adios2: 2.10.2 -> 2.11.0 (#463788)

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

@@ -25,7 +25,9 @@
   libffi,
   yaml-cpp,
   nlohmann_json,
+  openssl,
   llvmPackages,
+  gtest,
   ctestCheckHook,
   mpiCheckPhaseHook,
   testers,
@@ -51,24 +53,24 @@ let
   };
 in
 stdenv.mkDerivation (finalAttrs: {
-  version = "2.10.2";
+  version = "2.11.0";
   pname = "adios2";
 
   src = fetchFromGitHub {
     owner = "ornladios";
     repo = "adios2";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-NVyw7xoPutXeUS87jjVv1YxJnwNGZAT4QfkBLzvQbwg=";
+    hash = "sha256-yHPI///17poiCEb7Luu5qfqxTWm9Nh+o9r57mZT26U0=";
   };
 
   postPatch = ''
     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 ''
-    substituteInPlace bindings/Python/py11{Attribute,Engine,Variable}.cpp \
-      --replace-fail "dynamic_cast" "reinterpret_cast"
+
+    # use upstream GoogleTest.cmake
+    # see https://github.com/ornladios/ADIOS2/issues/4659
+    substituteInPlace cmake/GoogleTest.cmake \
+      --replace-fail 'CMAKE_VERSION VERSION_LESS 4' 'TRUE'
   '';
 
   nativeBuildInputs = [
@@ -98,6 +100,7 @@ stdenv.mkDerivation (finalAttrs: {
     zlib
     yaml-cpp
     nlohmann_json
+    openssl
 
     # Todo: add these optional dependencies in nixpkgs.
     # sz
@@ -141,11 +144,10 @@ stdenv.mkDerivation (finalAttrs: {
     (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_OpenSSL" 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
@@ -171,51 +173,29 @@ stdenv.mkDerivation (finalAttrs: {
   doCheck = false;
   dontUseNinjaCheck = true;
 
-  preCheck = ''
-    export adios2_DIR=$PWD
-  '';
-
   enableParallelChecking = false;
 
-  enabledTestPaths = [
-    "../testing/adios2/python/Test*.py"
-  ];
-
   __darwinAllowLocalNetworking = finalAttrs.finalPackage.doCheck && mpiSupport;
 
   nativeCheckInputs = [
     python3Packages.python
+    gtest
     ctestCheckHook
     mpiCheckPhaseHook
   ];
 
-  # required for finding the generated adios2-config.cmake file
-  preInstall = ''
-    export adios2_DIR=$out/lib/cmake/adios2
-  '';
-
   pythonImportsCheck = [ "adios2" ];
 
   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;
     };
+  }
+  // lib.optionalAttrs stdenv.hostPlatform.isLinux {
+    withCheck = finalAttrs.finalPackage.overrideAttrs {
+      doCheck = true;
+    };
   };
 
   meta = {

pkgs/by-name/do/dolfinx/package.nix

@@ -12,7 +12,6 @@
   kahip,
   adios2,
   python3Packages,
-  darwinMinVersionHook,
   catch2_3,
   withParmetis ? false,
 }:
@@ -26,20 +25,16 @@ let
   );
 in
 stdenv.mkDerivation (finalAttrs: {
-  version = "0.10.0.post3";
+  version = "0.10.0.post4";
   pname = "dolfinx";
 
   src = fetchFromGitHub {
     owner = "fenics";
     repo = "dolfinx";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-YsFya92lz9Twc1PsSLGj6tJNvKb+MQfpmN/qOFxbe34=";
+    hash = "sha256-vzP5vBZpUR4HW6yJw1wFtbo/TiZ/k02TXV2Zk42b5aQ=";
   };
 
-  preConfigure = ''
-    cd cpp
-  '';
-
   nativeBuildInputs = [
     cmake
     pkg-config
@@ -49,7 +44,6 @@ stdenv.mkDerivation (finalAttrs: {
     dolfinxPackages.kahip
     dolfinxPackages.scotch
   ]
-  ++ lib.optional stdenv.hostPlatform.isDarwin (darwinMinVersionHook "13.3")
   ++ lib.optional withParmetis dolfinxPackages.parmetis;
 
   propagatedBuildInputs = [
@@ -64,6 +58,8 @@ stdenv.mkDerivation (finalAttrs: {
     python3Packages.fenics-ffcx
   ];
 
+  cmakeDir = "../cpp";
+
   cmakeFlags = [
     (lib.cmakeBool "DOLFINX_ENABLE_ADIOS2" true)
     (lib.cmakeBool "DOLFINX_ENABLE_PETSC" true)
@@ -81,9 +77,7 @@ stdenv.mkDerivation (finalAttrs: {
       pname = "${finalAttrs.pname}-unittests";
       inherit (finalAttrs) version src;
 
-      preConfigure = ''
-        cd cpp/test
-      '';
+      cmakeDir = "../cpp/test";
 
       nativeBuildInputs = [
         cmake