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 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 scripts/uberenv/uberenv.py
to help setup your development environment. This script 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
python scripts/uberenv/uberenv.py
# run the configure helper script and give it the
# path to a host-config file
./config-build.sh uberenv_libs/`hostname`*.cmake
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
.
Building Conduit with pip¶
Conduit provides a setup.py that allows pip to use CMake to build and install Conduit and the Conduit Python module. This script assumes that CMake is in your path.
Example Basic Build:
pip install . --user
Or for those with certificate woes:
pip install --trusted-host pypi.org --trusted-host files.pythonhosted.org . --user
You can enable Conduit features using the following environment variables:
Option Description Default HDF5_DIR Path to HDF5 install for HDF5 Support IGNORE ENABLE_MPI Build Conduit with MPI Support OFF
Example Build with MPI and HDF5 Support:
env ENABLE_MPI=ON HDF5_DIR={path/to/hdf5/install} pip install . --user
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.
Notes for using OpenMPI in a container as root¶
By default OpenMPI prevents the root user from launching MPI jobs. If you are running as root in a container you can use the following env vars to turn off this restriction:
OMPI_ALLOW_RUN_AS_ROOT=1
OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1