* 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>
