Add clsparse

m/common/base/env.nix

@@ -5,8 +5,8 @@
     vim wget git htop tmux pciutils tcpdump ripgrep nix-index nixos-option
     nix-diff ipmitool freeipmi ethtool lm_sensors cmake gnumake file tree
     ncdu config.boot.kernelPackages.perf ldns pv
-    # From jungle overlay
+    # From bsckgs overlay
-    osumb nixgen
+    osumb
   ];
 
   programs.direnv.enable = true;

overlay.nix

@@ -17,6 +17,7 @@ let
     clangOmpss2NodesOmpv = callPackage ./pkgs/llvm-ompss2/default.nix { ompss2rt = final.nodes; openmp = final.openmpv; };
     clangOmpss2Unwrapped = callPackage ./pkgs/llvm-ompss2/clang.nix { };
     cudainfo = prev.callPackage ./pkgs/cudainfo/default.nix { };
+    clsparse = callPackage ./pkgs/clsparse/package.nix { };
     #extrae = callPackage ./pkgs/extrae/default.nix { }; # Broken and outdated
     gpi-2 = callPackage ./pkgs/gpi-2/default.nix { };
     intelPackages_2023 = callPackage ./pkgs/intel-oneapi/2023.nix { };
@@ -37,7 +38,6 @@ let
     nanos6 = callPackage ./pkgs/nanos6/default.nix { };
     nanos6Debug = final.nanos6.override { enableDebug = true; };
     nixtools = callPackage ./pkgs/nixtools/default.nix { };
-    nixgen = callPackage ./pkgs/nixgen/default.nix { };
     # Broken because of pkgsStatic.libcap
     # See: https://github.com/NixOS/nixpkgs/pull/268791
     #nix-wrap = callPackage ./pkgs/nix-wrap/default.nix { };

pkgs/clsparse/install_target.patch

@@ -0,0 +1,53 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3d139ed..15ffc14 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -176,32 +179,22 @@ if( BUILD_clSPARSE OR BUILD_SAMPLES )
+   if( BUILD_clSPARSE )
+     message( STATUS "Setting up clSPARSE external..." )
+ 
+-    if ( BUILD_SAMPLES )
+-      # If the user elects to build samples, then we must build and install clSPARSE
+-      # The install location is set as a subdirectory of the SuperBuild
+-      ExternalProject_Add(
+-        clSPARSE
+-        DEPENDS ${clSPARSE.Dependencies}
+-        SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
+-        BINARY_DIR clSPARSE-build
+-        INSTALL_DIR clSPARSE-package
+-        CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-        -DBUILD_CLVERSION=${BUILD_CLVERSION} -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+-        -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
+-      )
+-    else( )
+-      # If the user does not want to build samples, then build clSPARSE but don't automatically
+-      # install it
+-      ExternalProject_Add(
+-        clSPARSE
+-        DEPENDS ${clSPARSE.Dependencies}
+-        SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
+-        BINARY_DIR clSPARSE-build
+-        CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-        -DBUILD_CLVERSION=${BUILD_CLVERSION} -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
+-        INSTALL_COMMAND ""
+-      )
+-    endif( )
++    ExternalProject_Add(
++      clSPARSE
++      DEPENDS ${clSPARSE.Dependencies}
++      SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
++      BINARY_DIR clSPARSE-build
++      INSTALL_DIR clSPARSE-package
++      CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
++      -DBUILD_CLVERSION=${BUILD_CLVERSION} -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
++      -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
++    )
++
++    install(
++      DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/clSPARSE-package/
++      DESTINATION ${CMAKE_INSTALL_PREFIX}
++      USE_SOURCE_PERMISSIONS
++    )
+ 
+   endif( )
+ 

pkgs/clsparse/package.nix

@@ -0,0 +1,70 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  boost,
+  gtest,
+  ocl-icd,
+  opencl-headers,
+  opencl-clhpp,
+  cmake,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "clsparse";
+  version = "0.10.2.0";
+
+  src = fetchFromGitHub {
+    owner = "clMathLibraries";
+    repo = "clSPARSE";
+    rev = "v${version}";
+    hash = "sha256-jIauCtUyPEIx7pFI3qH0WagV+t/fvro0OsGgONBJm0s=";
+  };
+
+  patches = [
+    ./pass_include_dir.patch
+    ./install_target.patch
+    (fetchpatch {
+      name = "remove-gettypecode.patch";
+      url = "https://patch-diff.githubusercontent.com/raw/clMathLibraries/clSPARSE/pull/210.patch";
+      hash = "sha256-9Q+tk7RMdWE4MCnbvWlsI0MIgBYKIWR2jIC1bICtIjU=";
+    })
+  ];
+
+  postInstallPhase = ''
+    mv $installDir/lib64 lib
+    ln -s lib/ lib64
+  '';
+
+  env.NIX_CFLAGS_COMPILE = "-std=c++17";
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  buildInputs = [
+    boost
+    ocl-icd
+    opencl-headers
+    opencl-clhpp
+  ];
+
+  cmakeFlags = [
+    "-DBUILD_Boost=OFF"
+    "-DBUILD_gMock=OFF"
+    "-DBUILD_MTX=OFF"
+    "-DBUILD_SAMPLES=OFF"
+    "-DUSE_SYSTEM_CL2HPP=ON"
+    "-DGMOCK_ROOT=${gtest}"
+    "-DGTEST_INCLUDE_DIR=${gtest.src}/googletest/include"
+  ];
+
+  meta = {
+    description = "A software library containing Sparse functions written in OpenCL";
+    homepage = "https://github.com/clMathLibraries/clSPARSE";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ leixb ];
+    platforms = lib.platforms.all;
+  };
+}

pkgs/clsparse/pass_include_dir.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3d139ed..b7ea2d3 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -132,6 +132,9 @@ else( )
+       set( GMOCK_ROOT "$ENV{GMOCK_ROOT}" )
+     endif( )
+     list( APPEND clSPARSE.Cmake.Args -DGTEST_ROOT=${GMOCK_ROOT} )
++    if( DEFINED GTEST_INCLUDE_DIR )
++      list( APPEND clSPARSE.Cmake.Args -DGTEST_INCLUDE_DIR=${GTEST_INCLUDE_DIR} )
++    endif( )
+   endif( )
+ endif( )
+ 

pkgs/gpi-2/default.nix

@@ -9,6 +9,7 @@
 , automake
 , libtool
 , mpi
+, rsync
 , gfortran
 }:
 
@@ -43,24 +44,13 @@ stdenv.mkDerivation rec {
 
   configureFlags = [
     "--with-infiniband=${rdma-core-all}"
-    "--with-mpi=yes"
+    "--with-mpi=${mpiAll}"
     "--with-slurm"
     "CFLAGS=-fPIC"
     "CXXFLAGS=-fPIC"
   ];
 
-  nativeBuildInputs = [
+  buildInputs = [ slurm mpiAll rdma-core-all autoconf automake libtool rsync gfortran ];
-    autoconf
-    automake
-    gfortran
-    libtool
-  ];
-
-  buildInputs = [
-    slurm
-    mpiAll
-    rdma-core-all
-  ];
 
   hardeningDisable = [ "all" ];
 
@@ -70,6 +60,5 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
-    cross = false;
   };
 }

pkgs/llvm-ompss2/clang.nix

@@ -16,19 +16,19 @@
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/llvm-ompss/llvm-mono.git"
 , gitBranch ? "master"
-, gitCommit ? "872ba63f86edaefc9787984ef3fae9f2f94e0124" # github-release-2025.11
+, gitCommit ? "880e2341c56bad1dc14e8c369fb3356bec19018e"
 }:
 
 let
   stdenv = llvmPackages_latest.stdenv;
 
   release = rec {
-    version = "2025.11";
+    version = "2025.06";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "llvm";
       rev = "refs/tags/github-release-${version}";
-      hash = "sha256-UgwMTUkM9Z87dDH205swZFBeFhrcbLAxginViG40pBM=";
+      hash = "sha256-ww9PpRmtz/M9IyLiZ8rAehx2UW4VpQt+svf4XfKBzKo=";
     };
   };
 

pkgs/mpich/default.nix

@@ -6,12 +6,6 @@
 , pmix
 , gfortran
 , symlinkJoin
-# Disabled when cross-compiling
-# To fix cross compilation, we should fill the values in:
-# https://github.com/pmodels/mpich/blob/main/maint/fcrosscompile/cross_values.txt.in
-# For each arch
-, enableFortran ? stdenv.hostPlatform == stdenv.buildPlatform
-, perl
 }:
 
 let
@@ -21,13 +15,10 @@ let
     paths = [ pmix.dev pmix.out ];
   };
 in mpich.overrideAttrs (old: {
-  buildInputs = old.buildInputs ++ [
+  buildInput = old.buildInputs ++ [
     libfabric
     pmixAll
   ];
-  nativeBuildInputs = old.nativeBuildInputs ++ [
-    perl
-  ];
   configureFlags = [
     "--enable-shared"
     "--enable-sharedlib"
@@ -40,21 +31,10 @@ in mpich.overrideAttrs (old: {
   ] ++ lib.optionals (lib.versionAtLeast gfortran.version "10") [
     "FFLAGS=-fallow-argument-mismatch" # https://github.com/pmodels/mpich/issues/4300
     "FCFLAGS=-fallow-argument-mismatch"
-  ] ++ lib.optionals (!enableFortran) [
-    "--disable-fortran"
   ];
-
-  preFixup = ''
-    sed -i 's:^CC=.*:CC=''${CC:-gcc}:' $out/bin/mpicc
-    sed -i 's:^CXX=.*:CXX=''${CXX:-g++}:' $out/bin/mpicxx
-  '' + lib.optionalString enableFortran ''
-    sed -i 's:^FC=.*:FC=''${FC:-gfortran}: $out/bin/mpifort
-  '';
-
   hardeningDisable = [ "all" ];
 
   meta = old.meta // {
     maintainers = old.meta.maintainers ++ (with lib.maintainers.bsc; [ rarias ]);
-    cross = true;
   };
 })

pkgs/nixgen/default.nix

@@ -1,22 +0,0 @@
-{
-  stdenv
-, lib
-}:
-
-stdenv.mkDerivation {
-  pname = "nixgen";
-  version = "0.0.1";
-  src = ./nixgen;
-  dontUnpack = true;
-  phases = [ "installPhase" ];
-  installPhase = ''
-    mkdir -p $out/bin
-    cp -a $src $out/bin/nixgen
-  '';
-  meta = {
-    description = "Quickly generate flake.nix from command line";
-    maintainers = with lib.maintainers.bsc; [ rarias ];
-    platforms = lib.platforms.linux;
-    license = lib.licenses.gpl3Plus;
-  };
-}

pkgs/nixgen/nixgen

@@ -1,97 +0,0 @@
-#!/bin/sh
-#
-# Copyright (c) 2025, Barcelona Supercomputing Center (BSC)
-# SPDX-License-Identifier: GPL-3.0+
-# Author: Rodrigo Arias Mallo <rodrigo.arias@bsc.es>
-
-function usage() {
-  echo "USAGE: nixgen [-f] [package [...]] [-b package [...]]" >&2
-  echo "  Generates a flake.nix file with the given packages." >&2
-  echo "  After flake.nix is created, use 'nix develop' to enter the shell." >&2
-  echo "OPTIONS" >&2
-  echo "  -f               Overwrite existing flake.nix (default: no)." >&2
-  echo "  packages...      Add these packages to the shell." >&2
-  echo "  -b packages...   Add the dependencies needed to build these packages." >&2
-  echo "EXAMPLE" >&2
-  echo "  $ nixgen ovni bigotes -b nosv tampi" >&2
-  echo "  Adds the packages ovni and bigotes as well as all required dependencies" >&2
-  echo "  to build nosv and tampi." >&2
-  echo "AUTHOR" >&2
-  echo "  Rodrigo Arias Mallo <rodrigo.arias@bsc.es>" >&2
-  exit 1
-}
-
-mode=package
-packages=
-inputsFrom=
-force=
-
-if [[ $# -eq 0 ]]; then
-  usage
-fi
-
-while [[ $# -gt 0 ]]; do
-    case $1 in -b)
-      mode=build
-      shift
-      ;;
-    -f)
-      force=1
-      shift
-      ;;
-    -h)
-      usage
-      ;;
-    -*|--*)
-      echo "error: unknown option $1" >&2
-      exit 1
-      ;;
-    *)
-      if [ "$mode" == "package" ]; then
-        packages+="${packages:+ }$1"
-      else
-        inputsFrom+="${inputsFrom:+ }$1"
-      fi
-      shift
-      ;;
-  esac
-done
-
-if [ ! "$force" -a -e flake.nix ]; then
-  echo "error: flake.nix exists, force overwrite with -f" >&2
-  exit 1
-fi
-
-cat > flake.nix <<EOF
-{
-  inputs.jungle.url = "git+https://jungle.bsc.es/git/rarias/jungle";
-  outputs = { self, jungle }:
-  let
-    nixpkgs = jungle.inputs.nixpkgs;
-    customOverlay = (final: prev: {
-      # Example overlay, for now empty
-    });
-    pkgs = import nixpkgs {
-      system = "x86_64-linux";
-      overlays = [
-        # Apply jungle overlay to get our BSC custom packages
-        jungle.outputs.bscOverlay
-        # And on top apply our local changes to customize for cluster
-        customOverlay
-      ];
-    };
-  in {
-    devShells.x86_64-linux.default = pkgs.mkShell {
-      pname = "devshell";
-      # Include these packages in the shell
-      packages = with pkgs; [
-        $packages
-      ];
-      # The dependencies needed to build these packages will be also included
-      inputsFrom = with pkgs; [
-        $inputsFrom
-      ];
-    };
-  };
-}
-EOF

pkgs/nodes/default.nix

@@ -14,19 +14,19 @@
 , useGit ? false
 , gitUrl ? "ssh://git@gitlab-internal.bsc.es/nos-v/nodes.git"
 , gitBranch ? "master"
-, gitCommit ? "511489e71504a44381e0930562e7ac80ac69a848" # version-1.4
+, gitCommit ? "6002ec9ae6eb876d962cc34366952a3b26599ba6"
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "1.4";
+    version = "1.3";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nodes";
       rev = "version-${version}";
-      hash = "sha256-+lR/R0l3fGZO3XG7whMorFW2y2YZ0ZFnLeOHyQYrAsQ=";
+      hash = "sha256-cFb9pxcjtkMmH0CsGgUO9LTdXDNh7MCqicgGWawLrsU=";
     };
   };
 

pkgs/nosv/default.nix

@@ -13,19 +13,19 @@
 , useGit ? false
 , gitUrl ? "git@gitlab-internal.bsc.es:nos-v/nos-v.git"
 , gitBranch ? "master"
-, gitCommit ? "1108e4786b58e0feb9a16fa093010b763eb2f8e8" # version 4.0.0
+, gitCommit ? "9f47063873c3aa9d6a47482a82c5000a8c813dd8"
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "4.0.0";
+    version = "3.2.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nos-v";
       rev = "${version}";
-      hash = "sha256-llaq73bd/YxLVKNlMebnUHKa4z3sdcsuDUoVwUxNuw8=";
+      hash = "sha256-yaz92426EM8trdkBJlISmAoG9KJCDTvoAW/HKrasvOw=";
     };
   };
 

pkgs/osu/default.nix

@@ -44,6 +44,5 @@ stdenv.mkDerivation rec {
     homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/";
     maintainers = [ ];
     platforms = lib.platforms.all;
-    cross = true;
   };
 }

pkgs/ovni/default.nix

@@ -7,7 +7,7 @@
 , useGit ? false
 , gitBranch ? "master"
 , gitUrl ? "ssh://git@bscpm04.bsc.es/rarias/ovni.git"
-, gitCommit ? "06432668f346c8bdc1006fabc23e94ccb81b0d8b" # version 1.13.0
+, gitCommit ? "e4f62382076f0cf0b1d08175cf57cc0bc51abc61"
 , enableDebug ? false
 # Only enable MPI if the build is native (fails on cross-compilation)
 , useMpi ? (stdenv.buildPlatform.canExecute stdenv.hostPlatform)
@@ -15,13 +15,13 @@
 
 let
   release = rec {
-    version = "1.13.0";
+    version = "1.12.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "ovni";
       rev = "${version}";
-      hash = "sha256-0l2ryIyWNiZqeYdVlnj/WnQGS3xFCY4ICG8JedX424w=";
+      hash = "sha256-H04JvsVKrdqr3ON7JhU0g17jjlg/jzQ7eTfx9vUNd3E=";
-    } // { shortRev = "0643266"; };
+    } // { shortRev = "a73afcf"; };
   };
 
   git = rec {

pkgs/sonar/default.nix

@@ -35,6 +35,5 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.mit;
-    cross = true;
   };
 }

pkgs/tagaspi/default.nix

@@ -5,14 +5,23 @@
 , automake
 , autoconf
 , libtool
+, mpi
 , autoreconfHook
 , gpi-2
 , boost
 , numactl
 , rdma-core
 , gfortran
+, symlinkJoin
 }:
 
+let
+  mpiAll = symlinkJoin {
+    name = "mpi-all";
+    paths = [ mpi.all ];
+  };
+in
+
 stdenv.mkDerivation rec {
   pname = "tagaspi";
   enableParallelBuilding = true;
@@ -26,18 +35,16 @@ stdenv.mkDerivation rec {
     hash = "sha256-RGG/Re2uM293HduZfGzKUWioDtwnSYYdfeG9pVrX9EM=";
   };
 
-  nativeBuildInputs = [
+  buildInputs = [
     autoreconfHook
     automake
     autoconf
     libtool
-    gfortran
-  ];
-
-  buildInputs = [
     boost
     numactl
     rdma-core
+    gfortran
+    mpiAll
   ];
 
   dontDisableStatic = true;
@@ -56,6 +63,5 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
-    cross = false; # gpi-2 cannot cross
   };
 }

pkgs/tampi/default.nix

@@ -68,6 +68,5 @@ in stdenv.mkDerivation {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
-    cross = true;
   };
 }