Building

This page provides details on several ways to build Conduit from source.

For the shortest path from zero to Conduit, see Quick Start.

If you are building features that depend on third party libraries we recommend using uberenv which leverages Spack or Spack directly. We also provide info about building for known HPC clusters using uberenv. and a Docker example that leverages Spack.

Obtain the Conduit source

Clone the Conduit repo from Github:

git clone --recursive https://github.com/llnl/conduit.git

--recursive is necessary because we are using a git submodule to pull in BLT (https://github.com/llnl/blt). If you cloned without --recursive, you can checkout this submodule using:

cd conduit
git submodule init
git submodule update

Configure a build

Conduit uses CMake for its build system. These instructions assume cmake is in your path. We recommend CMake 3.9 or newer, for more details see Supported CMake Versions.

config-build.sh is a simple wrapper for the cmake call to configure conduit. This creates a new out-of-source build directory build-debug and a directory for the install install-debug. It optionally includes a host-config.cmake file with detailed configuration options.

cd conduit
./config-build.sh

Build, test, and install Conduit:

cd build-debug
make -j 8
make test
make install

Build Options

The core Conduit library has no dependencies outside of the repo, however Conduit provides optional support for I/O and Communication (MPI) features that require externally built third party libraries.

Conduit’s build system supports the following CMake options:

  • BUILD_SHARED_LIBS - Controls if shared (ON) or static (OFF) libraries are built. (default = ON)
  • ENABLE_TESTS - Controls if unit tests are built. (default = ON)
  • ENABLE_EXAMPLES - Controls if examples are built. (default = ON)
  • ENABLE_UTILS - Controls if utilities are built. (default = ON)
  • ENABLE_TESTS - Controls if unit tests are built. (default = ON)
  • ENABLE_DOCS - Controls if the Conduit documentation is built (when sphinx and doxygen are found ). (default = ON)
  • ENABLE_COVERAGE - Controls if code coverage compiler flags are used to build Conduit. (default = OFF)
  • ENABLE_PYTHON - Controls if the Conduit Python module is built. (default = OFF)
  • CONDUIT_ENABLE_TESTS - Extra control for if Conduit unit tests are built. Useful for in cases where Conduit is pulled into a larger CMake project (default = ON)

The Conduit Python module can be built for Python 2 or Python 3. To select a specific Python, set the CMake variable PYTHON_EXECUTABLE to path of the desired python binary. The Conduit Python module requires Numpy. The selected Python instance must provide Numpy, or PYTHONPATH must be set to include a Numpy install compatible with the selected Python install. Note: You can not use compiled Python modules built with Python 2 in Python 3 and vice versa. You need to compile against the version you expect to use.

  • ENABLE_MPI - Controls if the conduit_relay_mpi library is built. (default = OFF)

We are using CMake’s standard FindMPI logic. To select a specific MPI set the CMake variables MPI_C_COMPILER and MPI_CXX_COMPILER, or the other FindMPI options for MPI include paths and MPI libraries.

To run the mpi unit tests on LLNL’s LC platforms, you may also need change the CMake variables MPIEXEC and MPIEXEC_NUMPROC_FLAG, so you can use srun and select a partition. (for an example see: src/host-configs/chaos_5_x86_64.cmake)

Warning

Starting in CMake 3.10, the FindMPI MPIEXEC variable was changed to MPIEXEC_EXECUTABLE. FindMPI will still set MPIEXEC, but any attempt to change it before calling FindMPI with your own cached value of MPIEXEC will not survive, so you need to set MPIEXEC_EXECUTABLE [reference].

  • HDF5_DIR - Path to a HDF5 install (optional).
Controls if HDF5 I/O support is built into conduit_relay.
  • SILO_DIR - Path to a Silo install (optional).

Controls if Silo I/O support is built into conduit_relay. When used, the following CMake variables must also be set:

  • HDF5_DIR - Path to a HDF5 install. (Silo support depends on HDF5)
  • ADIOS_DIR - Path to an ADIOS install (optional).

Controls if ADIOS I/O support is built into conduit_relay. When used, the following CMake variables must also be set:

  • HDF5_DIR - Path to a HDF5 install. (ADIOS support depends on HDF5)
  • BLT_SOURCE_DIR - Path to BLT. (default = “blt”)
Defaults to “blt”, where we expect the blt submodule. The most compelling reason to override is to share a single instance of BLT across multiple projects.

Installation Path Options

Conduit’s build system provides an install target that installs the Conduit libraires, headers, python modules, and documentation. These CMake options allow you to control install destination paths:

  • CMAKE_INSTALL_PREFIX - Standard CMake install path option (optional).
  • PYTHON_MODULE_INSTALL_PREFIX - Path to install Python modules into (optional).
When present and ENABLE_PYTHON is ON, Conduit’s Python modules will be installed to ${PYTHON_MODULE_INSTALL_PREFIX} directory instead of ${CMAKE_INSTALL_PREFIX}/python-modules.

Host Config Files

To handle build options, third party library paths, etc we rely on CMake’s initial-cache file mechanism.

cmake -C config_file.cmake

We call these initial-cache files host-config files, since we typically create a file for each platform or specific hosts if necessary.

The config-build.sh script uses your machine’s hostname, the SYS_TYPE environment variable, and your platform name (via uname) to look for an existing host config file in the host-configs directory at the root of the conduit repo. If found, it passes the host config file to CMake via the -C command line option.

cmake {other options} -C host-configs/{config_file}.cmake ../

You can find example files in the host-configs directory.

These files use standard CMake commands. To properly seed the cache, CMake set commands need to specify CACHE as follows:

set(CMAKE_VARIABLE_NAME {VALUE} CACHE PATH "")

Building Conduit and Third Party Dependencies

We use Spack (http://software.llnl.gov/spack) to help build Conduit’s third party dependencies on OSX and Linux. Conduit builds on Windows as well, but there is no automated process to build dependencies necessary to support Conduit’s optional features.

Uberenv (scripts/uberenv/uberenv.py) automates fetching spack, building and installing third party dependencies, and can optionally install Conduit as well. To automate the full install process, Uberenv uses the Conduit Spack package along with extra settings such as Spack compiler and external third party package details for common HPC platforms.

Building Third Party Dependencies for Development

Note

Conduit developers use bootstrap-env.sh and scripts/uberenv/uberenv.py to setup third party libraries for Conduit development. For info on how to use the Conduit Spack package see Building Conduit and its Dependencies with Spack.

On OSX and Linux, you can use bootstrap-env.sh (located at the root of the conduit repo) to help setup your development environment. This script uses scripts/uberenv/uberenv.py, which leverages Spack to build all of the external third party libraries and tools used by Conduit. Fortran support is optional and all dependencies should build without a fortran compiler. After building these libraries and tools, it writes an initial host-config file and adds the Spack built CMake binary to your PATH so can immediately call the config-build.sh helper script to configure a conduit build.

#build third party libs using spack
source bootstrap-env.sh

#copy the generated host-config file into the standard location
cp uberenv_libs/`hostname`*.cmake host-configs/

# run the configure helper script
./config-build.sh

# or you can run the configure helper script and give it the
# path to a host-config file
./config-build.sh uberenv_libs/`hostname`*.cmake

When bootstrap-env.sh runs uberenv.py, all command line arguments are forwarded:

python scripts/uberenv/uberenv.py $@

So any options to bootstrap-env.sh are effectively uberenv.py options.

Uberenv Options for Building Third Party Dependencies

uberenv.py has a few options that allow you to control how dependencies are built:

Option Description Default
–prefix Destination directory uberenv_libs
–spec Spack spec linux: %gcc osx: %clang
–spack-config-dir Folder with Spack settings files linux: (empty) osx: scripts/uberenv_configs/spack_configs/config/darwin/
-k Ignore SSL Errors False
–install Fully install conduit, not just dependencies False
–run_tests Invoke tests during build and against install False

The -k option exists for sites where SSL certificate interception undermines fetching from github and https hosted source tarballs. When enabled, uberenv.py clones spack using:

git -c http.sslVerify=false clone https://github.com/llnl/spack.git

And passes -k to any spack commands that may fetch via https.

Default invocation on Linux:

python scripts/uberenv/uberenv.py --prefix uberenv_libs \
                                  --spec %gcc

Default invocation on OSX:

python scripts/uberenv/uberenv.py --prefix uberenv_libs \
                                  --spec %clang \
                                  --spack-config-dir scripts/uberenv_configs/spack_configs/configs/darwin/

The uberenv –install installs conduit@develop (not just the development dependencies):

python scripts/uberenv/uberenv.py --install

To run tests during the build process to validate the build and install, you can use the --run_tests option:

python scripts/uberenv/uberenv.py --install \
                                  --run_tests

For details on Spack’s spec syntax, see the Spack Specs & dependencies documentation.

You can edit yaml files under scripts/uberenv/spack_config/{platform} or use the –spack-config-dir option to specify a directory with compiler and packages yaml files to use with Spack. See the Spack Compiler Configuration and Spack System Packages documentation for details.

For OSX, the defaults in spack_configs/darwin/compilers.yaml are X-Code’s clang and gfortran from https://gcc.gnu.org/wiki/GFortranBinaries#MacOS.

Note

The bootstrapping process ignores ~/.spack/compilers.yaml to avoid conflicts and surprises from a user’s specific Spack settings on HPC platforms.

When run, uberenv.py checkouts a specific version of Spack from github as spack in the destination directory. It then uses Spack to build and install Conduit’s dependencies into spack/opt/spack/. Finally, it generates a host-config file {hostname}.cmake in the destination directory that specifies the compiler settings and paths to all of the dependencies.

Building with Uberenv on Known HPC Platforms

To support testing and installing on common platforms, we maintain sets of Spack compiler and package settings for a few known HPC platforms. Here are the commonly tested configurations:

System OS Tested Configurations (Spack Specs)
pascal.llnl.gov Linux: TOSS3

%gcc

%gcc~shared

lassen.llnl.gov Linux: BlueOS %clang@coral~python~fortran
cori.nersc.gov Linux: SUSE / CNL %gcc

See scripts/spack_build_tests/ for the exact invocations used to test on these platforms.

Building Conduit and its Dependencies with Spack

As of 1/4/2017, Spack’s develop branch includes a recipe to build and install Conduit.

To install the latest released version of Conduit with all options (and also build all of its dependencies as necessary) run:

spack install conduit

To build and install Conduit’s github develop branch run:

spack install conduit@develop

The Conduit Spack package provides several variants that customize the options and dependencies used to build Conduit:

Variant Description Default
shared Build Conduit as shared libraries ON (+shared)
cmake Build CMake with Spack ON (+cmake)
python Enable Conduit Python support ON (+python)
mpi Enable Conduit MPI support ON (+mpi)
hdf5 Enable Conduit HDF5 support ON (+hdf5)
silo Enable Conduit Silo support ON (+silo)
adios Enable Conduit ADIOS support OFF (+adios)
doc Build Conduit’s Documentation OFF (+docs)

Variants are enabled using + and disabled using ~. For example, to build Conduit with the minimum set of options (and dependencies) run:

spack install conduit~python~mpi~hdf5~silo~docs

You can specify specific versions of a dependency using ^. For Example, to build Conduit with Python 3:

spack install conduit+python ^python@3

Supported CMake Versions

We recommend CMake 3.9 or newer. We test building Conduit with CMake 3.9 and 3.14. Other versions of CMake may work, however CMake 3.18.0 and 3.18.1 have known issues that impact HDF5 support. CMake 3.18.2 resolved the HDF5 issues.

Using Conduit in Another Project

Under src/examples there are examples demonstrating how to use Conduit in a CMake-based build system (using-with-cmake) and via a Makefile (using-with-make).

Building Conduit in a Docker Container

Under src/examples/docker/ubuntu there is an example Dockerfile which can be used to create an ubuntu-based docker image with a build of the Conduit. There is also a script that demonstrates how to build a Docker image from the Dockerfile (example_build.sh) and a script that runs this image in a Docker container (example_run.sh). The Conduit repo is cloned into the image’s file system at /conduit, the build directory is /conduit/build-debug, and the install directory is /conduit/install-debug.

Notes for Cray systems

HDF5 and gtest use runtime features such as dlopen. Because of this, building static on Cray systems commonly yields the following flavor of compiler warning:

Using 'zzz' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking

You can avoid related linking warnings by adding the -dynamic compiler flag, or by setting the CRAYPE_LINK_TYPE environment variable:

export CRAYPE_LINK_TYPE=dynamic

Shared Memory Maps are read only on Cray systems, so updates to data using Node::mmap will not be seen between processes.