Update license year range to 2025

.gitlab-ci.yml

@@ -3,4 +3,4 @@ build:bsc-ci.all:
   tags:
     - nix
   script:
-    - nix build -L "jungle#bsc-ci.all" --override-input bscpkgs . -v --show-trace
+    - nix build -L --no-link --print-out-paths .#bsc-ci.all

COPYING

@@ -1,4 +1,4 @@
-Copyright (c) 2020-2021 Barcelona Supercomputing Center
+Copyright (c) 2020-2025 Barcelona Supercomputing Center
 Copyright (c) 2003-2020 Eelco Dolstra and the Nixpkgs/NixOS contributors
 
 Permission is hereby granted, free of charge, to any person obtaining

README.md

@@ -1 +1,9 @@
-Nix overlay with BSC packages.
+# Jungle
+
+This repository provides two components that can be used independently:
+
+- A Nix overlay with packages used at BSC (formerly known as bscpkgs). Access
+  them directly with `nix shell .#<pkgname>`.
+
+- NixOS configurations for jungle machines. Use `nixos-rebuild switch --flake .`
+  to upgrade the current machine.

flake.lock

@@ -23,26 +23,6 @@
         "type": "github"
       }
     },
-    "bscpkgs": {
-      "inputs": {
-        "nixpkgs": [
-          "nixpkgs"
-        ]
-      },
-      "locked": {
-        "lastModified": 1749650500,
-        "narHash": "sha256-2MHfVPV6RA7qPSCtXh4+KK0F0UjN+J4z8//+n6NK7Xs=",
-        "ref": "refs/heads/master",
-        "rev": "9d1944c658929b6f98b3f3803fead4d1b91c4405",
-        "revCount": 961,
-        "type": "git",
-        "url": "https://git.sr.ht/~rodarima/bscpkgs"
-      },
-      "original": {
-        "type": "git",
-        "url": "https://git.sr.ht/~rodarima/bscpkgs"
-      }
-    },
     "darwin": {
       "inputs": {
         "nixpkgs": [
@@ -105,7 +85,6 @@
     "root": {
       "inputs": {
         "agenix": "agenix",
-        "bscpkgs": "bscpkgs",
         "nixpkgs": "nixpkgs"
       }
     },

flake.nix

@@ -3,17 +3,22 @@
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.05";
     agenix.url = "github:ryantm/agenix";
     agenix.inputs.nixpkgs.follows = "nixpkgs";
-    bscpkgs.url = "git+https://git.sr.ht/~rodarima/bscpkgs";
-    bscpkgs.inputs.nixpkgs.follows = "nixpkgs";
   };
 
-  outputs = { self, nixpkgs, agenix, bscpkgs, ... }:
+  outputs = { self, nixpkgs, agenix, ... }:
 let
   mkConf = name: nixpkgs.lib.nixosSystem {
     system = "x86_64-linux";
-    specialArgs = { inherit nixpkgs bscpkgs agenix; theFlake = self; };
+    specialArgs = { inherit nixpkgs agenix; theFlake = self; };
     modules = [ "${self.outPath}/m/${name}/configuration.nix" ];
   };
+  # For now we only support x86
+  system = "x86_64-linux";
+  pkgs = import nixpkgs {
+    inherit system;
+    overlays = [ self.overlays.default ];
+    config.allowUnfree = true;
+  };
 in
   {
     nixosConfigurations = {
@@ -31,36 +36,17 @@ in
       weasel  = mkConf "weasel";
     };
 
-    packages.x86_64-linux = self.nixosConfigurations.hut.pkgs // {
-      bscpkgs = bscpkgs.packages.x86_64-linux;
-      nixpkgs = nixpkgs.legacyPackages.x86_64-linux;
-    };
-  };
+    bscOverlay = import ./overlay.nix;
+    overlays.default = self.bscOverlay;
 
-# TODO: Merge from bscpkgs:
-#
-#  inputs.nixpkgs.url = "nixpkgs";
-#
-#  outputs = { self, nixpkgs, ...}:
-#    let
-#      # For now we only support x86
-#      system = "x86_64-linux";
-#      pkgs = import nixpkgs {
-#        inherit system;
-#        overlays = [ self.overlays.default ];
-#      };
-#    in
-#    {
-#      bscOverlay = import ./overlay.nix;
-#      overlays.default = self.bscOverlay;
-#      # full nixpkgs with our overlay applied
-#      legacyPackages.${system} = pkgs;
-#
-#      hydraJobs = {
-#        inherit (self.legacyPackages.${system}.bsc-ci) tests pkgs cross;
-#      };
-#
-#      # propagate nixpkgs lib, so we can do bscpkgs.lib
-#      inherit (nixpkgs) lib;
-#    };
+    # full nixpkgs with our overlay applied
+    legacyPackages.${system} = pkgs;
+
+    hydraJobs = {
+      inherit (self.legacyPackages.${system}.bsc-ci) tests pkgs cross;
+    };
+
+    # propagate nixpkgs lib, so we can do bscpkgs.lib
+    inherit (nixpkgs) lib;
+  };
 }

m/common/base/nix.nix

@@ -1,9 +1,8 @@
-{ pkgs, nixpkgs, bscpkgs, theFlake,  ... }:
+{ pkgs, nixpkgs, theFlake,  ... }:
 
 {
   nixpkgs.overlays = [
-    bscpkgs.bscOverlay
-    (import ../../../pkgs/overlay.nix)
+    (import ../../../overlay.nix)
   ];
 
   nixpkgs.config.allowUnfree = true;

overlay.nix

@@ -7,6 +7,7 @@ let
   callPackage = final.callPackage;
 
   bscPkgs = {
+    amd-uprof = prev.callPackage ./pkgs/amd-uprof/default.nix { };
     bench6 = callPackage ./pkgs/bench6/default.nix { };
     bigotes = callPackage ./pkgs/bigotes/default.nix { };
     clangOmpss2 = callPackage ./pkgs/llvm-ompss2/default.nix { };
@@ -14,12 +15,24 @@ let
     clangOmpss2Nodes = callPackage ./pkgs/llvm-ompss2/default.nix { ompss2rt = final.nodes; openmp = final.openmp; };
     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 { };
     #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 { };
     jemallocNanos6 = callPackage ./pkgs/nanos6/jemalloc.nix { };
+    # FIXME: Extend this to all linuxPackages variants. Open problem, see:
+    # https://discourse.nixos.org/t/whats-the-right-way-to-make-a-custom-kernel-module-available/4636
+    linuxPackages = prev.linuxPackages.extend (_final: _prev: {
+      amd-uprof-driver = _prev.callPackage ./pkgs/amd-uprof/driver.nix { };
+    });
+    linuxPackages_latest = prev.linuxPackages_latest.extend(_final: _prev: {
+      amd-uprof-driver = _prev.callPackage ./pkgs/amd-uprof/driver.nix { };
+    });
     lmbench = callPackage ./pkgs/lmbench/default.nix { };
     mcxx = callPackage ./pkgs/mcxx/default.nix { };
+    meteocat-exporter = prev.callPackage ./pkgs/meteocat-exporter/default.nix { };
+    mpi = final.mpich; # Set MPICH as default
+    mpich = callPackage ./pkgs/mpich/default.nix { mpich = prev.mpich; };
     nanos6 = callPackage ./pkgs/nanos6/default.nix { };
     nanos6Debug = final.nanos6.override { enableDebug = true; };
     nixtools = callPackage ./pkgs/nixtools/default.nix { };
@@ -34,6 +47,7 @@ let
     ovni = callPackage ./pkgs/ovni/default.nix { };
     ovniGit = final.ovni.override { useGit = true; };
     paraverKernel = callPackage ./pkgs/paraver/kernel.nix { };
+    prometheus-slurm-exporter = prev.callPackage ./pkgs/slurm-exporter/default.nix { };
     #pscom = callPackage ./pkgs/parastation/pscom.nix { }; # Unmaintaned
     #psmpi = callPackage ./pkgs/parastation/psmpi.nix { }; # Unmaintaned
     sonar = callPackage ./pkgs/sonar/default.nix { };
@@ -43,6 +57,7 @@ let
     stdenvClangOmpss2NodesOmpv = final.stdenv.override { cc = final.clangOmpss2NodesOmpv; allowedRequisites = null; };
     tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
     tampi = callPackage ./pkgs/tampi/default.nix { };
+    upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
     wxparaver = callPackage ./pkgs/paraver/default.nix { };
   };
 

pkgs/mpich/default.nix

@@ -1,68 +1,36 @@
 {
   stdenv
 , lib
-, fetchurl
-, perl
-, gfortran
-, openssh
-, hwloc
 , libfabric
-, enableDebug ? false
+, mpich
+, pmix
+, gfortran
+, symlinkJoin
 }:
 
-with lib;
-
-stdenv.mkDerivation  rec {
-  pname = "mpich";
-  version = "3.3.2";
-
-  src = fetchurl {
-    url = "https://www.mpich.org/static/downloads/${version}/mpich-${version}.tar.gz";
-    sha256 = "1farz5zfx4cd0c3a0wb9pgfypzw0xxql1j1294z1sxslga1ziyjb";
+let
+  # pmix comes with the libraries in .out and headers in .dev
+  pmixAll = symlinkJoin {
+    name = "pmix-all";
+    paths = [ pmix.dev pmix.out ];
   };
-
+in mpich.overrideAttrs (old: {
+  buildInput = old.buildInputs ++ [
+    libfabric
+    pmixAll
+  ];
   configureFlags = [
     "--enable-shared"
     "--enable-sharedlib"
+    "--with-pm=no"
     "--with-device=ch4:ofi"
+    "--with-pmi=pmix"
+    "--with-pmix=${pmixAll}"
     "--with-libfabric=${libfabric}"
-  ]
-  ++ optional enableDebug "--enable-g=dbg,log";
-
-  enableParallelBuilding = true;
-
-  buildInputs = [ perl gfortran openssh hwloc libfabric ];
+    "--enable-g=log"
+  ] ++ lib.optionals (lib.versionAtLeast gfortran.version "10") [
+    "FFLAGS=-fallow-argument-mismatch" # https://github.com/pmodels/mpich/issues/4300
+    "FCFLAGS=-fallow-argument-mismatch"
+  ];
   hardeningDisable = [ "all" ];
-
-  # doCheck = true; # Fails
-
-  preFixup = ''
-    # Ensure the default compilers are the ones mpich was built with
-    sed -i 's:CC="gcc":CC=${stdenv.cc}/bin/gcc:' $out/bin/mpicc
-    sed -i 's:CXX="g++":CXX=${stdenv.cc}/bin/g++:' $out/bin/mpicxx
-    sed -i 's:FC="gfortran":FC=${gfortran}/bin/gfortran:' $out/bin/mpifort
-  ''
-  + lib.optionalString (!stdenv.isDarwin) ''
-    # /tmp/nix-build... ends up in the RPATH, fix it manually
-    for entry in $out/bin/mpichversion $out/bin/mpivars; do
-      echo "fix rpath: $entry"
-      patchelf --set-rpath "$out/lib" $entry
-    done
-    '';
-
-  meta = with lib; {
-    description = "Implementation of the Message Passing Interface (MPI) standard";
-
-    longDescription = ''
-      MPICH is a high-performance and widely portable implementation of
-      the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).
-    '';
-    homepage = "http://www.mpich.org";
-    license = {
-      url = "https://github.com/pmodels/mpich/blob/v${version}/COPYRIGHT";
-      fullName = "MPICH license (permissive)";
-    };
-    maintainers = [ ];
-    platforms = platforms.linux ++ platforms.darwin;
-  };
-}
+})

pkgs/overlay.nix

@@ -1,67 +0,0 @@
-final: prev:
-{
-  # Set MPICH as default
-  mpi = final.mpich;
-
-  # Configure the network for MPICH
-  mpich = with final; let
-    # pmix comes with the libraries in .out and headers in .dev
-    pmixAll = symlinkJoin {
-      name = "pmix-all";
-      paths = [ pmix.dev pmix.out ];
-    };
-  in prev.mpich.overrideAttrs (old: {
-    buildInput = old.buildInputs ++ [
-      libfabric
-      pmixAll
-    ];
-    configureFlags = [
-      "--enable-shared"
-      "--enable-sharedlib"
-      "--with-pm=no"
-      "--with-device=ch4:ofi"
-      "--with-pmi=pmix"
-      "--with-pmix=${pmixAll}"
-      "--with-libfabric=${libfabric}"
-      "--enable-g=log"
-    ] ++ lib.optionals (lib.versionAtLeast gfortran.version "10") [
-      "FFLAGS=-fallow-argument-mismatch" # https://github.com/pmodels/mpich/issues/4300
-      "FCFLAGS=-fallow-argument-mismatch"
-    ];
-  });
-
-  slurm = prev.slurm.overrideAttrs (old: {
-    patches = (old.patches or []) ++ [
-      # See https://bugs.schedmd.com/show_bug.cgi?id=19324
-      ./slurm-rank-expansion.patch
-    ];
-    # Install also the pam_slurm_adopt library to restrict users from accessing
-    # nodes with no job allocated.
-    postBuild = (old.postBuild or "") + ''
-      pushd contribs/pam_slurm_adopt
-        make "PAM_DIR=$out/lib/security"
-      popd
-    '';
-    postInstall = (old.postInstall or "") + ''
-      pushd contribs/pam_slurm_adopt
-        make "PAM_DIR=$out/lib/security" install
-      popd
-    '';
-  });
-
-  prometheus-slurm-exporter = prev.callPackage ./slurm-exporter.nix { };
-  meteocat-exporter = prev.callPackage ./meteocat-exporter/default.nix { };
-  upc-qaire-exporter = prev.callPackage ./upc-qaire-exporter/default.nix { };
-  cudainfo = prev.callPackage ./cudainfo/default.nix { };
-
-  amd-uprof = prev.callPackage ./amd-uprof/default.nix { };
-
-  # FIXME: Extend this to all linuxPackages variants. Open problem, see:
-  # https://discourse.nixos.org/t/whats-the-right-way-to-make-a-custom-kernel-module-available/4636
-  linuxPackages = prev.linuxPackages.extend (_final: _prev: {
-    amd-uprof-driver = _prev.callPackage ./amd-uprof/driver.nix { };
-  });
-  linuxPackages_latest = prev.linuxPackages_latest.extend(_final: _prev: {
-    amd-uprof-driver = _prev.callPackage ./amd-uprof/driver.nix { };
-  });
-}

pkgs/slurm/default.nix

@@ -1,80 +1,22 @@
-{ stdenv, lib, fetchFromGitHub, pkg-config, libtool, curl
-, python, munge, perl, pam, openssl
-, ncurses, libmysqlclient, gtk2, lua, hwloc, numactl
-, readline, freeipmi, libssh2, xorg
-, pmix
-# enable internal X11 support via libssh2
-, enableX11 ? true
-}:
+{ slurm }:
 
-stdenv.mkDerivation rec {
-  name = "slurm-${version}";
-  version = "17.11.9-2";
-
-  # N.B. We use github release tags instead of https://www.schedmd.com/downloads.php
-  # because the latter does not keep older releases.
-  src = fetchFromGitHub {
-    owner = "SchedMD";
-    repo = "slurm";
-    # The release tags use - instead of .
-    rev = "${builtins.replaceStrings ["."] ["-"] name}";
-    sha256 = "1lq4ac6yjai6wh979dciw8v3d99zbd3w36rfh0vpncqm672fg1qy";
-  };
-
-  outputs = [ "out" "dev" ];
-
-  prePatch = lib.optional enableX11 ''
-    substituteInPlace src/common/x11_util.c \
-        --replace '"/usr/bin/xauth"' '"${xorg.xauth}/bin/xauth"'
+slurm.overrideAttrs (old: {
+  patches = (old.patches or []) ++ [
+    # See https://bugs.schedmd.com/show_bug.cgi?id=19324
+    # Still unmerged as of 2025-10-03, another corpo-cancer.
+    ./slurm-rank-expansion.patch
+  ];
+  # Install also the pam_slurm_adopt library to restrict users from accessing
+  # nodes with no job allocated.
+  # TODO: Review pam_slurm_adopt, I don't trust their code much.
+  postBuild = (old.postBuild or "") + ''
+    pushd contribs/pam_slurm_adopt
+      make "PAM_DIR=$out/lib/security"
+    popd
   '';
-
-  # nixos test fails to start slurmd with 'undefined symbol: slurm_job_preempt_mode'
-  # https://groups.google.com/forum/#!topic/slurm-devel/QHOajQ84_Es
-  # this doesn't fix tests completely at least makes slurmd to launch
-  hardeningDisable = [ "bindnow" ];
-
-  nativeBuildInputs = [ pkg-config libtool ];
-  buildInputs = [
-    curl python munge perl pam openssl
-      libmysqlclient ncurses gtk2
-      lua hwloc numactl readline freeipmi
-      pmix
-  ] ++ lib.optionals enableX11 [ libssh2 xorg.xauth ];
-
-  configureFlags = with lib;
-    [ "--with-munge=${munge}"
-      "--with-ssl=${openssl.dev}"
-      "--with-hwloc=${hwloc.dev}"
-      "--with-freeipmi=${freeipmi}"
-      "--sysconfdir=/etc/slurm"
-      "--with-pmix=${pmix}"
-    ] ++ (optional (gtk2 == null)  "--disable-gtktest")
-      ++ (optional enableX11 "--with-libssh2=${libssh2.dev}");
-
-
-  preConfigure = ''
-    patchShebangs ./doc/html/shtml2html.py
-    patchShebangs ./doc/man/man2html.py
-    patchShebangs ./configure
+  postInstall = (old.postInstall or "") + ''
+    pushd contribs/pam_slurm_adopt
+      make "PAM_DIR=$out/lib/security" install
+    popd
   '';
-
-#  postBuild = ''
-#    pushd contrib/pmi2
-#      make -j install
-#    popd
-#  '';
-
-  postInstall = ''
-    rm -f $out/lib/*.la $out/lib/slurm/*.la
-  '';
-
-  enableParallelBuilding = true;
-
-  meta = with lib; {
-    homepage = http://www.schedmd.com/;
-    description = "Simple Linux Utility for Resource Management";
-    platforms = platforms.linux;
-    license = licenses.gpl2;
-    maintainers = with maintainers; [ jagajaga markuskowa ];
-  };
-}
+})