* 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>
124 lines
3.6 KiB
YAML
124 lines
3.6 KiB
YAML
name: LBPM CI
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on:
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push:
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branches: [ master ]
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pull_request:
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branches: [ master ]
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jobs:
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build-and-test:
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runs-on: ubuntu-latest
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env:
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LBPM_ZLIB_DIR: /home/runner/extlib/zlib
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LBPM_HDF5_DIR: /home/runner/extlib/hdf5
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LBPM_SILO_DIR: /home/runner/extlib/silo
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MPI_DIR: /home/runner/.openmpi
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steps:
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- name: download dependencies
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run: |
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echo $LBPM_ZLIB_DIR
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echo $LBPM_HDF5_DIR
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echo $LBPM_SILO_DIR
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echo $GITHUB_PATH
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echo $GITHUB_WORKSPACE
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sudo apt-get update -y
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wget https://bitbucket.org/AdvancedMultiPhysics/tpl-builder/downloads/silo-4.10.2.tar.gz
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wget https://www.zlib.net/fossils/zlib-1.2.11.tar.gz
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wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz
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#wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.10/src/hdf5-1.8.10.tar.gz
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tar -xzvf zlib-1.2.11.tar.gz
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tar -xzvf hdf5-1.8.12.tar.gz
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tar -xzvf silo-4.10.2.tar.gz
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- name: check out commit
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uses: actions/checkout@v2
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with:
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path: LBPM
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- name: install-openmpi
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run: |
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wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.2.tar.gz
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tar -xvf ./openmpi-3.1.2.tar.gz
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./openmpi-3.1.2/configure --prefix="$HOME/.openmpi"
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make -j
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sudo make install
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echo "$HOME/.openmpi/bin" >> $GITHUB_PATH
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- name: install zlib dependencies
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run: |
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cd zlib-1.2.11
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./configure --prefix=$LBPM_ZLIB_DIR
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make
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sudo make install
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cd ..
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- name: install hdf5 dependencies
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run: |
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cd hdf5-1.8.12
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CC=/home/runner/.openmpi/bin/mpicc CXX=/home/runner/.openmpi/bin/mpicxx CXXFLAGS="-fPIC -O3 -std=c++14" \
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./configure --prefix=$LBPM_HDF5_DIR --enable-parallel --enable-shared --with-zlib=$LBPM_ZLIB_DIR
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make
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sudo make install
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cd ..
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- name: install silo dependencies
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run: |
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cd silo-4.10.2
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CC=$MPI_DIR/bin/mpicc CXX=$MPI_DIR/bin/mpicxx CXXFLAGS="-fPIC -O3 -std=c++14" \
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./configure --prefix=$LBPM_SILO_DIR -with-hdf5="$LBPM_HDF5_DIR/include,$LBPM_HDF5_DIR/lib" --enable-static
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make
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sudo make install
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cd ..
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- name: configure cmake
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run: |
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mkdir build
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cd build
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rm -rf CMake*
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cmake \
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-D CMAKE_BUILD_TYPE:STRING=Release \
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-D CMAKE_C_COMPILER:PATH=$MPI_DIR/bin/mpicc \
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-D CMAKE_CXX_COMPILER:PATH=$MPI_DIR/bin/mpicxx \
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-D MPI_CXX_COMPILER=$MPI_DIR/bin/mpicxx \
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-D CMAKE_C_FLAGS="-fPIC" \
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-D CMAKE_CXX_FLAGS="-fPIC" \
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-D CMAKE_CXX_STD=14 \
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-D TEST_MAX_PROCS=1 \
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-D USE_TIMER=0 \
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-D TIMER_DIRECTORY=$LBPM_TIMER_DIR \
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-D USE_NETCDF=0 \
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-D NETCDF_DIRECTORY=$LBPM_NETCDF_DIR \
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-D USE_SILO=1 \
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-D HDF5_DIRECTORY=$LBPM_HDF5_DIR \
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-D SILO_DIRECTORY=$LBPM_SILO_DIR \
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-D USE_CUDA=0 \
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$GITHUB_WORKSPACE/LBPM
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- name: build and make
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run: |
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cd build
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make
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sudo make install
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cd ..
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- name: tests
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run: |
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cd build
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ctest
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