add support for mixed element unstructured meshes (#1309)

* add start of test for mixed ele topos * fixes for dset construction * add support for processing mixed element topos * add vtkm to bp mixed ele support and round trip tests * fix memory access issue * new docker build with clang asan build recipe * separation of concerns, wait on 2d zoom discovery * adj mixed tests to work around path bug in conduit on windows * add test that exercises bad shape ids
Alpine-DAV · Jul 17, 2024 · abb6ecd · abb6ecd
1 parent 628d171
commit abb6ecd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project aspires to adhere to [Semantic Versioning](https://semver.org/s
 - kokkos@3.7.02
 
 ### Added
+- Added support for unstructured topologies with mixed elements types (for example, hexs and tets).
+- Added support for `pyramid` and `wedge` elements.
 - Added a `topologies` option to the relay extract. This allows you to select which topologies are saved. This option can be used with the existing `fields` option, the result is the union of the selected topologies and fields.
 - Added `near_plane` and `far_plane` to the camera details provided in Ascent::info()
 

diff --git a/scripts/ci/docker/alpinedav_ubuntu_20.04_cuda_11.4.3_devel_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_20.04_cuda_11.4.3_devel_tpls/Dockerfile
@@ -2,8 +2,8 @@
 # Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
 # other details. No copyright assignment is required to contribute to Ascent.
 
-ARG ARCH_TAG="x86_64"
-FROM alpinedav/ascent-devel:ubuntu-20.04-cuda-11.4.3-${ARCH_TAG}
+ARG TAG_ARCH="x86_64"
+FROM alpinedav/ascent-devel:ubuntu-20.04-cuda-11.4.3-${TAG_ARCH}
 
 # obtain a copy of ascent source from host env,
 # which we use to call uberenv

diff --git a/scripts/ci/docker/alpinedav_ubuntu_20.04_cuda_12.1.1_devel_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_20.04_cuda_12.1.1_devel_tpls/Dockerfile
@@ -2,8 +2,8 @@
 # Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
 # other details. No copyright assignment is required to contribute to Ascent.
 
-ARG ARCH_TAG="x86_64"
-FROM alpinedav/ascent-devel:ubuntu-20.04-cuda-12.1.1-${ARCH_TAG}
+ARG TAG_ARCH="x86_64"
+FROM alpinedav/ascent-devel:ubuntu-20.04-cuda-12.1.1-${TAG_ARCH}
 
 # obtain a copy of ascent source from host env,
 # which we use to call uberenv

diff --git a/scripts/ci/docker/alpinedav_ubuntu_20.04_devel_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_20.04_devel_tpls/Dockerfile
@@ -2,8 +2,8 @@
 # Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
 # other details. No copyright assignment is required to contribute to Ascent.
 
-ARG ARCH_TAG="x86_64"
-FROM alpinedav/ascent-devel:ubuntu-20.04-${ARCH_TAG}
+ARG TAG_ARCH="x86_64"
+FROM alpinedav/ascent-devel:ubuntu-20.04-${TAG_ARCH}
 
 # obtain a copy of ascent source from host env,
 # which we use to call uberenv

diff --git a/scripts/ci/docker/alpinedav_ubuntu_20.04_rocm_5.1.3_devel_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_20.04_rocm_5.1.3_devel_tpls/Dockerfile
@@ -2,8 +2,8 @@
 # Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
 # other details. No copyright assignment is required to contribute to Ascent.
 
-ARG ARCH_TAG="x86_64"
-FROM alpinedav/ascent-devel:ubuntu-20.04-rocm-5.1.3-${ARCH_TAG}
+ARG TAG_ARCH="x86_64"
+FROM alpinedav/ascent-devel:ubuntu-20.04-rocm-5.1.3-${TAG_ARCH}
 
 # obtain a copy of ascent source from host env,
 # which we use to call uberenv

diff --git a/scripts/ci/docker/alpinedav_ubuntu_20.04_rocm_6.0.0_devel_build_ascent_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_20.04_rocm_6.0.0_devel_build_ascent_tpls/Dockerfile
@@ -2,8 +2,8 @@
 # Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
 # other details. No copyright assignment is required to contribute to Ascent.
 
-ARG ARCH_TAG="x86_64"
-FROM alpinedav/ascent-devel:ubuntu-20.04-rocm-6.0.0-${ARCH_TAG}
+ARG TAG_ARCH="x86_64"
+FROM alpinedav/ascent-devel:ubuntu-20.04-rocm-6.0.0-${TAG_ARCH}
 
 # obtain a copy of ascent source from host env,
 # which we use to call uberenv

diff --git a/.../docker/alpinedav_ubuntu_20.04_rocm_6.0.0_devel_build_ascent_tpls/docker_uberenv_build.sh b/.../docker/alpinedav_ubuntu_20.04_rocm_6.0.0_devel_build_ascent_tpls/docker_uberenv_build.sh
@@ -1,12 +1,17 @@
 #!/bin/bash
 set -ev
 
-cmake_install_dir=/cmake-3.23.2-linux-x86_64
+export CMAKE_ARCH=`uname -m`
+
+if [[ ${CMAKE_ARCH} == "arm64" ]]; then
+  export CMAKE_ARCH="aarch64"
+fi
+
+cmake_install_dir=/cmake-3.23.2-linux-${CMAKE_ARCH}
 if [ ! -d ${cmake_install_dir} ]; then
-  echo "**** Downloading ${hdf5_tarball}"
   # setup cmake in container
-  curl -L https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-x86_64.tar.gz -o cmake-3.23.2-linux-x86_64.tar.gz
-  tar -xzf cmake-3.23.2-linux-x86_64.tar.gz
+  curl -L https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz -o cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz
+  tar -xzf cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz
 fi
 
 export PATH=$PATH:/${cmake_install_dir}/bin/

diff --git a/scripts/ci/docker/alpinedav_ubuntu_22.04_devel/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_22.04_devel/Dockerfile
@@ -18,6 +18,8 @@ RUN apt-get update && apt-get -y install \
              python3 \
              python3-dev \
              python-is-python3 \
+             clang \
+             llvm \
              perl \
              git \
              git-lfs \

diff --git a/scripts/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/Dockerfile b/scripts/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/Dockerfile
@@ -0,0 +1,22 @@
+# Copyright (c) Lawrence Livermore National Security, LLC and other Ascent
+# Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
+# other details. No copyright assignment is required to contribute to Ascent.
+
+ARG TAG_ARCH=x86_64
+FROM alpinedav/ascent-devel:ubuntu-22.04-${TAG_ARCH}
+
+ENV TAG_ARCH ${TAG_ARCH}
+
+# obtain a copy of ascent source from host env,
+# which we use to call uberenv
+COPY ascent.docker.src.tar.gz /
+# extract 
+RUN tar -xzf ascent.docker.src.tar.gz
+
+# copy spack build script in
+COPY docker_uberenv_build.sh docker_env_setup.sh /
+RUN chmod -R a+x /*.sh
+
+RUN /docker_uberenv_build.sh
+
+RUN /docker_env_setup.sh
diff --git a/scripts/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/build.sh b/scripts/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/build.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+# Copyright (c) Lawrence Livermore National Security, LLC and other Ascent
+# Project developers. See top-level LICENSE AND COPYRIGHT files for dates and
+# other details. No copyright assignment is required to contribute to Ascent.
+set -ev
+
+export REPO_NAME="ascent"
+export TAG_ARCH=`uname -m`
+export TAG_BASE=alpinedav/ascent-devel:ubuntu-22.04-clang-14-asan-${TAG_ARCH}-build-ascent-tpls
+
+date
+
+python3 ../../../docker_build_and_tag.py ${REPO_NAME} ${TAG_ARCH} ${TAG_BASE}
+
+date
diff --git a/...s/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/docker_env_setup.sh b/...s/ci/docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/docker_env_setup.sh
@@ -0,0 +1,7 @@
+# create some helper scripts
+python ascent/scripts/gen_spack_env_script.py cmake mpi
+echo "git clone --recursive https://github.com/Alpine-DAV/ascent.git" > clone.sh
+chmod +x clone.sh
+
+# delete copy of source from host (ci will fetch new from repo)
+rm -rf ascent
diff --git a/.../docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/docker_uberenv_build.sh b/.../docker/alpinedav_ubuntu_22.04_devel_clang_asan_build_ascent_tpls/docker_uberenv_build.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+set -ev
+
+export CMAKE_ARCH=`uname -m`
+
+if [[ ${CMAKE_ARCH} == "arm64" ]]; then
+  export CMAKE_ARCH="aarch64"
+fi
+
+cmake_install_dir=/cmake-3.23.2-linux-${CMAKE_ARCH}
+if [ ! -d ${cmake_install_dir} ]; then
+  # setup cmake in container
+  curl -L https://github.com/Kitware/CMake/releases/download/v3.23.2/cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz -o cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz
+  tar -xzf cmake-3.23.2-linux-${CMAKE_ARCH}.tar.gz
+fi
+
+export PATH=$PATH:/${cmake_install_dir}/bin/
+
+export CFLAGS="-fsanitize=address"
+export CXXFLAGS="-fsanitize=address"
+
+# build tpls with helper script /w clang and 
+chmod +x ascent/scripts/build_ascent/build_ascent.sh
+# bi
+env CXX=clang++ CC=clang enable_tests=OFF build_ascent=false ascent/scripts/build_ascent/build_ascent.sh
+