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ats-short-course's Introduction

Amanzi

Master: Build Status

BACKGROUND

Amanzi provides a flexible and extensible parallel flow and reactive transport simulation capability for environmental applications. It includes general polyhedral mesh infrastructure, which leverages MSTK, advanced discretizations of process models, including traditional finite volume schemes, mimetic finite differences, and nonlinear finite volumes. In addition, it provides advanced nonlinear solvers, such as Nonlinear Krylov Acceleration (NKA) and Anderson Acceleration, and leverages Trilinos-ML and Hypre Algebraic Multigrid for scalable solvers. The reaction of contaminants and minerals carried by the flow through the surrounding rock and soil is modeled through a general software interface called Alquimia that allows Amanzi to interface with a variety of powerful geochemistry engines including PFLOTRAN and CrunchFlow. The code is parallel and leverages open-source parallel frameworks such as Trilinos, PETSc. Amanzi has been used to model contaminant migration at various DOE waste sites (e.g., Nevada National Security Site, and Savannah River), and is generally applicable to groundwater contaminant migration under partially saturated, nonisothermal conditions and its interaction with surface water.

The multiphysics framework in Amanzi is called Arcos, and it provides modelers with the flexibility they need to creatively decompose complex problems and explore a variety of mixed-dimensional model configurations to develop understanding and make predictions of environmental systems. In particular, Arcos provides flexibility for hierarchical weak and strong coupling of processes with subcycling of mixed dimensions. This capability in conjuction with Amanzi's powerful mesh infrastructure, which supports the splitting and subsetting of meshes, enables creative conceptual modeling. Applications in Amanzi include, coupling flow and transport on discrete-fracture-networks (DFNs) and the background matrix, while applications in the Advanced Terrestrial Simulator (ATS) include, integrated hydrology coupling surface and subsurface processes; and an intermediate scale thermal hydrology model of polygonal tundra based on one-dimensional columns coupled to the two-dimensional surface.

BUILDING/INSTALLING AND RUNNING AMANZI

See the INSTALL.md file in this directory.

COPYRIGHT AND LICENSE

The copyright and license are contained in the top-level file COPYRIGHT.md. The copyright is held jointly by the DOE laboratories that are contributing code to the development of Amanzi.

ats-short-course's People

Contributors

daniellivingston avatar dasvyat avatar ecoon avatar gaobhub avatar jd-moulton avatar pinshuai avatar saubhagya-gatech avatar smolins avatar zexuanxu avatar

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ats-short-course's Issues

Notebook requirements, configuration, and demos

The Jupyter Notebooks are wonderful, but do have some limitations. It would be great to tap into the expertise here to figure out a reasonable set of requirements, how to configure the notebook to support these requirements (i.e., do we need extensions and if so, which ones), and then include a demo notebook with simple examples covering these requirements.

For example, we could create a subdirectory to work on both the requirements and the demo notebook. The requirements doc could be laid out as

Requirements

Markdown cells

  • Math equations in isolation (standard)
  • Math equations with labels
  • ...

Code cells

  • Need certain module for reason x
  • ...

PYTHONPATH still messed up

In current main branch, we still have a few PYTHONPATH issues.

  1. TINerator and WW directories appear twice. Likely this is because we use both ENV docker command and echo "export PYTHONPATH=..." >> .bashrc calls.
  2. The following should also be in the PYTHONPATH: ${ATS_SRC_DIR}/tools/utils:${ATS_SRC_DIR}/tools/meshing/meshing_ats:${AMANZI_SRC_DIR}/tools/amanzi_xml At least the first used to be, but isn't anymore.

PETSc fails to install

With the current container (59665e6), PETSc appears to build successfully, but fails to install:

#14 4104.4 [ 92%] No update step for 'pflotran'
#14 4104.4 [ 92%] Performing patch step for 'pflotran'
#14 4104.4 Applying patch: /.build/amanzi/config/SuperBuild/templates/pflotran-program.patch
#14 4104.4 patching file src/pflotran/pflotran_rxn.F90
#14 4104.4 Hunk #1 succeeded at 258 (offset -46 lines).
#14 4104.4 Hunk #2 succeeded at 333 (offset -46 lines).
#14 4104.4 [ 92%] No configure step for 'pflotran'
#14 4104.4 [ 92%] Performing build step for 'pflotran'
#14 4133.2 -- pflotran build command succeeded.  See also /.build/tpls/pflotran/pflotran-timestamps/pflotran-build-*.log
#14 4133.2 [ 92%] Performing install step for 'pflotran'
#14 4133.3 CMake Error at /.build/tpls/pflotran/pflotran-timestamps/pflotran-install-Release.cmake:49 (message):
#14 4133.3   Command failed: 1
#14 4133.3
#14 4133.3    '/usr/bin/cmake' '-P' '/.build/tpls/pflotran/pflotran-install-step.cmake'
#14 4133.3
#14 4133.3   See also
#14 4133.3
#14 4133.3     /.build/tpls/pflotran/pflotran-timestamps/pflotran-install-*.log
#14 4133.3
#14 4133.3
#14 4133.3 make[2]: *** [CMakeFiles/pflotran.dir/build.make:74: pflotran/pflotran-timestamps/pflotran-install] Error 1
#14 4133.3 make[1]: *** [CMakeFiles/Makefile2:3125: CMakeFiles/pflotran.dir/all] Error 2
#14 4133.3 make: *** [Makefile:130: all] Error 2
#14 4133.3 Amanzi Bootstrap ERROR: Failed to build TPLs

See attached log file: docker-err.log

errors downloading the container

Hi - I'm getting the following error message when I try to download the container for the short course:

$ docker pull metsi/ats-short-course:latest
error during connect: This error may indicate that the docker daemon is not running.: Post "http://%2F%2F.%2Fpipe%2Fdocker_engine/v1.24/images/create?fromImage=metsi%2Fats-short-course&tag=latest": open //./pipe/docker_engine: The system cannot find the file specified.

Does anyone have suggestions of what to try?

If I try to open Docker Desktop from the start menu, I get an error that access is denied because I'm not in the "docker-users" group.

I'm working on a windows machine and just installed docker desktop this afternoon.

I don't have administrative rights to my computer, but could reach out to our IT specialist if that is needed.

Thanks in advance for any suggestions!

PS I tried to post to the users group using the link from the email but got a message that the group doesn't exist or I don't have permission to post there

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