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@@ -9,135 +9,6 @@ A collection of closure models and tools useful for multiphysics codes. | |
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| More complete documentation is available [here](https://lanl.github.io/singularity-eos/). | ||
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| ## Components | ||
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| - `eos` contains the analytic and tabular equation of state infrastructure | ||
| - `eospac-wrapper` is a wrapper for eospac | ||
| - `closure` contains mixed cell closure models. Currently pressure-temperature equilibrium is supported. Requires `eos`. | ||
| - `sesame2spiner` converts sesame tables to spiner tables | ||
| - `stellarcollaspe2spiner` converts tables found on stellarcollapse.org to spiner tables | ||
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| ## To Build | ||
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| At its most basic: | ||
| ```bash | ||
| git clone --recursive [email protected]:lanl/singularity-eos.git | ||
| cd singularity-eos | ||
| mkdir bin | ||
| cd bin | ||
| cmake .. | ||
| make | ||
| ``` | ||
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| ### To Make tests | ||
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| Then, in the singularity-eos root directory: | ||
| ```bash | ||
| mkdir -p bin | ||
| cd bin | ||
| cmake -DSINGULARITY_BUILD_TESTS=ON .. | ||
| make -j | ||
| make test | ||
| ``` | ||
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| ### Build Options | ||
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| A number of options are avaialable for compiling: | ||
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| | Option | Default | Comment | | ||
| | --------------------------------- | ------- | ------------------------------------------------------------------------------------ | | ||
| | SINGULARITY_USE_HDF5 | ON | Enables HDF5. Required for SpinerEOS, StellarCollapseEOS, and sesame2spiner | | ||
| | SINGULARITY_USE_FORTRAN | ON | Enable Fortran API for equation of state | | ||
| | SINGULARITY_USE_KOKKOS | OFF | Uses Kokkos as the portability backend. Currently only Kokkos is supported for GPUs. | | ||
| | SINGULARITY_USE_EOSPAC | OFF | Link against EOSPAC. Needed for sesame2spiner and some tests. | | ||
| | SINGULARITY_USE_CUDA | OFF | Target nvidia GPUs via cuda. Currently requires Kokkos. | | ||
| | SINGULARITY_USE_KOKKOSKERNELS | OFF | Use Kokkos Kernels for linear algebra. Needed for mixed cell closure models on GPU | | ||
| | SINGULARITY_BUILD_CLOSURE | ON | Builds mixed cell closure machinery for multi-material problems | | ||
| | SINGULARITY_BUILD_TESTS | OFF | Build test infrastructure. | | ||
| | SINGULARITY_BUILD_PYTHON | OFF | Build Python bindings | | ||
| | SINGULARITY_TEST_SESAME | OFF | Test the Sesame table readers | | ||
| | SINGULARITY_TEST_STELLAR_COLLAPSE | OFF | Test the Stellar Collapse table readers | | ||
| | SINGULARITY_TEST_PYTHON | OFF | Test the Python bindings | | ||
| | SINGULARITY_BUILD_SESAME2SPINER | OFF | Builds the conversion tool sesame2spiner which makes files readable by SpinerEOS | | ||
| | SINGULARITY_BUILD_STELLARCOLLAPSE2SPINER | OFF | Builds the conversion tool stellarcollapse2spiner which optionally makes stellar collapse files faster to read | | ||
| | SINGULARITY_INVERT_AT_SETUP | OFF | For tests, pre-invert eospac tables. | | ||
| | SINGULARITY_BETTER_DEBUG_FLAGS | ON | Enables nicer GPU debug flags. May interfere with in-tree builds as a submodule | | ||
| | SINGULARITY_HIDE_MORE_WARNINGS | OFF | Makes warnings less verbose. May interfere with in-tree builds as a submodule | | ||
| | SINGULARITY_SUBMODULE_MODE | OFF | Sets cmake flags for in-tree builds | | ||
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| #### Dependency overriding | ||
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| `singularity-eos` will do it's utmost to import all it's dependencies with as little user prompts as possible. | ||
| However, there may be situations where `singularity-eos` cannot find either an install or a source tree of a dependency. | ||
| Furthermore, users may wish to use a modified dependency that `singularity-eos` lacks the foreknowledge to know how to find or otherwise does not utilize. | ||
| Therefore the `singularity-eos` build system provides an "override" option for dependencies. | ||
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| | Option | Default | Comment | | ||
| | --------------------------------- | ------- | ------------------------------------------------------------------------------------ | | ||
| | SINGULARITY_PKG_INSTALL_DIR | empty | Specifies a path where a CMake install of `PKG` is located | | ||
| | SINGULARITY_PKG_IMPORT_DIR | empty | Specifies a path where a CMake source tree of `PKG` is located | | ||
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| Notes on using these options: | ||
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| - These options are intended for `singularity-eos` developers. Users are encouraged to let `singularity-eos` use it's own build system to find and configure dependencies | ||
| - `PKG` should be in all uppercase, for example `-DSINGULARITY_KOKKOSKERNELS_IMPORT_DIR=...` | ||
| - Dashes in package names should be given as underscores, e.g. for `ports-of-call`, use `-DSINGULARITY_PORTS_OF_CALL_INSTALL_DIR=...` | ||
| - `_INSTALL_DIR` points to a directory where the package has been installed by CMake. It expects to find a CMake configuration file in a standard location. If this option is specified and the configuration file cannot be found at that location, the build will produce and error and halt | ||
| - `_IMPORT_DIR` points to a directory that is the top-level of a source-tree of `PKG`. The directory will be imported into the build "as-though" it was an "in-tree" directory | ||
| - using `_IMPORT_DIR` will only check for the existence of a top-level `CMakeLists.txt` file. It does no other evaluation on the directory (e.g. there is no check that this path points to the "correct" package source) | ||
| - `_INSTALL_DIR` and `_IMPORT_DIR` cannot be used for the same package | ||
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| ### Building on Darwin power9 nodes with the IBM xl compiler | ||
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| ```bash | ||
| git clone --recursive https://gitlab.lanl.gov/singularity/singularity-eos.git | ||
| cd singularity-eos | ||
| mkdir bin && cd bin | ||
| source /usr/projects/eap/dotfiles/.bashrc xl reset | ||
| module switch ibm/xlc-16.1.1.5-xlf-16.1.1.5 ibm/xlc-16.1.1.7-xlf-16.1.1.7-gcc-7.4.0 | ||
| export FC="xlf_r -F/usr/projects/opt/ppc64le/ibm/xlf-16.1.1.7/xlf/16.1.1/etc/xlf.cfg.rhel.7.8.gcc.7.4.0.cuda.10.1" | ||
| module load cmake/3.17.3 | ||
| cd /build/directory | ||
| cmake -DCMAKE_BUILD_TYPE=Release -DSINGULARITY_USE_KOKKOS=ON -DSINGULARITY_USE_HDF5=ON -DSINGULARITY_USE_EOSPAC=ON -DSINGULARITY_EOSPAC_INSTALL_DIR=/usr/projects/eap/spack/spack-develop_20191010/opt/spack/linux-rhel7-power9le/xl_r-16.1.1.7-plain/eospac-6.4.0beta.2-mp6hd267l4iokwr6ght2kp5ukk5zc6vq -DSINGULARITY_BUILD_TESTS=ON .. | ||
| make -j | ||
| make test | ||
| ``` | ||
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| ## Formatting | ||
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| This project is formatted with `clang-format` using `clang-format` | ||
| version 12. If contributing, please run clang-format on the files | ||
| you modify. | ||
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| To run formatting automatically, call `make format_singularity-eos` | ||
| at the build step. Cmake automatically makes a target. | ||
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| You can also call the bash script `format.sh` in the `utils/scripts` | ||
| directory as | ||
| ```bash | ||
| utils/scripts/format.sh | ||
| ``` | ||
| The script optionally sets the `clang-format` binary from an | ||
| environment variable, e.g., | ||
| ```bash | ||
| CFM=clang-format=12 utils/scripts/format.sh | ||
| ``` | ||
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| ## Units | ||
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| singularity-eos, prior to unit modifiers, always uses CGS units internally. For | ||
| concreteness, the internal units of each quantity are: | ||
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| | Quantity | Alternate names | Units | | ||
| | ------------------------- | -------------------- | ------------- | | ||
| | Mass density | rho | g cm^-3 | | ||
| | Temperature | temperature | K | | ||
| | Specific Internal Energy | sie, Internal Energy | erg g^-1 | | ||
| | Pressure | | erg cm^-3 | | ||
| | Specific Heat | | erg g^-1 K^-1 | | ||
| | Bulk Modulus | | erg cm^-3 | | ||
| | Gruneisen Parameter | | | | ||
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| ## Copyright | ||
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| © 2021-2023. Triad National Security, LLC. All rights reserved. This | ||
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