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12 changed files with 674 additions and 25 deletions

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@@ -51,6 +51,7 @@ let
ovniGit = final.ovni.override { useGit = true; };
paraverKernel = callPackage ./pkgs/paraver/kernel.nix { };
pocl = callPackage ./pkgs/pocl/default.nix { };
pocl-noicd = callPackage ./pkgs/pocl/default.nix { enableICD = false; };
prometheus-slurm-exporter = prev.callPackage ./pkgs/slurm-exporter/default.nix { };
#pscom = callPackage ./pkgs/parastation/pscom.nix { }; # Unmaintaned
#psmpi = callPackage ./pkgs/parastation/psmpi.nix { }; # Unmaintaned
@@ -63,7 +64,16 @@ let
tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
tampi = callPackage ./pkgs/tampi/default.nix { };
upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
taopencl = callPackage ./pkgs/taopencl/default.nix { };
wxparaver = callPackage ./pkgs/paraver/default.nix { };
gromacs = callPackage ./pkgs/gromacs/default.nix { enableSYCL = true; };
_cuda = prev._cuda.extend (_: _prev: final.lib.recursiveUpdate _prev {
extensions = _prev.extensions ++ [(finalAttrs: _: {
tacuda = finalAttrs.callPackage ./pkgs/tacuda/default.nix { };
})];
});
};
tests = rec {
@@ -98,7 +108,12 @@ let
stdenv = final.stdenvClangOmpss2NodesOmpv;
};
ocl-build = callPackage ./test/compilers/opencl.nix { };
ocl-build-noicd = callPackage ./test/compilers/opencl.nix { ocl-icd = final.pocl-noicd; };
pocl = callPackage ./test/compilers/pocl.nix { };
ocl-run-pocl = ocl-build.test-icd;
ocl-run-pocl-noicd = ocl-build-noicd.test-noicd;
};
# For now, only build toplevel packages in CI/Hydra

190
pkgs/gromacs/default.nix Normal file
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@@ -0,0 +1,190 @@
{
lib,
stdenv,
fetchurl,
cmake,
hwloc,
fftw,
perl,
blas,
lapack,
llvmPackages,
intelPackages ? null,
mpi,
cudaPackages,
plumed,
singlePrec ? true,
config,
enableSYCL ? false,
enableCuda ? config.cudaSupport,
enableMpi ? false,
enablePlumed ? false,
cpuAcceleration ? null,
}:
# CUDA is only implemented for single precission
assert enableCuda -> singlePrec;
assert !(enableSYCL && enableCuda);
assert enableSYCL -> intelPackages != null;
let
inherit (cudaPackages.flags) cmakeCudaArchitecturesString;
# 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
# AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD
SIMD =
x:
if (cpuAcceleration != null) then
x
else if stdenv.hostPlatform.system == "i686-linux" then
"SSE2"
else if stdenv.hostPlatform.system == "x86_64-linux" then
"SSE4.1"
else if stdenv.hostPlatform.system == "x86_64-darwin" then
"SSE4.1"
else if stdenv.hostPlatform.system == "aarch64-linux" then
"ARM_NEON_ASIMD"
else
"None";
source =
if enablePlumed then
{
version = "2024.2";
hash = "sha256-gCp+M18uiVdw9XsVnk7DaOuw/yzm2sz3BsboAlw2hSs=";
}
else
{
version = "2025.3";
hash = "sha256-i9/KAmjz8Qp8o8BuWbYvc+oCQgxnIRwP85EvMteDPGU=";
};
stdenv' = if enableSYCL then intelPackages.stdenv else stdenv;
in
stdenv'.mkDerivation rec {
pname = "gromacs";
version = source.version;
src = fetchurl {
url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz";
inherit (source) hash;
};
patches = [ (if enablePlumed then ./pkgconfig-2024.patch else ./pkgconfig-2025.patch) ];
postPatch = lib.optionalString enablePlumed ''
plumed patch -p -e gromacs-${source.version}
'';
outputs = [
"out"
"dev"
"man"
];
nativeBuildInputs = [
cmake
]
++ lib.optional enablePlumed plumed
++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
env.MKLROOT = intelPackages.mkl;
buildInputs = [
fftw
perl
hwloc
blas
lapack
]
++ lib.optional enableMpi mpi
++ lib.optionals enableCuda [
cudaPackages.cuda_cccl
cudaPackages.cuda_cudart
cudaPackages.libcufft
cudaPackages.cuda_profiler_api
]
++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;
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"
]
++ (
if singlePrec then
[
"-DGMX_DOUBLE=OFF"
]
else
[
"-DGMX_DOUBLE=ON"
"-DGMX_DEFAULT_SUFFIX=OFF"
]
)
++ (
if enableMpi then
[
"-DGMX_MPI:BOOL=TRUE"
"-DGMX_THREAD_MPI:BOOL=FALSE"
]
else
[
"-DGMX_MPI:BOOL=FALSE"
]
)
++ (lib.optionals enableSYCL [
"-DGMX_GPU=SYCL"
"-DGMX_OPENMP=OFF" # TODO: enable OpenMP with SYCL?
])
++ lib.optionals enableCuda [
"-DGMX_GPU=CUDA"
(lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString)
# Gromacs seems to ignore and override the normal variables, so we add this ad hoc:
(lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" cmakeCudaArchitecturesString)
];
postInstall = ''
moveToOutput share/cmake $dev
'';
meta = with lib; {
homepage = "https://www.gromacs.org";
license = licenses.lgpl21Plus;
description = "Molecular dynamics software package";
longDescription = ''
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems
with hundreds to millions of particles.
It is primarily designed for biochemical molecules like
proteins, lipids and nucleic acids that have a lot of
complicated bonded interactions, but since GROMACS is
extremely fast at calculating the nonbonded interactions (that
usually dominate simulations) many groups are also using it
for research on non-biological systems, e.g. polymers.
GROMACS supports all the usual algorithms you expect from a
modern molecular dynamics implementation, (check the online
reference or manual for details), but there are also quite a
few features that make it stand out from the competition.
See: https://www.gromacs.org/about.html for details.
'';
platforms = platforms.unix;
maintainers = with maintainers; [
sheepforce
markuskowa
];
};
}

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@@ -0,0 +1,24 @@
diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
index 646787cb53..9b97ad57f7 100644
--- a/src/external/muparser/muparser.pc.in
+++ b/src/external/muparser/muparser.pc.in
@@ -1,7 +1,5 @@
-prefix=@CMAKE_INSTALL_PREFIX@
-exec_prefix=${prefix}
-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
Name: @PACKAGE_NAME@
Description: Mathematical expressions parser library
diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
index ec1ed6684e..ca1105474a 100644
--- a/src/gromacs/libgromacs.pc.cmakein
+++ b/src/gromacs/libgromacs.pc.cmakein
@@ -1,4 +1,4 @@
-libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
Name: libgromacs@GMX_LIBS_SUFFIX@
Description: Gromacs library

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@@ -0,0 +1,36 @@
diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
index 646787cb53..d26e84de8f 100644
--- a/src/external/muparser/muparser.pc.in
+++ b/src/external/muparser/muparser.pc.in
@@ -1,11 +1,9 @@
-prefix=@CMAKE_INSTALL_PREFIX@
-exec_prefix=${prefix}
-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
-
-Name: @PACKAGE_NAME@
-Description: Mathematical expressions parser library
-Version: @MUPARSER_VERSION@
-Requires:
-Libs: -L${libdir} -lmuparser
-Cflags: -I${includedir} @PKG_CONFIG_FLAGS@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
+
+Name: @PACKAGE_NAME@
+Description: Mathematical expressions parser library
+Version: @MUPARSER_VERSION@
+Requires:
+Libs: -L${libdir} -lmuparser
+Cflags: -I${includedir} @PKG_CONFIG_FLAGS@
diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
index af9b5a6dc0..5f58d549bf 100644
--- a/src/gromacs/libgromacs.pc.cmakein
+++ b/src/gromacs/libgromacs.pc.cmakein
@@ -1,5 +1,4 @@
-prefix=@CMAKE_INSTALL_PREFIX@
-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
Name: libgromacs@GMX_LIBS_SUFFIX@
Description: Gromacs library

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@@ -13,6 +13,9 @@
libxml2, # required for statically linked llvm
python3,
writableTmpDirAsHomeHook,
writeText,
runCommand,
opencl-cts,
fetchFromGitHub,
@@ -194,22 +197,46 @@ stdenv.mkDerivation (finalAttrs: {
runHook postInstallCheck
'';
setupHook = ./setup-hook.sh;
setupHook = lib.optionalDrvAttr enableICD (
writeText "setup-hook" ''
addToSearchPath OCL_ICD_VENDORS @out@/etc/OpenCL/vendors
''
);
passthru = {
updateScript = nix-update-script { };
git = finalAttrs.finalPackage.override { useGit = true; };
test = finalAttrs.finalPackage.overrideAttrs { doCheck = true; };
};
passthru =
let
self = finalAttrs.finalPackage;
in
{
updateScript = nix-update-script { };
git = self.override { useGit = true; };
requiredSystemFeatures = lib.optionals (finalAttrs.finalPackage.doCheck && enableHWLOC) [
"sys-devices"
];
withICD = enableICD;
preCheck = ''
export POCL_DEBUG=error,warn
export NIX_DEBUG=1
'';
test = {
# Run builtin tests (causes a rebuild)
self = self.overrideAttrs { doCheck = true; };
# Run basic test from Khronos OpenCL Conformance Test Suite
# WARN: despite its name, test_basic is very exhaustive, and can take more
# than 1 hour in a marenostrum5 node.
cts =
assert enableICD;
lib.genAttrs [ "api" "basic" "c11_atomics" "printf" "svm" ] (
name:
runCommand "pocl-cts-test_${name}" {
nativeBuildInputs = [ self ];
requiredSystemFeatures = [ "sys-devices" ];
env = {
POCL_DEBUG = "error,warn";
POCL_CACHE_DIR = "/build/pocl_cache";
};
} "${opencl-cts}/bin/Release/test_${name} | tee $out"
);
};
};
env.HWLOC_SYNTHETIC = lib.optionalDrvAttr enableHWLOC "node:1 core:1 pu:1";
propagatedBuildInputs = [ stdenv.cc.cc ];

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@@ -1,6 +0,0 @@
preCheckHooks+=('setupPoclCheck')
preInstallCheckHooks+=('setupPoclCheck')
setupPoclCheck () {
export OCL_ICD_VENDORS="@out@/etc/OpenCL/vendors"
}

72
pkgs/tacuda/default.nix Normal file
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@@ -0,0 +1,72 @@
{
backendStdenv,
fetchFromGitHub,
automake,
autoconf,
libtool,
gnumake,
autoreconfHook,
boost,
cudatoolkit,
libcublas,
cuda_cudart,
useGit ? false,
gitUrl ? "git@gitlab-internal.bsc.es:task-awareness/tacuda/tacuda.git",
gitBranch ? "main",
gitCommit ? "35234f9445e6149a2bd38d119841e2485d6ee05e",
}:
let
release_ver = "2.1.0";
release = {
version = release_ver;
src = fetchFromGitHub {
owner = "bsc-pm";
repo = "tacuda";
rev = release_ver;
hash = "sha256-Cj3EiLVJSLvRv0ydeg7Vp4SpkniEqHkcWF+YOJQ8EcM=";
};
};
git = rec {
version = src.shortRev;
src = builtins.fetchGit {
url = gitUrl;
ref = gitBranch;
rev = gitCommit;
};
};
source = if (useGit) then git else release;
in
backendStdenv.mkDerivation {
pname = "tacuda";
inherit (source) src version;
enableParallelBuilding = true;
separateDebugInfo = true;
strictDeps = true;
nativeBuildInputs = [
autoreconfHook
automake
autoconf
libtool
gnumake
];
patches = [ ./fix_config.patch ];
configureFlags = [ "--with-cuda-include=${cudatoolkit}/include" ];
buildInputs = [
boost
libcublas
cuda_cudart
];
}

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@@ -0,0 +1,13 @@
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,

46
pkgs/taopencl/default.nix Normal file
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@@ -0,0 +1,46 @@
{
stdenv,
automake,
autoconf,
libtool,
gnumake,
boost,
mpi,
gcc,
autoreconfHook,
ocl-icd,
opencl-headers,
}:
stdenv.mkDerivation (finalAttrs: {
pname = "taopencl";
version = finalAttrs.src.shortRev;
src = builtins.fetchGit {
url = "git@gitlab-internal.bsc.es:task-awareness/taopencl/taopencl.git";
ref = "master";
rev = "c3b7b32ae8fa4af7ceff598532a881f8f1490aaf";
};
enableParallelBuilding = true;
separateDebugInfo = true;
configureFlags = [
"--with-opencl-lib=${ocl-icd}/lib"
"--with-opencl-include=${opencl-headers}/include"
];
buildInputs = [
autoreconfHook
automake
autoconf
libtool
gnumake
boost
mpi
gcc
];
dontDisableStatic = true;
hardeningDisable = [ "all" ];
})

127
test/compilers/opencl.c Normal file
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@@ -0,0 +1,127 @@
#include <CL/cl.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define BUF_LEN 128
cl_int exit_err = CL_SUCCESS;
#define CHECK(cmd) \
do { \
cl_int err = cmd; \
if (err != CL_SUCCESS) { \
printf("[ERROR] " #cmd " (Error code: %d)\n" \
"@ "__FILE__ \
":%d", \
err, __LINE__); \
exit_err = err; \
goto cleanup; \
} \
} while (0)
const char *kernel_source = "__kernel void vector_add(__global const float *a, "
"__global const float *b, __global float *c) {\n"
" int gid = get_global_id(0);\n"
" c[gid] = a[gid] + b[gid];\n"
"}\n";
cl_int test_kernel_compilation(cl_platform_id platform) {
cl_device_id device = NULL;
cl_context context = NULL;
cl_program program = NULL;
cl_int err = CL_SUCCESS;
char device_name[BUF_LEN];
// Get first device for this platform
CHECK(clGetDeviceIDs(platform, CL_DEVICE_TYPE_ALL, 1, &device, NULL));
// Get device name
CHECK(clGetDeviceInfo(device, CL_DEVICE_NAME, sizeof(device_name),
device_name, NULL));
printf(" Device: %s\n", device_name);
context = clCreateContext(NULL, 1, &device, NULL, NULL, &err);
CHECK(err);
program = clCreateProgramWithSource(context, 1, &kernel_source, NULL, &err);
CHECK(err);
err = clBuildProgram(program, 1, &device, NULL, NULL, NULL);
if (err != CL_SUCCESS) {
printf(" [ERROR] Kernel compilation failed (Error code: %d)\n", err);
// Build log
size_t log_size;
CHECK(clGetProgramBuildInfo(program, device, CL_PROGRAM_BUILD_LOG, 0, NULL,
&log_size));
char *log = (char *)malloc(log_size);
CHECK(clGetProgramBuildInfo(program, device, CL_PROGRAM_BUILD_LOG, log_size,
log, NULL));
printf(" Build log:\n%s\n", log);
free(log);
goto cleanup;
}
printf(" [OK] Kernel compiled successfully!\n");
cleanup:
if (program)
clReleaseProgram(program);
if (context)
clReleaseContext(context);
printf("\n");
return exit_err;
}
int main() {
cl_uint num_platforms;
cl_platform_id *platforms = NULL;
// Get number of platforms
CHECK(clGetPlatformIDs(0, NULL, &num_platforms));
printf("Found %d OpenCL platform(s)\n\n", num_platforms);
if (num_platforms == 0) {
printf("No OpenCL platforms found!\n");
return EXIT_FAILURE;
}
// Allocate memory for platforms
platforms = (cl_platform_id *)malloc(sizeof(cl_platform_id) * num_platforms);
// Get platform IDs
CHECK(clGetPlatformIDs(num_platforms, platforms, NULL));
// Query each platform and test kernel compilation
for (cl_uint i = 0; i < num_platforms; i++) {
char platform_name[BUF_LEN];
char platform_vendor[BUF_LEN];
char platform_version[BUF_LEN];
CHECK(clGetPlatformInfo(platforms[i], CL_PLATFORM_NAME,
sizeof(platform_name), platform_name, NULL));
CHECK(clGetPlatformInfo(platforms[i], CL_PLATFORM_VENDOR,
sizeof(platform_vendor), platform_vendor, NULL));
CHECK(clGetPlatformInfo(platforms[i], CL_PLATFORM_VERSION,
sizeof(platform_version), platform_version, NULL));
printf("Platform %d: %s\n", i, platform_name);
printf(" Vendor: %s\n", platform_vendor);
printf(" Version: %s\n", platform_version);
// Test kernel compilation
CHECK(test_kernel_compilation(platforms[i]));
}
cleanup:
if (platforms)
free(platforms);
if (exit_err == CL_SUCCESS)
return EXIT_SUCCESS;
return EXIT_FAILURE;
}

104
test/compilers/opencl.nix Normal file
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@@ -0,0 +1,104 @@
{
stdenv,
ocl-icd,
opencl-headers,
pocl,
clinfo,
runCommand,
lib,
}:
stdenv.mkDerivation (finalAttrs: {
pname = "opencl-pocl-test";
version = "1.0.0";
src = ./opencl.c;
dontUnpack = true;
dontConfigure = true;
buildInputs = [
ocl-icd
opencl-headers
];
buildPhase = ''
runHook preBuild
$CC -Wall -Wextra -D CL_TARGET_OPENCL_VERSION=100 $src -o ocl-hello -lOpenCL
runHook postBuild
'';
installPhase = ''
runHook preInstall
mkdir -p $out/bin
cp ocl-hello $out/bin
runHook postInstall
'';
passthru = {
test-icd =
runCommand "custom-clinfo"
{
nativeBuildInputs =
assert !(lib.hasPrefix "pocl" ocl-icd.pname);
[
clinfo
finalAttrs.finalPackage
pocl
];
env = {
POCL_DEBUG = "error,warn";
POCL_CACHE_DIR = "/build/pocl_cache";
};
requiredSystemFeatures = [ "sys-devices" ];
}
''
set -x
mkdir $out
clinfo -l >$out/clinfo
clinfo >$out/clinfo-full
ocl-hello >$out/hello
for i in $out/*; do
grep "Portable Computing Language" $i
done
echo $OCL_ICD_VENDORS >$out/env
grep "pocl.*/etc/OpenCL/vendors" $out/env
set +x
'';
# this needs: ocl-icd = pocl-noicd
test-noicd =
runCommand "custom-clinfo"
{
nativeBuildInputs = [
finalAttrs.finalPackage
];
env = {
POCL_DEBUG = "error,warn";
POCL_CACHE_DIR = "/build/pocl_cache";
};
requiredSystemFeatures = [ "sys-devices" ];
}
''
ocl-hello >$out
grep "Portable Computing Language" $out
'';
};
})

View File

@@ -2,25 +2,26 @@
runCommand,
pocl,
clinfo,
writableTmpDirAsHomeHook,
}:
runCommand "clinfo-pocl"
{
nativeBuildInputs = [
clinfo
writableTmpDirAsHomeHook
pocl
];
requiredSystemFeatures = [ "sys-devices" ];
env = {
POCL_DEBUG = "error,warn";
OCL_ICD_VENDORS = "${pocl}/etc/OpenCL/vendors";
POCL_CACHE_DIR = "/build/pocl_cache";
};
}
''
set -x
clinfo | tee $out
set +x
echo $OCL_ICD_VENDORS
clinfo >$out
# check that we have PoCL:
grep "Portable Computing Language" $out
''