Add clsparse

m/common/base.nix

@@ -11,13 +11,11 @@
     ./base/hw.nix
     ./base/net.nix
     ./base/nix.nix
-    ./base/sys-devices.nix
     ./base/ntp.nix
     ./base/rev.nix
     ./base/ssh.nix
     ./base/users.nix
     ./base/watchdog.nix
     ./base/zsh.nix
-    ./base/fish.nix
   ];
 }

m/common/base/env.nix

@@ -5,8 +5,6 @@
     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
-    nix-output-monitor
-    nixfmt-rfc-style
     # From bsckgs overlay
     osumb
   ];

m/common/base/fish.nix

@@ -1,4 +0,0 @@
-{ ... }:
-{
-  programs.fish.enable = true;
-}

m/common/base/sys-devices.nix

@@ -1,9 +0,0 @@
-{
-  nix.settings.system-features = [ "sys-devices" ];
-
-  programs.nix-required-mounts.enable = true;
-  programs.nix-required-mounts.allowedPatterns.sys-devices.paths = [
-    "/sys/devices/system/cpu"
-    "/sys/devices/system/node"
-  ];
-}

m/common/base/users.nix

@@ -87,12 +87,6 @@
         openssh.authorizedKeys.keys = [
           "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIIIFiqXqt88VuUfyANkZyLJNiuroIITaGlOOTMhVDKjf abonerib@bsc"
         ];
-        shell = pkgs.fish;
-        packages = with pkgs; [
-          starship
-          jujutsu
-          neovim
-        ];
       };
 
       vlopez = {

m/weasel/configuration.nix

@@ -1,11 +1,9 @@
-{ lib, pkgs, ... }:
+{ lib, ... }:
 
 {
   imports = [
     ../common/ssf.nix
     ../module/hut-substituter.nix
-    ./virtualization.nix
-    ./hydra.nix
   ];
 
   # Select this using the ID to avoid mismatches
@@ -32,23 +30,4 @@
       prefixLength = 24;
     } ];
   };
-
-  services.nix-serve = {
-    enable = true;
-    bindAddress = "0.0.0.0";
-    port = 5000;
-    package = pkgs.haskell.lib.overrideSrc (pkgs.haskell.packages.ghc96.nix-serve-ng.override { nix = pkgs.nixVersions.nix_2_28; }) {
-      src = pkgs.fetchgit {
-        url = "https://jungle.bsc.es/git/abonerib/nix-serve-ng.git";
-        rev = "9c056641300a826db66b66d7e584b2541d38927a";
-        hash = "sha256-y69ZchFiZOU71eyeljcQgLxkLk5JUzZfanq8Yzw4MkI=";
-      };
-      version = "unstable";
-    };
-
-    secretKeyFile = "/var/cache-priv-key.pem";
-    # Public key:
-    # 10.0.40.6:8jBhIdXEBap+Qo+vc1/fnV9vj43A2oDk839EEheRr/U=
-  };
-
 }

m/weasel/hydra.nix

@@ -1,52 +0,0 @@
-{ config, pkgs, lib, ... }:
-{
-  services.hydra = {
-    enable = true;
-
-    # Wrap hydra so it puts quiet flag every time... This is dumb and annoying,
-    # but i can't override the systemd ExecStart without running into infinite
-    # recursion.
-    package = pkgs.symlinkJoin {
-      name = "hydra-quiet";
-      paths = [ pkgs.hydra ];
-      postBuild = ''
-        for prog in hydra-queue-runner hydra-evaluator ; do
-          prev=$(realpath $out/bin/$prog)
-          rm $out/bin/$prog
-          cat >$out/bin/$prog <<EOF
-        #!/bin/sh
-        args=()
-        for arg in "\$@"; do
-          if [ "\$arg" != "-v" ]; then
-            args+=("\$arg")
-          fi
-        done
-        exec $prev --quiet "\''${args[@]}"
-        EOF
-
-          chmod +x $out/bin/$prog
-        done
-      '';
-    };
-
-    hydraURL = "http://localhost:3001"; # externally visible URL
-    notificationSender = "hydra@jungle.bsc.es"; # e-mail of Hydra service
-    port = 3001;
-    # a standalone Hydra will require you to unset the buildMachinesFiles list to avoid using a nonexistant /etc/nix/machines
-    buildMachinesFiles = [ ];
-    # you will probably also want, otherwise *everything* will be built from scratch
-    useSubstitutes = true;
-    listenHost = "0.0.0.0"; # Force IPv4
-  };
-
-  systemd.services.hydra-send-stats.enable = lib.mkForce false;
-
-  networking.firewall.allowedTCPPorts = [ config.services.hydra.port ];
-
-  nix.settings.extra-allowed-uris = [
-    "git+ssh://git@bscpm04.bsc.es"
-    "git+ssh://git@gitlab-internal.bsc.es"
-    "https://github.com"
-    "git+ssh://github.com"
-  ];
-}

m/weasel/virtualization.nix

@@ -1,40 +0,0 @@
-{
-  lib,
-  pkgs,
-  config,
-  ...
-}:
-
-{
-  # Enable common container config files in /etc/containers
-  virtualisation.containers.enable = true;
-  virtualisation = {
-    podman = {
-      enable = true;
-
-      # Required for containers under podman-compose to be able to talk to each other.
-      defaultNetwork.settings.dns_enabled = true;
-    };
-  };
-
-  # We cannot use /home since nfs does not support fileattrs needed by podman
-  systemd.tmpfiles.settings = {
-    "podman-users" = lib.mapAttrs' (
-      name: value:
-      lib.nameValuePair ("/var/lib/podman-users/" + name) {
-        d = {
-          group = value.group;
-          mode = value.homeMode;
-          user = name;
-        };
-      }
-    ) (lib.filterAttrs (_: x: x.isNormalUser) config.users.users);
-  };
-
-  # Useful other development tools
-  environment.systemPackages = with pkgs; [
-    dive # look into docker image layers
-    podman-tui # status of containers in the terminal
-    podman-compose # start group of containers for dev
-  ];
-}

overlay.nix

@@ -16,6 +16,7 @@ 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 { };
@@ -62,7 +63,7 @@ let
   };
 
   tests = rec {
-    hwloc = callPackage ./test/bugs/hwloc.nix { };
+    #hwloc = callPackage ./test/bugs/hwloc.nix { }; # Broken, no /sys
     #sigsegv = callPackage ./test/reproducers/sigsegv.nix { };
     hello-c = callPackage ./test/compilers/hello-c.nix { };
     hello-cpp = callPackage ./test/compilers/hello-cpp.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( )
+ 

test/bugs/hwloc.nix

@@ -6,7 +6,6 @@
 
 stdenv.mkDerivation {
   name = "hwloc-test";
-  requiredSystemFeatures = [ "sys-devices" ];
 
   src = ./.;
 
@@ -15,7 +14,7 @@ stdenv.mkDerivation {
   buildPhase = ''
     ls -l /sys
     gcc -lhwloc hwloc.c -o hwloc
-    strace ./hwloc > $out
+    strace ./hwloc
   '';
 
 }

test/compilers/clang-openmp-ld.nix

@@ -23,8 +23,9 @@ in stdenv.mkDerivation {
   dontUnpack = true;
   dontConfigure = true;
 
-  # nOS-V requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
+  # nOS-V requires access to /sys/devices to request NUMA information. It will
+  # fail to run otherwise, so we disable the sandbox for this test.
+  __noChroot = true;
 
   buildInputs = [ openmp ];
 

test/compilers/clang-openmp-nosv.nix

@@ -36,8 +36,9 @@ in stdenv.mkDerivation {
   dontUnpack = true;
   dontConfigure = true;
 
-  # nOS-V requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
+  # nOS-V requires access to /sys/devices to request NUMA information. It will
+  # fail to run otherwise, so we disable the sandbox for this test.
+  __noChroot = true;
 
   buildInputs = [ nosv ];
 

test/compilers/clang-openmp.nix

@@ -24,8 +24,9 @@ in stdenv.mkDerivation {
   dontUnpack = true;
   dontConfigure = true;
 
-  # nOS-V requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
+  # nOS-V requires access to /sys/devices to request NUMA information. It will
+  # fail to run otherwise, so we disable the sandbox for this test.
+  __noChroot = true;
 
   buildPhase = ''
     set -x

test/compilers/ompss2.nix

@@ -25,10 +25,9 @@ stdenv.mkDerivation rec {
   hardeningDisable = [ "all" ];
   #NIX_DEBUG = 1;
   buildInputs = [ ]; #strace gdb;
-
-  # NODES requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
-
+  # NODES requires access to /sys/devices to request NUMA information. It will
+  # fail to run otherwise, so we disable the sandbox for this test.
+  __noChroot = true;
   buildPhase = ''
     set -x
     #$CC -v