Updates needed for ScaLBL refactor / CPU build script on Eos

IO/Mesh.h

@@ -6,8 +6,8 @@
 #include <vector>
 
 #include "common/Array.h"
-#include "common/PointList.h"
 #include "common/Communication.h"
+#include "analysis/PointList.h"
 #include "shared_ptr.h"
 
 

analysis/eikonal.hpp

@@ -2,7 +2,7 @@
 #define Eikonal_HPP_INC
 
 #include "analysis/eikonal.h"
-#include "common/imfilter.h"
+#include "analysis/imfilter.h"
 
 
 

analysis/imfilter.h

@@ -153,7 +153,7 @@ Array<TYPE> create_filter( const std::vector<int>& N, const std::string &type, c
 }
 
 
-#include "common/imfilter.hpp"
+#include "analysis/imfilter.hpp"
 
 #endif
 

analysis/imfilter.hpp

@@ -1,4 +1,4 @@
-#include "common/imfilter.h"
+#include "analysis/imfilter.h"
 #include "ProfilerApp.h"
 #include <math.h>
 #include <string.h>

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<class T>

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  \

tests/BlobAnalysis.cpp

@@ -5,7 +5,7 @@
 
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "analysis/analysis.h"
 //#include "Domain.h"
 

tests/BlobIdentify.cpp

@@ -5,7 +5,7 @@
 
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "analysis/analysis.h"
 
 //#include "Domain.h"

tests/BlobIdentifyParallel.cpp

@@ -5,9 +5,9 @@
 
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
 #include "common/Communication.h"
 #include "analysis/analysis.h"
+#include "analysis/pmmc.h"
 #ifdef PROFILE
  #include "ProfilerApp.h"
 #endif

tests/ColorToBinary.cpp

@@ -6,7 +6,7 @@
 #include <iostream>
 #include <math.h>
 #include "analysis/analysis.h"
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 
 using namespace std;
 

tests/ComponentLabel.cpp

@@ -6,7 +6,7 @@
 #include <iostream>
 #include <math.h>
 #include "analysis/analysis.h"
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 
 #define NUM_AVERAGES 30
 

tests/TestBlobAnalyze.cpp

@@ -7,7 +7,7 @@
 #include <math.h>
 #include "common/Communication.h"
 #include "analysis/analysis.h"
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 
 //#include "Domain.h"
 

tests/TestBlobIdentify.cpp

@@ -5,7 +5,7 @@
 
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "common/Communication.h"
 #include "analysis/analysis.h"
 #include "IO/MeshDatabase.h"

tests/TestBubble.cpp

@@ -5,7 +5,7 @@
 #include <stdexcept>
 #include <fstream>
 
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "common/ScaLBL.h"
 #include "common/MPI_Helpers.h"
 #include "common/Communication.h"

tests/TestInterfaceSpeed.cpp

@@ -1,7 +1,7 @@
 #include <iostream>
 #include <math.h>
 
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 #include "common/MPI_Helpers.h"
 #include "common/Communication.h"
 #include "IO/Mesh.h"

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)

tests/TestSphereCurvature.cpp

@@ -1,6 +1,6 @@
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "common/Domain.h"
 
 using namespace std;

tests/TestTorus.cpp

@@ -7,7 +7,7 @@
 #include <math.h>
 #include "common/Communication.h"
 #include "analysis/analysis.h"
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 
 //#include "Domain.h"
 

tests/TestTwoPhase.cpp

@@ -7,7 +7,7 @@
 #include <stdexcept>
 #include <fstream>
 
-#include "common/TwoPhase.h"
+#include "analysis/TwoPhase.h"
 #include "common/MPI_Helpers.h"
 #include "common/Communication.h"
 #include "IO/Mesh.h"

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)

tests/lbpm_color_macro_simulator.cpp

@@ -7,7 +7,7 @@
 #include <fstream>
 
 #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"

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"

tests/lbpm_disc_pp.cpp

@@ -6,7 +6,7 @@
 #include <stdexcept>
 #include <fstream>
 
-#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

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)

tests/lbpm_juanes_bench_disc_pp.cpp

@@ -6,7 +6,7 @@
 #include <stdexcept>
 #include <fstream>
 
-#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

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

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

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)

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)
 {

tests/lbpm_sphere_pp.cpp

@@ -6,7 +6,7 @@
 #include <stdexcept>
 #include <fstream>
 
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 #include "common/Domain.h"
 #include "common/MPI_Helpers.h"
 #include "common/Communication.h"

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)

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"
 

tests/pmmc_cylinder.cpp

@@ -1,6 +1,6 @@
 #include <iostream>
 #include <math.h>
-#include "common/pmmc.h"
+#include "analysis/pmmc.h"
 //#include "common/PointList.h"
 //#include "common/Array.h"