Merge all branches

New apt list does not have Package: as the first entry for all packages

flake.nix

@@ -2,25 +2,34 @@
   inputs.nixpkgs.url = "nixpkgs";
 
   outputs = { self, nixpkgs, ...}:
-    let
+  let
+    system = "x86_64-linux";
+    pkgs = import nixpkgs {
+      inherit system;
       # For now we only support x86
-      system = "x86_64-linux";
-      pkgs = import nixpkgs {
-        inherit system;
-        overlays = [ self.overlays.default ];
-      };
-    in
+      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.${system}.bsc-ci) test pkgs cross;
-      };
-
-      # propagate nixpkgs lib, so we can do bscpkgs.lib
-      inherit (nixpkgs) lib;
+      # packages added by our overlay
+      packages.${system} =
+        let
+          inherit (builtins) attrNames removeAttrs;
+          inherit (nixpkgs.lib) flip filterAttrs getAttrs pipe isDerivation;
+        in
+          # extract the names of the packages from the overlay, then get the
+          # actual packages from the full package set with the overlay applied
+          pipe (self.overlays.default null null) [
+            attrNames
+            (flip getAttrs pkgs)
+            (flip removeAttrs [ "bsc" ])
+            (filterAttrs (_: isDerivation))
+          ];
     };
 }

overlay.nix

@@ -2,7 +2,7 @@ final: /* Future last stage */
 prev:  /* Previous stage */
 
 let
-  inherit (prev.lib) collect isDerivation mapAttrs filterAttrs;
+  inherit (prev.lib) collect isDerivation mapAttrs;
 
   inherit (final) callPackage;
 
@@ -26,7 +26,7 @@ let
     clangOmpss2Unwrapped = callPackage ./pkgs/llvm-ompss2/clang.nix { };
     clsparse = callPackage ./pkgs/clsparse/package.nix { };
     #extrae = callPackage ./pkgs/extrae/default.nix { }; # Broken and outdated
-    gpi-2 = callPackage ./pkgs/gpi-2/default.nix { };
+    #gpi-2 = callPackage ./pkgs/gpi-2/default.nix { }; # Broken: https://jungle.bsc.es/git/rarias/bscpkgs/issues/7
     intel-apt = callPackage ./pkgs/intel-oneapi/packages.nix { };
     intelPackages_2023 = callPackage ./pkgs/intel-oneapi/2023.nix { };
     intelPackages_2024 = final.intel-apt.hpckit_2024;
@@ -57,23 +57,12 @@ let
     stdenvClangOmpss2Nanos6 = final.stdenv.override { cc = final.clangOmpss2Nanos6; allowedRequisites = null; };
     stdenvClangOmpss2Nodes = final.stdenv.override { cc = final.clangOmpss2Nodes; allowedRequisites = null; };
     stdenvClangOmpss2NodesOmpv = final.stdenv.override { cc = final.clangOmpss2NodesOmpv; allowedRequisites = null; };
-    tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
+    #tagaspi = callPackage ./pkgs/tagaspi/default.nix { }; # Broken due gpi-2
     tampi = callPackage ./pkgs/tampi/default.nix { };
-    tacuda = callPackage ./pkgs/tacuda/default.nix { };
     taopencl = callPackage ./pkgs/taopencl/default.nix { };
     tasycl = callPackage ./pkgs/tasycl/default.nix { };
     tasycl-acpp = callPackage ./pkgs/tasycl/default.nix { useIntel = false; };
     wxparaver = callPackage ./pkgs/paraver/default.nix { };
-
-    # Fix for RISC-V cross compilation
-    # TODO: remove once we update to 25.11
-    # https://github.com/NixOS/nixpkgs/commit/d9c222c81435b
-    prrte = prev.prrte.overrideAttrs (prevAttrs: {
-      configureFlags = (prevAttrs.configureFlags or []) ++ [
-        "--with-pmix=${prev.lib.getDev final.pmix}"
-        "--with-pmix-libdir=${prev.lib.getLib final.pmix}/lib"
-      ];
-    });
   };
 
 in bscPkgs // {
@@ -126,21 +115,15 @@ in bscPkgs // {
       };
     };
 
-    pkgs = filterAttrs (_: isDerivation) bscPkgs;
-
-    pkgsList = final.runCommand "ci-pkgs" { }
+    pkgs = final.runCommand "ci-pkgs" { }
       "printf '%s\n' ${toString (collect isDerivation bscPkgs)} > $out";
 
     tests = final.runCommand "ci-tests" { }
       "printf '%s\n' ${toString (collect isDerivation final.bsc-ci.test)} > $out";
 
-    cross = prev.lib.genAttrs [ "riscv64" ] (target:
-      final.pkgsCross.${target}.bsc-ci.pkgs
-    );
-
     all = final.runCommand "ci-all" { }
     ''
-      deps="${toString [ final.bsc-ci.pkgsList final.bsc-ci.tests ]}"
+      deps="${toString [ final.bsc-ci.pkgs final.bsc-ci.tests ]}"
       cat $deps
       printf '%s\n' $deps > $out
     '';

pkgs/extrae/default.nix

@@ -20,7 +20,6 @@
 #, python3Packages
 , installShellFiles
 , symlinkJoin
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
 }:
 
 let
@@ -88,7 +87,7 @@ stdenv.mkDerivation rec {
       --enable-sampling
       --with-unwind=${libunwind.dev}
       --with-xml-prefix=${libxml2.dev}
-      ${lib.optionalString enablePapi "--with-papi=${papi}"}
+      --with-papi=${papi}
       ${if (mpi != null) then ''--with-mpi=${mpi}''
         else ''--without-mpi''}
       --without-dyninst)

pkgs/gpi-2/default.nix

@@ -34,8 +34,6 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  patches = [ ./rdma-core.patch ./max-mem.patch ];
-
   preConfigure = ''
     patchShebangs autogen.sh
     ./autogen.sh

pkgs/gpi-2/max-mem.patch

@@ -1,10 +0,0 @@
---- a/tests/tests/segments/max_mem.c	2025-09-12 13:30:53.449353591 +0200
-+++ b/tests/tests/segments/max_mem.c	2025-09-12 13:33:49.750352401 +0200
-@@ -1,5 +1,7 @@
- #include <test_utils.h>
- 
-+gaspi_size_t gaspi_get_system_mem (void);
-+
- /* Test allocates 45% of system memory and creates a segment that
-    large or if several ranks per node exist, divided among that
-    number */

pkgs/gpi-2/rdma-core.patch

@@ -1,12 +0,0 @@
---- a/src/devices/ib/GPI2_IB.h	2025-09-12 13:25:31.564181121 +0200
-+++ b/src/devices/ib/GPI2_IB.h	2025-09-12 13:24:49.105422150 +0200
-@@ -26,6 +26,9 @@ along with GPI-2. If not, see <http://ww
- 
- #include "GPI2_Dev.h"
- 
-+/* Missing prototype as driver.h is now private */
-+int ibv_read_sysfs_file(const char *dir, const char *file, char *buf, size_t size);
-+
- #define GASPI_GID_INDEX   (0)
- #define PORT_LINK_UP      (5)
- #define MAX_INLINE_BYTES  (128)

pkgs/llvm-ompss2/default.nix

@@ -2,7 +2,6 @@
   stdenv
 , lib
 , gcc
-, gcc13
 , clangOmpss2Unwrapped
 , writeShellScript
 , openmp ? null
@@ -11,9 +10,9 @@
 , ompss2rt ? null
 }:
 
-let
-  inherit (lib) assertMsg optional optionalString;
+with lib;
 
+let
   usingNodesAndOmpv = (openmp.pname == "openmp-v" && ompss2rt.pname == "nodes");
   sameNosv = openmp.nosv == ompss2rt.nosv;
 in
@@ -38,8 +37,7 @@ let
   targetConfig = stdenv.targetPlatform.config;
   inherit gcc;
   cc = clangOmpss2Unwrapped;
-
-  gccVersion = with lib.versions; let v = gcc.version; in concatStringsSep "." [(major v) (minor v) (patch v)];
+  gccVersion = with versions; let v = gcc.version; in concatStringsSep "." [(major v) (minor v) (patch v)];
 
   extraBuildCommands = ''
     echo "-target ${targetConfig}" >> $out/nix-support/cc-cflags
@@ -94,8 +92,7 @@ let
   '';
 
   wrappedCCIntel = wrapCCWith {
-    inherit bintools extraPackages;
-    cc = cc.override { gcc = gcc13; }; # Intel uses gcc13, so we have to match it
+    inherit cc bintools extraPackages;
     # extraPackages adds packages to depsTargetTargetPropagated
     extraBuildCommands = intelExtraBuildCommands + envExports;
   };

pkgs/lmbench/default.nix

@@ -22,11 +22,7 @@ stdenv.mkDerivation rec {
   '';
 
   buildInputs = [ libtirpc ];
-  patches = [
-    ./fix-install.patch
-    ./gcc-14.patch
-    ./fix-cross.patch
-  ];
+  patches = [ ./fix-install.patch ./gcc-14.patch ];
 
   hardeningDisable = [ "all" ];
 
@@ -39,8 +35,6 @@ stdenv.mkDerivation rec {
       CFLAGS=-Wno-implicit-int
       CPPFLAGS=-I${libtirpc.dev}/include/tirpc
       LDFLAGS=-ltirpc
-      CC=${stdenv.cc.targetPrefix}cc
-      AR=${stdenv.cc.targetPrefix}ar
     )
   '';
 

pkgs/lmbench/fix-cross.patch

@@ -1,13 +0,0 @@
-diff --git a/src/Makefile b/src/Makefile
-index 2555014..356eeb3 100644
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -36,7 +36,7 @@ SHELL=/bin/sh
- 
- CC=`../scripts/compiler`
- MAKE=`../scripts/make`
--AR=ar
-+AR?=ar
- ARCREATE=cr
- 
- # base of installation location

pkgs/nanos6/default.nix

@@ -16,7 +16,6 @@
 , jemallocNanos6 ? null
 , cachelineBytes ? 64
 , enableGlibcxxDebug ? false
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/nanos6/nanos6"
 , gitBranch ? "master"
@@ -48,8 +47,6 @@ let
   };
 
   source = if (useGit) then git else release;
-
-  isCross = stdenv.hostPlatform != stdenv.buildPlatform;
 in
   stdenv.mkDerivation (source // {
     pname = "nanos6";
@@ -74,11 +71,9 @@ in
       "--disable-all-instrumentations"
       "--enable-ovni-instrumentation"
       "--with-ovni=${ovni}"
-      "--with-boost=${boost.dev}"
     ] ++
       (optional enableJemalloc "--with-jemalloc=${jemallocNanos6}") ++
-      (optional enableGlibcxxDebug "CXXFLAGS=-D_GLIBCXX_DEBUG") ++
-      (optional isCross "--with-symbol-resolution=ifunc");
+      (optional enableGlibcxxDebug "CXXFLAGS=-D_GLIBCXX_DEBUG");
 
     postConfigure = lib.optionalString (!enableDebug) ''
       # Disable debug
@@ -102,14 +97,16 @@ in
       # TODO: papi_version is needed for configure:
       # ./configure: line 27378: papi_version: command not found
       # This probably breaks cross-compilation
-    ] ++ lib.optionals enablePapi [ papi ];
+      papi
+    ];
 
     buildInputs = [
       boost
       numactl
       hwloc
+      papi
       ovni
-    ] ++ lib.optionals enablePapi [ papi ];
+    ];
 
     # Create a script that sets NANOS6_HOME
     postInstall = ''

pkgs/nosv/default.nix

@@ -7,7 +7,7 @@
 , numactl
 , hwloc
 , papi
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
+, enablePapi ? true
 , cacheline ? 64 # bits
 , ovni ? null
 , useGit ? false

pkgs/ovni/default.nix

@@ -44,7 +44,6 @@ in
       patchShebangs --build test/
     '';
     nativeBuildInputs = [ cmake ] ++ lib.optionals (useMpi) [ mpi ];
-    buildInputs = lib.optionals (useMpi) [ mpi ];
     cmakeBuildType = if (enableDebug) then "Debug" else "Release";
     cmakeFlags = [
       "-DOVNI_GIT_COMMIT=${src.shortRev}"

pkgs/paraver/default.nix

@@ -1,4 +1,5 @@
-{ stdenv
+{
+  stdenv
 , fetchFromGitHub
 , autoreconfHook
 , boost
@@ -11,17 +12,14 @@
 , openssl
 , glibcLocales
 , wrapGAppsHook
-
-, enableDebug ? false
 }:
 
 let
   wx = wxGTK32;
-  version = "4.12.0";
 in
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   pname = "wxparaver";
-  inherit version;
+  version = "4.12.0";
 
   src = fetchFromGitHub {
     owner = "bsc-performance-tools";
@@ -38,26 +36,21 @@ stdenv.mkDerivation {
     ./fix-boost-87.patch
   ];
 
+  hardeningDisable = [ "all" ];
+
   # Fix the PARAVER_HOME variable
   postPatch = ''
     sed -i 's@^PARAVER_HOME=.*$@PARAVER_HOME='$out'@g' docs/wxparaver
     sed -i '1aexport LOCALE_ARCHIVE="${glibcLocales}/lib/locale/locale-archive"' docs/wxparaver
   '';
 
+  dontStrip = true;
   enableParallelBuilding = true;
 
-  hardeningDisable = [ "all" ];
-
-  dontStrip = true;
-
-  env =
-    let
-      flags = if enableDebug then "-ggdb -Og" else "-O3";
-    in
-    {
-      CFLAGS = flags;
-      CXXFLAGS = flags;
-    };
+  preConfigure = ''
+    export CFLAGS="-O3"
+    export CXXFLAGS="-O3"
+  '';
 
   configureFlags = [
     "--with-boost=${boost}"
@@ -75,11 +68,11 @@ stdenv.mkDerivation {
 
   buildInputs = [
     boost
-    libxml2
+    libxml2.dev
     xml2
     wx
     paraverKernel
-    openssl
+    openssl.dev
   ];
 
   postInstall = ''

pkgs/paraver/kernel.nix

@@ -1,4 +1,5 @@
-{ stdenv
+{
+  stdenv
 , fetchFromGitHub
 , autoreconfHook
 , boost
@@ -8,16 +9,11 @@
 , automake
 , pkg-config
 , zlib
-
-, enableDebug ? false
 }:
 
-let
-  version = "4.12.0";
-in
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   pname = "paraver-kernel";
-  inherit version;
+  version = "4.12.0";
 
   src = fetchFromGitHub {
     owner = "bsc-performance-tools";
@@ -38,14 +34,10 @@ stdenv.mkDerivation {
 
   dontStrip = true;
 
-  env =
-    let
-      flags = "-DPARALLEL_ENABLED " + (if enableDebug then "-ggdb -Og" else "-O3");
-    in
-    {
-      CFLAGS = flags;
-      CXXFLAGS = flags;
-    };
+  preConfigure = ''
+    export CFLAGS="-O3 -DPARALLEL_ENABLED"
+    export CXXFLAGS="-O3 -DPARALLEL_ENABLED"
+  '';
 
   configureFlags = [
     "--with-boost=${boost}"

pkgs/tacuda/default.nix

@@ -1,4 +1,6 @@
 { stdenv
+, lib
+, withCFlags
 , fetchFromGitHub
 , automake
 , autoconf
@@ -6,24 +8,21 @@
 , gnumake
 , autoreconfHook
 , boost
-, cudaPackages
 
 , useGit ? false
 , gitUrl ? "git@gitlab-internal.bsc.es:task-awareness/tacuda/tacuda.git"
 , gitBranch ? "main"
-, gitCommit ? "35234f9445e6149a2bd38d119841e2485d6ee05e"
+, gitCommit ? ""
 }:
 
 let
-
-  release_ver = "2.1.0";
-  release = {
-    version = release_ver;
+  release = rec {
+    version = "2.1.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "tacuda";
-      rev = release_ver;
-      hash = "sha256-Cj3EiLVJSLvRv0ydeg7Vp4SpkniEqHkcWF+YOJQ8EcM=";
+      rev = version;
+      hash = "";
     };
   };
 
@@ -55,14 +54,8 @@ stdenv.mkDerivation {
     gnumake
   ];
 
-  patches = [ ./fix_config.patch ];
-
-  configureFlags = [ "--with-cuda-include=${cudaPackages.cudatoolkit}/include" ];
-
   buildInputs = [
     boost
-    cudaPackages.libcublas
-    cudaPackages.cuda_cudart
   ];
 
 }

pkgs/tacuda/fix_config.patch

@@ -1,13 +0,0 @@
-diff --git a/m4/cuda.m4 b/m4/cuda.m4
-index 23f5c94..8f9b534 100644
---- a/m4/cuda.m4
-+++ b/m4/cuda.m4
-@@ -40,7 +40,7 @@ search_libs="cuda cublas cudart"
- required_libs=""
- 
- m4_foreach([function],
--           [cuInit,
-+           [
- 	    cublasSgemm,
-             cudaStreamCreate,
-             cudaLaunchKernel,

pkgs/taopencl/default.nix

@@ -17,7 +17,7 @@ stdenv.mkDerivation (finalAttrs: {
   version = finalAttrs.src.shortRev;
 
   src = builtins.fetchGit {
-    url = "git@gitlab-internal.bsc.es:task-awareness/taopencl/taopencl.git";
+    url =  "git@gitlab-internal.bsc.es:task-awareness/taopencl/taopencl.git";
     ref = "master";
     rev = "c3b7b32ae8fa4af7ceff598532a881f8f1490aaf";
   };