+  buildInputs = [
+    autoreconfHook
+    gfortran
+    libunwind
+    binutils-unwrapped
+    boost
+    boost.dev
+    libiberty
+    mpi
+    xml2
+    which
+    libxml2.dev
+    libbfd
+    #python3Packages.sphinx
+  ]
+  ++ lib.optional stdenv.cc.isClang llvmPackages.openmp;
+    
+  preConfigure = ''
+    configureFlagsArray=(
+      --enable-posix-clock
+      --with-binutils="${binutils-unwrapped} ${libiberty}"
+      --with-dwarf=${libdwarfBundle}
+      --with-elf=${libelf}
+      --with-boost=${boost.dev}
+      --enable-instrument-io
+      --enable-instrument-dynamic-memory
+      --without-memkind
+      --enable-merge-in-trace
+      --disable-online
+      --without-opencl
+      --enable-pebs-sampling
+      --enable-sampling
+      --with-unwind=${libunwind.dev}
+      --with-xml-prefix=${libxml2.dev}
+      --with-papi=${papi}
+      ${if (mpi != null) then ''--with-mpi=${mpi}''
+        else ''--without-mpi''}
+      --without-dyninst)
+  '';
+
+  # Install the manuals only by hand, as we don't want to pull the complete
+  # LaTeX world
+
+  # FIXME: sphinx is broken
+  #postBuild = ''
+  #  make -C docs man
+  #'';
+  #
+  #postInstall = ''
+  #  installManPage docs/builds/man/*/*
+  #'';
+
+#  ++ (
+#    if (openmp)
+#    then [ "--enable-openmp" ]
+#    else []
+#  );
+}

pkgs/extrae/use-command.patch

@@ -0,0 +1,24 @@
+diff --git a/substitute b/substitute
+index d5615606..82ca91a5 100755
+--- a/substitute
++++ b/substitute
+@@ -16,7 +16,7 @@ UNAME=`uname`
+ if [ "${UNAME}" = "Darwin" -o "${UNAME}" = "AIX" ] ; then
+ 	TMPFILE=substitute-$$
+ 	${SED} "s|${KEY}|${VALUE}|g" < ${FILE} >${TMPFILE}
+-	/bin/mv -f ${TMPFILE} ${FILE}
++	command mv -f ${TMPFILE} ${FILE}
+ else
+ 	${SED} "s|${KEY}|${VALUE}|g" -i ${FILE}
+ fi
+diff --git a/substitute-all b/substitute-all
+index 48c6b76a..eda7a0f2 100755
+--- a/substitute-all
++++ b/substitute-all
+@@ -23,5 +23,5 @@ fi
+ 
+ echo "Applying modification in ${PATHTOCHANGE} - Key = ${KEY} for value = ${VALUE}"
+ 
+-/usr/bin/find ${PATHTOCHANGE} -type f -exec ${SCRIPT_LOCATION} "${SED}" "${KEY}" "${VALUE}" {} \;
++command find ${PATHTOCHANGE} -type f -exec ${SCRIPT_LOCATION} "${SED}" "${KEY}" "${VALUE}" {} \;
+