https://github.com/lanl/jali

A parallel unstructured mesh framework for multiphysics application
https://github.com/lanl/jali

Last synced: 9 months ago
JSON representation

A parallel unstructured mesh framework for multiphysics application

• Host: GitHub
• URL: https://github.com/lanl/jali
• Owner: lanl
• License: bsd-3-clause
• Created: 2017-05-01T01:06:57.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2023-05-11T02:01:37.000Z (about 3 years ago)
• Last Synced: 2025-06-26T22:13:49.389Z (12 months ago)
• Language: C++
• Size: 1.9 MB
• Stars: 16
• Watchers: 11
• Forks: 12
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
Copyright (c) 2019, Triad National Security, LLC

All rights reserved.

Copyright 2019. Triad National Security, LLC. This software was

produced under U.S. Government contract 89233218CNA000001 for Los

Alamos National Laboratory (LANL), which is operated by Triad

National Security, LLC for the U.S. Department of Energy. 

All rights in the program are reserved by Triad National Security,

LLC, and the U.S. Department of Energy/National Nuclear Security

Administration. The Government is granted for itself and others acting

on its behalf a nonexclusive, paid-up, irrevocable worldwide license

in this material to reproduce, prepare derivative works, distribute

copies to the public, perform publicly and display publicly, and to

permit others to do so

This is open source software distributed under the 3-clause BSD license.

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are

met:

1. Redistributions of source code must retain the above copyright notice,

   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright

   notice, this list of conditions and the following disclaimer in the

   documentation and/or other materials provided with the distribution.

3. Neither the name of Triad National Security, LLC, Los Alamos

   National Laboratory, LANL, the U.S. Government, nor the names of its

   contributors may be used to endorse or promote products derived from this

   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY TRIAD NATIONAL SECURITY, LLC AND

CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING,

BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND

FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL

TRIAD NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY

DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE

GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER

IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR

OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF

ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# Summary

Jali is a parallel unstructured mesh infrastructure library designed

for use by multi-physics simulations. It supports 2D and 3D arbitrary

polyhedral meshes distributed over hundreds to thousands of

nodes. Jali can read and write Exodus II meshes along with fields and

sets on the mesh and support for other formats is partially

implemented or is in the plans. Jali is built upon MSTK

(https://github.com/MeshToolkit/MSTK), an open source general purpose

unstructured mesh infrastructure library from Los Alamos National

Laboratory. While it has been made to work with other mesh frameworks

such as MOAB and STKmesh in the past, support for maintaining the

interface to these frameworks has been suspended for now. Jali

supports distributed as well as on-node parallelism. Support of

on-node parallelism is through direct use of the mesh calls in

multi-threaded constructs or through use of "tiles" which are

submeshes or sub-partitions of a partition destined for a compute

node.

Jali is derived from the mesh infrastructure of the early versions of

the open source software Amanzi (whose three-part BSD open source

copyright assertion included Los Alamos National Laboratory, Pacific

Northwest National Laboratory and Lawrence Berkeley

Laboratory). Jali's copyright is being asserted solely under Los

Alamos National Laboratory having been rewritten to include only code

written by Los Alamos National Laboratory developers.

# Authors

Jali is derived from the unstructured mesh infrastructure in Amanzi (https://github.com/amanzi/amanzi) with non-LANL contributions stripped out. While much of the unstructured mesh infrastructure in  Amanzi (and subsequently Jali) was developed by Rao Garimella, its design was influenced by the entire Amanzi team. Additionally, contributions to the Amanzi or Jali code base have been made by Markus Berndt, Konstantin Lipnikov, Ethan Coon, Daniil Svyatsky, Chris Malone, Chris Sewell, Charles Ferenbaugh and Ondrej Certik. In addition, most of the build system in Jali was taken as-is from Amanzi. This build system was largely developed by Lori Pritchett-Sheats.

# Third Party Libraries

Jali uses a number of third party libraries (TPLs) primarily for mesh

import/export, mesh partitioning and MPI communication. To build Jali,

you must point the build system to a directory containing the TPLs or

build the third party libraries as described below.

Jali *1.0.0*  uses version *1.1.0* or higher of the TPL set. See

$JALI_SOURCE/config/SuperBuild/TPLVersions.cmake for details.

# Installation instructions

There are a few configuration examples in

`config/configure-examples/`. Below we list copy & paste instructions

for several machines. The first option is the *easy* option in which

pre-installed third-party libraries (TPLs) are used to build Jali. The

second option is for cases where you want to build all the TPLs used

by Jali and build Jali using these custom TPLs. Naturally, in the

following instructions, you may use your choice of compiler, openmpi

libraries and cmake version, subject to compatibility requirements of Jali

## Darwin

If you want to build only Jali, execute the following from the Jali

root directory (you may have to modify the exact version number of the

TPLs directory depending on how out-of-sync this file is with whats on

your system):

    /bin/tcsh

    module load openmpi/2.1.2-intel_17.0.6 cmake

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX /usr/projects/ngc/private/jali-tpl/1.1.0-intel-17.0.6-openmpi-2.1.2

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit

If you want to build a custom set of Jali TPLs and build Jali using

these TPLs, execute the following from the Jali root directory: 

    /bin/tcsh

    module load openmpi/2.1.2-intel_17.0.6 cmake

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX $SOURCE/inst-tpl

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-tpl

    cd build-tpl

    cmake \

        -D CMAKE_C_COMPILER=`which mpicc` \

        -D CMAKE_CXX_COMPILER=`which mpiCC` \

        -D CMAKE_Fortran_COMPILER=`which mpif90` \

        -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \

        -D TPL_DOWNLOAD_DIR:PATH=/usr/projects/ngc/private/tpl-downloads/ \

        -D CMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \

        $SOURCE/config/SuperBuild/

    make -j

    make install

    cd ..

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit

## Snow

If you want to build only Jali, execute the following from the Jali

root directory (you may have to modify the exact version number of the

TPLs directory depending on how out-of-sync this file is with whats on

your system):

    /bin/tcsh

    module load intel/17.0.4 openmpi/2.1.2

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX /usr/projects/ngc/private/jali-tpl/1.1.0-intel-17.0.4-openmpi-2.1.2

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit

If you want to build a custom set of Jali TPLs and build Jali using

these TPLs, execute the following from the Jali root directory: 

    /bin/tcsh

    module load intel/17.0.4 openmpi/2.1.2

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX $SOURCE/inst-tpl

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-tpl

    cd build-tpl

    cmake \

        -D CMAKE_C_COMPILER=`which mpicc` \

        -D CMAKE_CXX_COMPILER=`which mpiCC` \

        -D CMAKE_Fortran_COMPILER=`which mpif90` \

        -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \

        -D TPL_DOWNLOAD_DIR:PATH=/usr/projects/ngc/private/tpl-downloads/ \

        -D CMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \

        $SOURCE/config/SuperBuild/

    make -j

    make install

    cd ..

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit

## XLAN (Varan or Barugon)

If you want to build only Jali, execute the following from the Jali

root directory (you may have to modify the exact version number of the

TPLs directory depending on how out-of-sync this file is with whats on

your system):

    /bin/tcsh

    /opt/local/packages/Modules/default/init/sh

    module load intel/17.0.1 openmpi/1.10.5

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX /usr/local/codes/ngc/private/jali-tpl/1.1.0-intel-17.0.1-openmpi-1.10.5

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit

If you want to build a custom set of Jali TPLs and build Jali using

these TPLs, execute the following from the Jali root directory: 

    /bin/tcsh

    /opt/local/packages/Modules/default/init/sh

    module load intel/17.0.1 openmpi/1.10.5

    setenv SOURCE `pwd`

    setenv CMAKE_INSTALL_PREFIX $SOURCE/inst-tpl

    setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali

    mkdir build-tpl

    cd build-tpl

    cmake \

        -D CMAKE_C_COMPILER=`which mpicc` \

        -D CMAKE_CXX_COMPILER=`which mpiCC` \

        -D CMAKE_Fortran_COMPILER=`which mpif90` \

        -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \

        -D TPL_DOWNLOAD_DIR:PATH=/usr/local/codes/ngc/private/tpl-downloads/ \

        -D CMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX \

        $SOURCE/config/SuperBuild/

    make -j

    make install

    cd ..

    mkdir build-jali

    cd build-jali

    cmake \

      -C $CMAKE_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \

      -D CMAKE_BUILD_TYPE=Release \

      -D CMAKE_CXX_FLAGS='-std=c++11' \

      -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \

      -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \

      -D BOOST_ROOT:FILEPATH=$CMAKE_INSTALL_PREFIX \

      -D ENABLE_MSTK_Mesh:BOOL=TRUE \

      -D ENABLE_STK_Mesh:BOOL=FALSE \

      -D ENABLE_MOAB_Mesh:BOOL=FALSE \

      ${SOURCE}

    make -j

    make test

    make install

    exit