From 31f1b517cdea429dc7a6c212ca650ea184c75a93 Mon Sep 17 00:00:00 2001
From: Someone Serge <sergei.kozlukov@aalto.fi>
Date: Tue, 28 Nov 2023 00:12:07 +0000
Subject: [PATCH] gromacs: drop cudatoolkit.run

---
 .../molecular-dynamics/gromacs/default.nix    | 32 ++++++++++++++++---
 pkgs/development/libraries/hwloc/default.nix  |  5 +--
 pkgs/top-level/all-packages.nix               |  1 -
 3 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index e669562c9cc7..1daeeb81410a 100644
--- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -1,4 +1,14 @@
-{ lib, stdenv, fetchurl, cmake, hwloc, fftw, perl, blas, lapack, mpi, cudatoolkit
+{ lib
+, stdenv
+, fetchurl
+, cmake
+, hwloc
+, fftw
+, perl
+, blas
+, lapack
+, mpi
+, cudaPackages
 , plumed
 , singlePrec ? true
 , config
@@ -9,6 +19,8 @@
 }:
 
 let
+  inherit (cudaPackages.cudaFlags) cudaCapabilities dropDot;
+
   # Select reasonable defaults for all major platforms
   # The possible values are defined in CMakeLists.txt:
   # AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256
@@ -52,7 +64,7 @@ in stdenv.mkDerivation rec {
   nativeBuildInputs =
     [ cmake ]
     ++ lib.optional enablePlumed plumed
-    ;
+    ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
 
   buildInputs = [
     fftw
@@ -61,13 +73,17 @@ in stdenv.mkDerivation rec {
     blas
     lapack
   ] ++ lib.optional enableMpi mpi
-    ++ lib.optional enableCuda cudatoolkit
-  ;
+  ++ lib.optionals enableCuda [
+    cudaPackages.cuda_cudart
+    cudaPackages.libcufft
+    cudaPackages.cuda_profiler_api
+  ];
 
   propagatedBuildInputs = lib.optional enableMpi mpi;
   propagatedUserEnvPkgs = lib.optional enableMpi mpi;
 
   cmakeFlags = [
+    (lib.cmakeBool "GMX_HWLOC" true)
     "-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"
     "-DGMX_OPENMP:BOOL=TRUE"
     "-DBUILD_SHARED_LIBS=ON"
@@ -87,7 +103,13 @@ in stdenv.mkDerivation rec {
      else [
        "-DGMX_MPI:BOOL=FALSE"
      ]
-  ) ++ lib.optional enableCuda "-DGMX_GPU=CUDA";
+  ) ++ lib.optionals enableCuda [
+    "-DGMX_GPU=CUDA"
+    (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities)))
+
+    # Gromacs seems to ignore and override the normal variables, so we add this ad hoc:
+    (lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" (builtins.concatStringsSep ";" (map dropDot cudaCapabilities)))
+  ];
 
   postInstall = ''
     moveToOutput share/cmake $dev
diff --git a/pkgs/development/libraries/hwloc/default.nix b/pkgs/development/libraries/hwloc/default.nix
index 67048167d6bf..626d0b7cca94 100644
--- a/pkgs/development/libraries/hwloc/default.nix
+++ b/pkgs/development/libraries/hwloc/default.nix
@@ -22,12 +22,13 @@ stdenv.mkDerivation rec {
   ];
 
   # XXX: libX11 is not directly needed, but needed as a propagated dep of Cairo.
-  nativeBuildInputs = [ pkg-config ];
+  nativeBuildInputs = [ pkg-config ]
+  ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
 
   buildInputs = [ expat ncurses ]
     ++ lib.optionals x11Support [ cairo libX11 ]
     ++ lib.optionals stdenv.isLinux [ numactl ]
-    ++ lib.optional enableCuda cudaPackages.cudatoolkit;
+    ++ lib.optionals enableCuda [ cudaPackages.cuda_cudart ];
 
   # Since `libpci' appears in `hwloc.pc', it must be propagated.
   propagatedBuildInputs = lib.optional stdenv.isLinux pciutils;
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 65bb876dd6fe..75e47757a8eb 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -39447,7 +39447,6 @@ with pkgs;
     singlePrec = true;
     enableMpi = true;
     enableCuda = true;
-    cudatoolkit = cudatoolkit_11;
     fftw = fftwSinglePrec;
   });