Merge all branches

Currently, we can use bscpkgs similarly to nixpkgs either through
the flake outputs or with import bscpkgs:

```nix
# currently supported:
bscpkgs.legacyPackages.x86_64-linux.hello
let pkgs = import bscpkgs { system = "x86_64-linux"; }; in pkgs.hello
```
The missing piece is nixpkgs.lib (not pkgs.lib, the system agnostic
one). The workaround is to do bscpkgs.inputs.nixpkgs.lib instead. We can
simplify this by forwarding the lib to our outputs.

This enables us to use bscpkgs as a drop-in
replacing the inputs to our flake from nixpkgs to bscpkgs.
(inputs.nixpkgs.url = "<*BSC*pkgs url>").


Reviewed-by: Rodrigo Arias Mallo <rodrigo.arias@bsc.es>

flake.nix

@@ -2,23 +2,36 @@
   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";
+      overlays = [ self.overlays.default ];
-      pkgs = import nixpkgs {
+    };
-        inherit system;
+  in
-        overlays = [ self.overlays.default ];
-      };
-    in
     {
       bscOverlay = import ./overlay.nix;
       overlays.default = self.bscOverlay;
+
       # full nixpkgs with our overlay applied
       legacyPackages.${system} = pkgs;
 
-      hydraJobs = {
+      # packages added by our overlay
-        inherit (self.legacyPackages.${system}.bsc-ci) test pkgs cross;
+      packages.${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))
+          ];
+       legacyPackages.x86_64-linux = pkgs;
 
       # propagate nixpkgs lib, so we can do bscpkgs.lib
       inherit (nixpkgs) lib;

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;
+    pkgs = final.runCommand "ci-pkgs" { }
-
-    pkgsList = 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
+with lib;
-  inherit (lib) assertMsg optional optionalString;
 
+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 versions; let v = gcc.version; in concatStringsSep "." [(major v) (minor v) (patch v)];
-  gccVersion = with lib.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;
+    inherit cc bintools extraPackages;
-    cc = cc.override { gcc = gcc13; }; # Intel uses gcc13, so we have to match it
     # extraPackages adds packages to depsTargetTargetPropagated
     extraBuildCommands = intelExtraBuildCommands + envExports;
   };

pkgs/lmbench/default.nix

@@ -22,11 +22,7 @@ stdenv.mkDerivation rec {
   '';
 
   buildInputs = [ libtirpc ];
-  patches = [
+  patches = [ ./fix-install.patch ./gcc-14.patch ];
-    ./fix-install.patch
-    ./gcc-14.patch
-    ./fix-cross.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 enableGlibcxxDebug "CXXFLAGS=-D_GLIBCXX_DEBUG");
-      (optional isCross "--with-symbol-resolution=ifunc");
 
     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/paraver/default.nix

@@ -1,18 +1,19 @@
-{ stdenv
+{
-, fetchFromGitHub
+  stdenv,
-, autoreconfHook
+  fetchFromGitHub,
-, boost
+  autoreconfHook,
-, libxml2
+  boost,
-, xml2
+  libxml2,
-, wxGTK32
+  xml2,
-, autoconf
+  wxGTK32,
-, automake
+  autoconf,
-, paraverKernel
+  automake,
-, openssl
+  paraverKernel,
-, glibcLocales
+  openssl,
-, wrapGAppsHook
+  glibcLocales,
+  wrapGAppsHook,
 
-, enableDebug ? false
+  enableDebug ? false,
 }:
 
 let

pkgs/paraver/kernel.nix

@@ -1,15 +1,16 @@
-{ stdenv
+{
-, fetchFromGitHub
+  stdenv,
-, autoreconfHook
+  fetchFromGitHub,
-, boost
+  autoreconfHook,
-, libxml2
+  boost,
-, xml2
+  libxml2,
-, autoconf
+  xml2,
-, automake
+  autoconf,
-, pkg-config
+  automake,
-, zlib
+  pkg-config,
+  zlib,
 
-, enableDebug ? false
+  enableDebug ? false,
 }:
 
 let

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 = rec {
-  release_ver = "2.1.0";
+    version = "2.1.0";
-  release = {
-    version = release_ver;
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "tacuda";
-      rev = release_ver;
+      rev = version;
-      hash = "sha256-Cj3EiLVJSLvRv0ydeg7Vp4SpkniEqHkcWF+YOJQ8EcM=";
+      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";
   };