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jali's Introduction

Copyright (c) 2017, Los Alamos National Security, LLC All rights reserved.

Copyright 2017. Los Alamos National Security, LLC. This software was produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos National Laboratory (LANL), which is operated by Los Alamos National Security, LLC for the U.S. Department of Energy. The U.S. Government has rights to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from LANL.

Additionally, 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 Los Alamos 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 LOS ALAMOS 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 LOS ALAMOS 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 1.0.9 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/1.10.0-intel_15.0.3 cmake
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX /usr/projects/ngc/private/jali-tpl/1.0.9-intel-15.0.3-openmpi-1.10.3
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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/1.10.0-intel_15.0.3 cmake
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX $SOURCE/inst-tpl
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-tpl
cd build-tpl
cmake \
    -D CMAKE_C_COMPILER=`which mpicc` \
    -D CMAKE_CXX_COMPILER=`which mpiCC` \
    -D CMAKE_Fortran_COMPILER=`which mpif90` \
    -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \
    -D TPL_DOWNLOAD_DIR:PATH=/usr/projects/ngc/private/tpl-downloads/ \
    -D TPL_INSTALL_PREFIX=$TPL_INSTALL_PREFIX \
    $SOURCE/config/SuperBuild/
make -j
make install
cd ..
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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

Moonlight (or Pinto)

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/16.0.3 openmpi/1.10.5
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX /usr/projects/ngc/private/jali-tpl/intel-16.0.3-openmpi-1.10.5
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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/16.0.3 openmpi/1.10.5
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX $SOURCE/inst-tpl
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-tpl
cd build-tpl
cmake \
    -D CMAKE_C_COMPILER=`which mpicc` \
    -D CMAKE_CXX_COMPILER=`which mpiCC` \
    -D CMAKE_Fortran_COMPILER=`which mpif90` \
    -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \
    -D TPL_DOWNLOAD_DIR:PATH=/usr/projects/ngc/private/tpl-downloads/ \
    -D TPL_INSTALL_PREFIX=$TPL_INSTALL_PREFIX \
    $SOURCE/config/SuperBuild/
make -j
make install
cd ..
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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/16.0.3 openmpi/1.10.3
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX /usr/local/codes/ngc/private/jali-tpl/intel-16.0.3-openmpi-1.10.3
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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/16.0.3 openmpi/1.10.3
setenv SOURCE `pwd`
setenv TPL_INSTALL_PREFIX $SOURCE/inst-tpl
setenv JALI_INSTALL_PREFIX $SOURCE/inst-jali
mkdir build-tpl
cd build-tpl
cmake \
    -D CMAKE_C_COMPILER=`which mpicc` \
    -D CMAKE_CXX_COMPILER=`which mpiCC` \
    -D CMAKE_Fortran_COMPILER=`which mpif90` \
    -D DISABLE_EXTERNAL_DOWNLOAD:BOOL=TRUE \
    -D TPL_DOWNLOAD_DIR:PATH=/usr/local/codes/ngc/private/tpl-downloads/ \
    -D TPL_INSTALL_PREFIX=$TPL_INSTALL_PREFIX \
    $SOURCE/config/SuperBuild/
make -j
make install
cd ..
mkdir build-jali
cd build-jali
cmake \
  -C $TPL_INSTALL_PREFIX/share/cmake/Jali-tpl-config.cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D CMAKE_CXX_FLAGS='-std=c++11' \
  -D CMAKE_INSTALL_PREFIX:FILEPATH=$JALI_INSTALL_PREFIX \
  -D HDF5_NO_SYSTEM_PATHS:BOOL=TRUE \
  -D BOOST_ROOT:FILEPATH=$TPL_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

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