Pore scale modelling
fac681dffe
* summit configure * add spock scripts to FOM * get new models to build with hip * add hip slipping bc * testing communication on spock * update spock build based on olcf docs * update configure & test scripts for spock * Fixing potential bugs with communication * Adding simple test of GPU aware MPI * some changes to configure for spock * Modifying GPU aware MPI test to send multiple messages * playing with spock Gpu test * added gpu wrapper test * Cleaning up some compiler warnings * add barrier between pack / MPI send * Updating build to support HIP as a language * fixing gpu mpi sync * Adding script * local spock changes * add membrane class * update membrane structure * membrane communications * working on new comm data structures * add membrane unit test * membrane compiles * membrane test * Updating hip port to match cuda * update summit config * update summit config * add configure script for crusher * update membrane test * update membrane test * convention for inside / outside membrane link direction * working on membrane comm * try to fix time conversion factor for Poisson solver; to be built and tested * fix dumb typo * update summit config * tune launch for crusher * tune launch for mrt on crusher * update color * summit script with specific module versions * update crusher config * add crusher examples * add dense case for crusher * Fixing some quick annoying compile warnings * fix binding in example * working on fix * Adding simple crusher test * Adding new crusher MPI test * disable MPI thread multiple for crusher * updates to crusher configure * cpu test for crusher * Working on standalone reproducer for MPI bug * More work on creating standalone test * More work on creating standalone test * More work on creating standalone test * Reverting TestCrusher2, standalone version passes (TestCrusher3.cpp), need to figure out why * Working on standalone MPI test on crusher * Working on standalone MPI test on crusher * Getting closer to stand alone test * Still trying to create standalone reproducer * hang fix / workaround * Created standalone MPI failure test * Removing TestCrusher tests, the bug deals with the StackTrace which we disable the multistack trace for now. Moving the test out of LBPM * fix sendcount / recvcount * Testing persistent communication * Updating calculation of bandwidth * crusher hackathon final version * working on membrane communication structures * add cell simulator * added cell simulator * make sure halo is filled when measuring object * add membrane transport function for d3q7 * add membrane unpack function * poking at MF issue * update crusher build * membrane data structures compiling * update to membrane capability * update comments in ion model * fix dumb print bug * clean up relabel * adding membrane functions * move membrane to common folder * membrane structure in IonModel * membrane structure in IonModel * try at membrane simulator * add python script to generate bubble * add python script to generate bubble * cell simulator runs * read input files * add single cell example * refining cell example * start on cuda function * werkin * start on cuda function * start on hip function * updates and fix for user input reader * update cell example * add sigmoid to ion equilibrium dist * cuda build succeeds * update crusher script * getting ready to merge gpu * refactor compact AA routines for testing * add testing functions to ScaLBL * testing membrane ion transport * membrane transport test passing * membrane starts working ok... * original wang poisson solver (broken) * rex d3q19 (broken) * tau from wang paper * still broken wang * d319 poisson works good * Poisson working pretty good now * initialize nernst-planck simulator; to be built subject to debugging * fix a few syntax bugs and build passed * Poisson solver; enable specifying initial values * update cell example * add GPU functions for d3q19 poisson * fix dumb bugs * fix bugs in initializing electric potential; the Psi on solid was accidentally overwritten before. * small change * fix bugs in importing ion model's dummy velocity * add membrane concentration init * remove bad warnings * remove print staetements * add barriers to poisson solver * update print * print membrane input concentration * read Membrane ion concentration list * fix bad ref to D3Q7 * update error analysis for Poisson solver * fix typo * update hip poisson solver * deprecate old error methods * a bunch of summit debug things to roll back later * fix poisson typo * update hip * debug crusher * debug charge density problems on crusher * fix charge density (i think) * remove Stokes solver from cell simulator; need to test build * update cpu ion valence * added membrane properties to input db * update cell db * update executable list and NP_cell simulator * correct use_membrane functionality * add functionality for user to choose either D3Q7 or D3Q19 lattice for Poisson;to be built and tested * build passed * make further corrections * correct D3Q7 Poisson LB algorithm * correct ion LB collison * udpate output precision * add more tweaks for cell simulator * update print-out * this makes mpi hang error explicit;to be debugged * cleanup with help from valgrind * update to cell vis routine * add hip for ion update * fix missing bracket * add new ion code for cuda * add barrier to membrane transport * debug gpu launch issue for ion * debug gpu * add functions to copy send / recv list from ScaLBL * updating membrane communication structure * membrane test works with new comm * communication seems to work * add sample files for plane membrane * update gpu routines first try * update hip * multiple nvidia gpu working with membrane * added membrane analysis capability * added support for swc file * support for SWC input format * swc reader works with MPI * shift swc data * SWC reader update * SWC reader update 2 * add offset to Domain for swc * add input files for simple bacteria * add performance counters to ion / poisson solvers * fix bug with SWC * add BC to poisson solver * fix compiler warnings * fix memory leaks * fix zlib download path * Fixing memory leak * Fixing memory leaks * restart for Poisson model * fix bug in ion model restart * trying to fix yaml * fix workflow indentation * porosity factor in effperm * porosity factor in effperm * porosity factor in effperm * porosity factor in effperm Co-authored-by: James E McClure <mcclurej@vt.edu> Co-authored-by: Mark Berrill <berrillma@ornl.gov> Co-authored-by: Zhe Rex Li <zhe.rex.li@gmail.com> Co-authored-by: Zhe Li <zzl109@gadi-login-01.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-04.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-02.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-06.gadi.nci.org.au> Co-authored-by: Zhe Li <zzl109@gadi-login-05.gadi.nci.org.au> |
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|---|---|---|
| .github/workflows | ||
| analysis | ||
| cmake | ||
| common | ||
| cpu | ||
| cuda | ||
| docs | ||
| doxygen | ||
| example | ||
| hip | ||
| IO | ||
| models | ||
| pmmc | ||
| sample_scripts | ||
| StackTrace | ||
| tests | ||
| threadpool | ||
| workflows | ||
| .clang-format | ||
| .clang-format-2 | ||
| .gitignore | ||
| .project | ||
| clang-format-all | ||
| CMakeLists.txt | ||
| ctest_script.cmake | ||
| LICENSE | ||
| README.md | ||
| README.titan | ||
| ValgrindSuppresionFile | ||
LBPM
Lattice Boltzmann Methods for Porous Media
========
Notes on installation
- example configure scripts for cmake are in the sample_scripts directory
- required dependencies - MPI, HDF5, SILO, C++14
- optional dependencies - NetCDF, CUDA, TimerUtility
Build dependencies (zlib, hdf5, silo) OR point to an existing installation
Configure, build & install procedure
-
create an empty directory to install (do not build in source!)
mkdir /path/to/my/installcd /path/to/my/install -
edit configure script from sample_scripts directory and configure (e.g.)
/path/to/LBPM/sample_scripts/configure_desktop -
compile and install
make -j4 && make install -
run the unit tests to make sure it works
ctest