adios2: doCheck with ctestCheckHook

pkgs/by-name/ad/adios2/package.nix

@@ -7,12 +7,12 @@
   ninja,
   gfortran,
   pkg-config,
-  python3,
   python3Packages,
   mpi,
+  catalyst,
   bzip2,
   c-blosc2,
-  hdf5-mpi,
+  hdf5,
   libfabric,
   libpng,
   libsodium,
@@ -25,9 +25,25 @@
   yaml-cpp,
   nlohmann_json,
   llvmPackages,
+  ctestCheckHook,
+  mpiCheckPhaseHook,
+  testers,
+  mpiSupport ? true,
   pythonSupport ? false,
   withExamples ? false,
 }:
+let
+  adios2Packages = {
+    hdf5 = hdf5.override {
+      inherit mpi mpiSupport;
+      cppSupport = !mpiSupport;
+    };
+    catalyst = catalyst.override {
+      inherit mpi mpiSupport pythonSupport;
+    };
+    mpi4py = python3Packages.mpi4py.override { inherit mpi; };
+  };
+in
 stdenv.mkDerivation (finalAttrs: {
   version = "2.10.2";
   pname = "adios2";
@@ -41,7 +57,8 @@ stdenv.mkDerivation (finalAttrs: {
 
   postPatch =
     ''
-      patchShebangs cmake/install/post/generate-adios2-config.sh.in
+      chmod +x cmake/install/post/adios2-config.pre.sh.in
+      patchShebangs cmake/install/post/{generate-adios2-config,adios2-config.pre}.sh.in
     ''
     # Dynamic cast to nullptr on darwin platform, switch to unsafe reinterpret cast.
     + lib.optionalString stdenv.hostPlatform.isDarwin ''
@@ -58,16 +75,17 @@ stdenv.mkDerivation (finalAttrs: {
       pkg-config
     ]
     ++ lib.optionals pythonSupport [
-      python3
+      python3Packages.python
       python3Packages.pybind11
+      python3Packages.pythonImportsCheckHook
     ];
 
   buildInputs =
     [
-      mpi
       bzip2
       c-blosc2
-      (hdf5-mpi.override { inherit mpi; })
+      adios2Packages.catalyst
+      adios2Packages.hdf5
       libfabric
       libpng
       libsodium
@@ -82,53 +100,114 @@ stdenv.mkDerivation (finalAttrs: {
       # Todo: add these optional dependencies in nixpkgs.
       # sz
       # mgard
-      # catalyst
     ]
     ++ lib.optional (lib.meta.availableOn stdenv.hostPlatform ucx) ucx
     # openmp required by zfp
     ++ lib.optional stdenv.cc.isClang llvmPackages.openmp;
 
-  propagatedBuildInputs = lib.optionals pythonSupport [
-    (python3Packages.mpi4py.override { inherit mpi; })
-    python3Packages.numpy
-  ];
+  propagatedBuildInputs =
+    lib.optional mpiSupport mpi
+    ++ lib.optional pythonSupport python3Packages.numpy
+    ++ lib.optional (mpiSupport && pythonSupport) adios2Packages.mpi4py;
 
   cmakeFlags = [
+    # adios2 builtin modules
+    (lib.cmakeBool "ADIOS2_USE_DataMan" true)
+    (lib.cmakeBool "ADIOS2_USE_MHS" true)
+    (lib.cmakeBool "ADIOS2_USE_SST" mpiSupport)
+
+    # declare thirdparty dependencies explicitly
+    (lib.cmakeBool "ADIOS2_USE_EXTERNAL_DEPENDENCIES" true)
+    (lib.cmakeBool "ADIOS2_USE_Blosc2" true)
+    (lib.cmakeBool "ADIOS2_USE_BZip2" true)
+    (lib.cmakeBool "ADIOS2_USE_ZFP" true)
+    (lib.cmakeBool "ADIOS2_USE_SZ" false)
+    (lib.cmakeBool "ADIOS2_USE_LIBPRESSIO" false)
+    (lib.cmakeBool "ADIOS2_USE_MGARD" false)
+    (lib.cmakeBool "ADIOS2_USE_PNG" true)
+    (lib.cmakeBool "ADIOS2_USE_CUDA" false)
+    (lib.cmakeBool "ADIOS2_USE_Kokkos" false)
+    (lib.cmakeBool "ADIOS2_USE_MPI" mpiSupport)
+    (lib.cmakeBool "ADIOS2_USE_DAOS" false)
+    (lib.cmakeBool "ADIOS2_USE_DataSpaces" false)
+    (lib.cmakeBool "ADIOS2_USE_ZeroMQ" true)
     (lib.cmakeBool "ADIOS2_USE_HDF5" true)
     (lib.cmakeBool "ADIOS2_USE_HDF5_VOL" true)
-    (lib.cmakeBool "BUILD_TESTING" false)
+    (lib.cmakeBool "ADIOS2_USE_IME" false)
+    (lib.cmakeBool "ADIOS2_USE_Python" pythonSupport)
+    (lib.cmakeBool "ADIOS2_USE_Fortran" true)
+    (lib.cmakeBool "ADIOS2_USE_UCX" (lib.meta.availableOn stdenv.hostPlatform ucx))
+    (lib.cmakeBool "ADIOS2_USE_Sodium" true)
+    (lib.cmakeBool "ADIOS2_USE_Catalyst" true)
+    (lib.cmakeBool "ADIOS2_USE_Campaign" true)
+    (lib.cmakeBool "ADIOS2_USE_AWSSDK" false)
+
+    # use vendored gtest as nixpkgs#gtest does not include <iomanip> in <gtest/gtest.h>
+    (lib.cmakeBool "ADIOS2_USE_EXTERNAL_GTEST" false)
+    (lib.cmakeBool "BUILD_TESTING" finalAttrs.finalPackage.doCheck)
+    # higher MPIEXEC_MAX_NUMPROCS>8 might cause tests failure in
+    #   - Engine.BP.BPJoinedArray.MultiBlock.BP4.MPI
+    #   - Engine.BP.BPJoinedArray.MultiBlock.BP5.MPI
+    #   - Bindings.Fortran.BPWriteReadHeatMap6D.MPI
+    # due to insufficiently robust data generation and comparison for larger MPI sizes.
+    (lib.cmakeFeature "MPIEXEC_MAX_NUMPROCS" "4")
+
+    # Enable support for Little/Big Endian Interoperability
+    (lib.cmakeBool "ADIOS2_USE_Endian_Reverse" true)
+
     (lib.cmakeBool "ADIOS2_BUILD_EXAMPLES" withExamples)
-    (lib.cmakeBool "ADIOS2_USE_EXTERNAL_DEPENDENCIES" true)
     (lib.cmakeFeature "CMAKE_INSTALL_BINDIR" "bin")
     (lib.cmakeFeature "CMAKE_INSTALL_LIBDIR" "lib")
     (lib.cmakeFeature "CMAKE_INSTALL_INCLUDEDIR" "include")
-    (lib.cmakeFeature "CMAKE_INSTALL_PYTHONDIR" python3.sitePackages)
+    (lib.cmakeFeature "CMAKE_INSTALL_PYTHONDIR" python3Packages.python.sitePackages)
   ];
 
-  # equired for finding the generated adios2-config.cmake file
-  env.adios2_DIR = "${placeholder "out"}/lib/cmake/adios2";
+  # Tests are time-consuming and moved to passthru.tests.withCheck.
+  doCheck = false;
+  dontUseNinjaCheck = true;
 
-  # Ctest takes too much time, so we only perform some smoke Python tests.
-  doInstallCheck = pythonSupport;
+  preCheck = ''
+    export adios2_DIR=$PWD
+  '';
 
-  preCheck =
-    ''
-      export PYTHONPATH=$out/${python3.sitePackages}:$PYTHONPATH
-    ''
-    + lib.optionalString (stdenv.hostPlatform.system == "aarch64-linux") ''
-      rm ../testing/adios2/python/TestBPWriteTypesHighLevelAPI.py
-    '';
+  enableParallelChecking = false;
 
-  pytestFlagsArray = [
-    "../testing/adios2/python/Test*.py"
+  __darwinAllowLocalNetworking = finalAttrs.finalPackage.doCheck && mpiSupport;
+
+  nativeCheckInputs = [
+    python3Packages.python
+    ctestCheckHook
+    mpiCheckPhaseHook
   ];
 
+  # required for finding the generated adios2-config.cmake file
+  preInstall = ''
+    export adios2_DIR=$out/lib/cmake/adios2
+  '';
+
   pythonImportsCheck = [ "adios2" ];
 
-  nativeInstallCheckInputs = lib.optionals pythonSupport [
-    python3Packages.pythonImportsCheckHook
-    python3Packages.pytestCheckHook
-  ];
+  passthru.tests = {
+    withCheck = finalAttrs.finalPackage.overrideAttrs {
+      doCheck = true;
+
+      disabledTests = lib.optionals stdenv.hostPlatform.isDarwin [
+        # TypeError: cannot pickle 'TextIOWrapper' instances
+        "Test.Engine.DataMan1xN.Serial"
+        "Test.Engine.DataManSingleValues"
+        # The test assumed to always contain n*64 byte-length records. Right now the length of index buffer is 71 bytes.
+        "Staging.1x1.Local2.BPS.BB.BP4_stream"
+        # Timeout
+        "Staging.3x5LockGeometry.FS.BB.FileStream"
+        "Engine.Staging.TestOnDemandMPI.ADIOS2OnDemandMPI.SST.MPI"
+      ];
+    };
+
+    cmake-config = testers.hasCmakeConfigModules {
+      moduleNames = [ "adios2" ];
+      package = finalAttrs.finalPackage;
+    };
+  };
 
   meta = {
     homepage = "https://adios2.readthedocs.io/en/latest/";

pkgs/top-level/python-packages.nix

@@ -93,7 +93,6 @@ self: super: with self; {
 
   adios2 = toPythonModule (
     pkgs.adios2.override {
-      python3 = python;
       python3Packages = self;
       pythonSupport = true;
     }