Merge pull request #262965 from markuskowa/upd-openmpi

openmpi: 4.1.5 -> 4.1.6 and pmix: 3.2.4 -> 5.0.1

pkgs/development/libraries/openmpi/default.nix

@@ -1,6 +1,6 @@
 { lib, stdenv, fetchurl, gfortran, perl, libnl
 , rdma-core, zlib, numactl, libevent, hwloc, targetPackages, symlinkJoin
-, libpsm2, libfabric, pmix, ucx
+, libpsm2, libfabric, pmix, ucx, ucc
 , config
 # Enable CUDA support
 , cudaSupport ? config.cudaSupport, cudatoolkit
@@ -25,11 +25,11 @@ let
   };
 in stdenv.mkDerivation rec {
   pname = "openmpi";
-  version = "4.1.5";
+  version = "4.1.6";
 
   src = with lib.versions; fetchurl {
     url = "https://www.open-mpi.org/software/ompi/v${major version}.${minor version}/downloads/${pname}-${version}.tar.bz2";
-    sha256 = "sha256-pkCYa8JXOJ3TeYhv2uYmTIz6VryYtxzjrj372M5h2+M=";
+    sha256 = "sha256-90CZRIVRbetjtTEa8SLCZRefUyig2FelZ7hdsAsR5BU=";
   };
 
   postPatch = ''
@@ -46,7 +46,7 @@ in stdenv.mkDerivation rec {
   outputs = [ "out" "man" ];
 
   buildInputs = [ zlib ]
-    ++ lib.optionals stdenv.isLinux [ libnl numactl pmix ucx ]
+    ++ lib.optionals stdenv.isLinux [ libnl numactl pmix ucx ucc ]
     ++ lib.optionals cudaSupport [ cudatoolkit ]
     ++ [ libevent hwloc ]
     ++ lib.optional (stdenv.isLinux || stdenv.isFreeBSD) rdma-core

pkgs/development/libraries/pmix/default.nix

@@ -1,16 +1,17 @@
 { lib, stdenv, fetchFromGitHub, perl, autoconf, automake
-, libtool, flex, libevent, hwloc, munge, zlib, pandoc
+, libtool, python3, flex, libevent, hwloc, munge, zlib, pandoc, gitMinimal
 } :
 
 stdenv.mkDerivation rec {
   pname = "pmix";
-  version = "3.2.4";
+  version = "5.0.1";
 
   src = fetchFromGitHub {
     repo = "openpmix";
     owner = "openpmix";
     rev = "v${version}";
-    sha256 = "sha256-79zTZm549VRsqeziCuBT6l4jTJ6D/gZaMAvgHZm7jn4=";
+    hash = "sha256-ZuuzQ8j5zqQ/9mBFEODAaoX9/doWB9Nt9Sl75JkJyqU=";
+    fetchSubmodules = true;
   };
 
   postPatch = ''
@@ -18,14 +19,25 @@ stdenv.mkDerivation rec {
     patchShebangs ./config
   '';
 
-  nativeBuildInputs = [ pandoc perl autoconf automake libtool flex ];
+  nativeBuildInputs = [
+    pandoc
+    perl
+    autoconf
+    automake
+    libtool
+    flex
+    gitMinimal
+    python3
+  ];
 
   buildInputs = [ libevent hwloc munge zlib ];
 
   configureFlags = [
     "--with-libevent=${lib.getDev libevent}"
+    "--with-libevent-libdir=${lib.getLib libevent}/lib"
     "--with-munge=${munge}"
     "--with-hwloc=${lib.getDev hwloc}"
+    "--with-hwloc-libdir=${lib.getLib hwloc}/lib"
   ];
 
   preConfigure = ''

pkgs/development/python-modules/pyslurm/default.nix

@@ -1,6 +1,7 @@
 { lib
 , pythonOlder
 , fetchFromGitHub
+, fetchpatch
 , buildPythonPackage
 , cython
 , slurm
@@ -20,9 +21,15 @@ buildPythonPackage rec {
     hash = "sha256-M8seh5pkw2OTiDU4O96D0Lg3+FrlB2w4ehy53kSxyoU=";
   };
 
+  patches = [ (fetchpatch {
+    name = "remove-undeclared-KILL_JOB_ARRAY";
+    url = "https://github.com/PySlurm/pyslurm/commit/f7a7d8beb8ceb4e4c1b248bab2ebb995dcae77e2.patch";
+    hash = "sha256-kQLGiGzAhqP8Z6pObz9vdTRdITd12w7KuUDXsfyLIU8=";
+  })];
+
   buildInputs = [ cython slurm ];
 
-  setupPyBuildFlags = [ "--slurm-lib=${slurm}/lib" "--slurm-inc=${slurm.dev}/include" ];
+  setupPyBuildFlags = [ "--slurm-lib=${lib.getLib slurm}/lib" "--slurm-inc=${lib.getDev slurm}/include" ];
 
   # Test cases need /etc/slurm/slurm.conf and require a working slurm installation
   doCheck = false;

pkgs/servers/computing/slurm/default.nix

@@ -32,8 +32,6 @@ stdenv.mkDerivation rec {
     # increase string length to allow for full
     # path of 'echo' in nix store
     ./common-env-echo.patch
-    # Required for configure to pick up the right dlopen path
-    ./pmix-configure.patch
   ];
 
   prePatch = ''
@@ -72,6 +70,7 @@ stdenv.mkDerivation rec {
       "--sysconfdir=/etc/slurm"
       "--with-pmix=${pmix}"
       "--with-bpf=${libbpf}"
+      "--without-rpath" # Required for configure to pick up the right dlopen path
     ] ++ (optional enableGtk2  "--disable-gtktest")
       ++ (optional (!enableX11) "--disable-x11");
 

pkgs/servers/computing/slurm/pmix-configure.patch

@@ -1,13 +0,0 @@
-diff --git a/configure b/configure
-index 1cf53bc..ab68441 100755
---- a/configure
-+++ b/configure
-@@ -21207,7 +21207,7 @@ rm -f conftest.err conftest.i conftest.$ac_ext
-                 as_fn_error $? "error processing $x_ac_cv_pmix_libdir: PMIx v3.x was already found in one of the previous paths" "$LINENO" 5
-               fi
-               _x_ac_pmix_v3_found="1"
--              PMIX_V3_CPPFLAGS="-I$x_ac_cv_pmix_dir/include"
-+              PMIX_V3_CPPFLAGS="-I$x_ac_cv_pmix_dir/include -DPMIXP_V3_LIBPATH=\\\"$x_ac_cv_pmix_libdir\\\""
-               if test "$ac_with_rpath" = "yes"; then
-                 PMIX_V3_LDFLAGS="-Wl,-rpath -Wl,$x_ac_cv_pmix_libdir -L$x_ac_cv_pmix_libdir"
-               else