diff --git a/IO/Mesh.h b/IO/Mesh.h index 969a9a61..604dddfd 100644 --- a/IO/Mesh.h +++ b/IO/Mesh.h @@ -6,8 +6,8 @@ #include #include "common/Array.h" -#include "common/PointList.h" #include "common/Communication.h" +#include "analysis/PointList.h" #include "shared_ptr.h" diff --git a/analysis/eikonal.hpp b/analysis/eikonal.hpp index 119677d3..fd96c7c0 100644 --- a/analysis/eikonal.hpp +++ b/analysis/eikonal.hpp @@ -2,7 +2,7 @@ #define Eikonal_HPP_INC #include "analysis/eikonal.h" -#include "common/imfilter.h" +#include "analysis/imfilter.h" diff --git a/analysis/imfilter.h b/analysis/imfilter.h index b0f5f9ee..b1c4040a 100644 --- a/analysis/imfilter.h +++ b/analysis/imfilter.h @@ -153,7 +153,7 @@ Array create_filter( const std::vector& N, const std::string &type, c } -#include "common/imfilter.hpp" +#include "analysis/imfilter.hpp" #endif diff --git a/analysis/imfilter.hpp b/analysis/imfilter.hpp index fb797aae..9816beca 100644 --- a/analysis/imfilter.hpp +++ b/analysis/imfilter.hpp @@ -1,4 +1,4 @@ -#include "common/imfilter.h" +#include "analysis/imfilter.h" #include "ProfilerApp.h" #include #include diff --git a/analysis/uCT.cpp b/analysis/uCT.cpp index c96511f4..efa43d47 100644 --- a/analysis/uCT.cpp +++ b/analysis/uCT.cpp @@ -2,8 +2,7 @@ #include "analysis/analysis.h" #include "analysis/eikonal.h" #include "analysis/filters.h" -#include "analysis/uCT.h" -#include "common/imfilter.h" +#include "analysis/imfilter.h" template diff --git a/sample_scripts/config_build_eos b/sample_scripts/config_build_eos index 0b886c87..2b93a789 100755 --- a/sample_scripts/config_build_eos +++ b/sample_scripts/config_build_eos @@ -2,25 +2,18 @@ #for var in ${LOADEDMODULES//:/ }; do if [ " ${var///*/}" != " modules" ]; then module unload " ${var///*/}" > /dev/null 2>&1; fi; done source $MODULESHOME/init/bash -module unload PrgEnv-intel -module load PrgEnv-gnu -module unload gcc -module load gcc/5.3.0 -module load cray-hdf5-parallel -module load cray-netcdf-hdf5parallel - # Set the modules and enviornmental variables -#module load DefApps -#module load PrgEnv-intel -#module unload cray-libsci -#module load cray-mpich ugni xpmem udreg altd -#module load moab torque +module unload PrgEnv-intel +module load PrgEnv-gnu/6.0.4 +module unload gcc cmake +module load gcc/6.3.0 +module load cray-hdf5-parallel/1.10.0.1 +module load cray-netcdf-hdf5parallel module load mercurial git -module load cmake +module load cmake3/3.6.1 export MPICH_RDMA_ENABLED_CUDA=0 - echo $GNU_VERSION module list @@ -42,9 +35,11 @@ cmake \ -D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \ -D USE_CUDA=0 \ -D CUDA_FLAGS="-arch sm_35" \ - -D USE_NETCDF=1 \ + -DBUILD_SHARED_LIBS=OFF \ + -D USE_NETCDF=0 \ -D NETCDF_DIRECTORY=$NETCDF_DIR \ -D HDF5_DIRECTORY=$HDF5_DIR \ + -D CMAKE_SKIP_RPATH=true \ ~/LBPM-WIA # -D PREFIX=$MEMBERWORK/geo106/eos-LBPM-WIA \ diff --git a/tests/BlobAnalysis.cpp b/tests/BlobAnalysis.cpp index 75ab154a..0a55c318 100644 --- a/tests/BlobAnalysis.cpp +++ b/tests/BlobAnalysis.cpp @@ -5,7 +5,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "analysis/analysis.h" //#include "Domain.h" diff --git a/tests/BlobIdentify.cpp b/tests/BlobIdentify.cpp index 155f8a7e..39a59954 100644 --- a/tests/BlobIdentify.cpp +++ b/tests/BlobIdentify.cpp @@ -5,7 +5,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "analysis/analysis.h" //#include "Domain.h" diff --git a/tests/BlobIdentifyParallel.cpp b/tests/BlobIdentifyParallel.cpp index 231b6595..b5127718 100644 --- a/tests/BlobIdentifyParallel.cpp +++ b/tests/BlobIdentifyParallel.cpp @@ -5,9 +5,9 @@ #include #include -#include "common/pmmc.h" #include "common/Communication.h" #include "analysis/analysis.h" +#include "analysis/pmmc.h" #ifdef PROFILE #include "ProfilerApp.h" #endif diff --git a/tests/ColorToBinary.cpp b/tests/ColorToBinary.cpp index fd8fa40c..6c3ac5e8 100644 --- a/tests/ColorToBinary.cpp +++ b/tests/ColorToBinary.cpp @@ -6,7 +6,7 @@ #include #include #include "analysis/analysis.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" using namespace std; diff --git a/tests/ComponentLabel.cpp b/tests/ComponentLabel.cpp index 067c40e4..16587699 100644 --- a/tests/ComponentLabel.cpp +++ b/tests/ComponentLabel.cpp @@ -6,7 +6,7 @@ #include #include #include "analysis/analysis.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #define NUM_AVERAGES 30 diff --git a/tests/TestBlobAnalyze.cpp b/tests/TestBlobAnalyze.cpp index b88010df..c5db51cf 100644 --- a/tests/TestBlobAnalyze.cpp +++ b/tests/TestBlobAnalyze.cpp @@ -7,7 +7,7 @@ #include #include "common/Communication.h" #include "analysis/analysis.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" //#include "Domain.h" diff --git a/tests/TestBlobIdentify.cpp b/tests/TestBlobIdentify.cpp index fbbae858..71e6f1cf 100644 --- a/tests/TestBlobIdentify.cpp +++ b/tests/TestBlobIdentify.cpp @@ -5,7 +5,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/Communication.h" #include "analysis/analysis.h" #include "IO/MeshDatabase.h" diff --git a/tests/TestBubble.cpp b/tests/TestBubble.cpp index dacd97f6..92b1a46c 100644 --- a/tests/TestBubble.cpp +++ b/tests/TestBubble.cpp @@ -5,7 +5,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/ScaLBL.h" #include "common/MPI_Helpers.h" #include "common/Communication.h" diff --git a/tests/TestInterfaceSpeed.cpp b/tests/TestInterfaceSpeed.cpp index efeca240..9ace6822 100644 --- a/tests/TestInterfaceSpeed.cpp +++ b/tests/TestInterfaceSpeed.cpp @@ -1,7 +1,7 @@ #include #include -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" #include "common/Communication.h" #include "IO/Mesh.h" diff --git a/tests/TestMassConservationD3Q7.cpp b/tests/TestMassConservationD3Q7.cpp index f21b2871..a08342a1 100644 --- a/tests/TestMassConservationD3Q7.cpp +++ b/tests/TestMassConservationD3Q7.cpp @@ -9,7 +9,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" int main(int argc, char **argv) diff --git a/tests/TestSphereCurvature.cpp b/tests/TestSphereCurvature.cpp index 7d11d052..dad87618 100644 --- a/tests/TestSphereCurvature.cpp +++ b/tests/TestSphereCurvature.cpp @@ -1,6 +1,6 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/Domain.h" using namespace std; diff --git a/tests/TestTorus.cpp b/tests/TestTorus.cpp index 004cc1b7..6dd55a67 100644 --- a/tests/TestTorus.cpp +++ b/tests/TestTorus.cpp @@ -7,7 +7,7 @@ #include #include "common/Communication.h" #include "analysis/analysis.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" //#include "Domain.h" diff --git a/tests/TestTwoPhase.cpp b/tests/TestTwoPhase.cpp index b19943e9..3ee6d7ef 100644 --- a/tests/TestTwoPhase.cpp +++ b/tests/TestTwoPhase.cpp @@ -7,7 +7,7 @@ #include #include -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" #include "common/Communication.h" #include "IO/Mesh.h" diff --git a/tests/lbpm_captube_pp.cpp b/tests/lbpm_captube_pp.cpp index db1adf66..9e6b8ebd 100644 --- a/tests/lbpm_captube_pp.cpp +++ b/tests/lbpm_captube_pp.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" int main(int argc, char **argv) diff --git a/tests/lbpm_color_macro_simulator.cpp b/tests/lbpm_color_macro_simulator.cpp index db4bcd71..8adceb6d 100644 --- a/tests/lbpm_color_macro_simulator.cpp +++ b/tests/lbpm_color_macro_simulator.cpp @@ -7,7 +7,7 @@ #include #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" #include "ProfilerApp.h" #include "threadpool/thread_pool.h" diff --git a/tests/lbpm_color_simulator.cpp b/tests/lbpm_color_simulator.cpp index da0ff608..6268b74f 100644 --- a/tests/lbpm_color_simulator.cpp +++ b/tests/lbpm_color_simulator.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" #include "ProfilerApp.h" diff --git a/tests/lbpm_disc_pp.cpp b/tests/lbpm_disc_pp.cpp index 25424dd6..6c427484 100644 --- a/tests/lbpm_disc_pp.cpp +++ b/tests/lbpm_disc_pp.cpp @@ -6,7 +6,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/Domain.h" #include "common/Communication.h" #include "common/MPI_Helpers.h" // This includes mpi.h diff --git a/tests/lbpm_drain_pp.cpp b/tests/lbpm_drain_pp.cpp new file mode 100644 index 00000000..e69de29b diff --git a/tests/lbpm_inkbottle_pp.cpp b/tests/lbpm_inkbottle_pp.cpp index 78cb74fb..4a1ca70a 100644 --- a/tests/lbpm_inkbottle_pp.cpp +++ b/tests/lbpm_inkbottle_pp.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" int main(int argc, char **argv) diff --git a/tests/lbpm_juanes_bench_disc_pp.cpp b/tests/lbpm_juanes_bench_disc_pp.cpp index cdfe54f1..843a1328 100644 --- a/tests/lbpm_juanes_bench_disc_pp.cpp +++ b/tests/lbpm_juanes_bench_disc_pp.cpp @@ -6,7 +6,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/Domain.h" #include "common/Communication.h" #include "common/MPI_Helpers.h" // This includes mpi.h diff --git a/tests/lbpm_nondarcy_simulator.cpp b/tests/lbpm_nondarcy_simulator.cpp index de5b961e..2e8da060 100644 --- a/tests/lbpm_nondarcy_simulator.cpp +++ b/tests/lbpm_nondarcy_simulator.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" //#define WRITE_SURFACES diff --git a/tests/lbpm_permeability_simulator.cpp b/tests/lbpm_permeability_simulator.cpp index 41a21460..cdb100d3 100644 --- a/tests/lbpm_permeability_simulator.cpp +++ b/tests/lbpm_permeability_simulator.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" //#define WRITE_SURFACES diff --git a/tests/lbpm_plates_pp.cpp b/tests/lbpm_plates_pp.cpp index eb9cff24..c43f6781 100644 --- a/tests/lbpm_plates_pp.cpp +++ b/tests/lbpm_plates_pp.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" int main(int argc, char **argv) diff --git a/tests/lbpm_refine_pp.cpp b/tests/lbpm_refine_pp.cpp index 95b9d679..d7e087b5 100644 --- a/tests/lbpm_refine_pp.cpp +++ b/tests/lbpm_refine_pp.cpp @@ -11,7 +11,7 @@ #include "common/Array.h" #include "common/Communication.h" #include "common/Domain.h" -#include "common/pmmc.h" +#include "analysis/pmmc.h" int main(int argc, char **argv) { diff --git a/tests/lbpm_sphere_pp.cpp b/tests/lbpm_sphere_pp.cpp index 7a639fb3..6f9e25ae 100644 --- a/tests/lbpm_sphere_pp.cpp +++ b/tests/lbpm_sphere_pp.cpp @@ -6,7 +6,7 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" #include "common/Domain.h" #include "common/MPI_Helpers.h" #include "common/Communication.h" diff --git a/tests/lbpm_squaretube_pp.cpp b/tests/lbpm_squaretube_pp.cpp index d506f7c2..c60079b9 100644 --- a/tests/lbpm_squaretube_pp.cpp +++ b/tests/lbpm_squaretube_pp.cpp @@ -8,7 +8,7 @@ #include "common/ScaLBL.h" #include "common/Communication.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "common/MPI_Helpers.h" int main(int argc, char **argv) diff --git a/tests/lbpm_uCT_maskfilter.cpp b/tests/lbpm_uCT_maskfilter.cpp index 22bcb45f..cd7763b4 100644 --- a/tests/lbpm_uCT_maskfilter.cpp +++ b/tests/lbpm_uCT_maskfilter.cpp @@ -23,7 +23,7 @@ #include "analysis/eikonal.h" #include "analysis/filters.h" #include "analysis/uCT.h" -#include "common/TwoPhase.h" +#include "analysis/TwoPhase.h" #include "ProfilerApp.h" diff --git a/tests/pmmc_cylinder.cpp b/tests/pmmc_cylinder.cpp index 8ad7c6f7..a573fee3 100644 --- a/tests/pmmc_cylinder.cpp +++ b/tests/pmmc_cylinder.cpp @@ -1,6 +1,6 @@ #include #include -#include "common/pmmc.h" +#include "analysis/pmmc.h" //#include "common/PointList.h" //#include "common/Array.h"