Commit 6b35584c authored by Giovanni La Mura's avatar Giovanni La Mura
Browse files

Merge branch 'wrap_output' into 'master' 

Wrap output

See merge request giacomo.mulas/np_tmcode!75
parents 6e1610f7 62cd0416

.gitlab-ci.yml

+34 −9
Original line number Diff line number Diff line
@@ -154,7 +154,7 @@ building_stage: 
      - cat /etc/os-release

      - cd build

      - echo "Configuring with default compilers (MAGMA disabled)..."

      - ./configure --without-magma --without-cublas --disable-offload --enable-refinement

      - ./configure --without-magma --without-cublas --disable-offload --enable-refinement --enable-shared

      - make wipe

      - echo "Building the default configuration..."

      - make -j
@@ -185,11 +185,19 @@ sanity_stage: 
      - hostname

      - echo $CI_COMMIT_SHA

      - echo $CI_COMMIT_BRANCH

      - cd build/testing

      - echo "Running memory sanity check"

      - cd build/libnptm

      - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"

      - cd ../testing

      - echo "Running memory sanity check for ParticleDescriptor"

      - chmod +x test_ParticleDescriptor

      - valgrind --leak-check=full --log-file=valgrind.log ./test_ParticleDescriptor

      - grep "no leaks are possible" valgrind.log

      - grep "0 errors from 0 contexts" valgrind.log

      - echo "Running memory sanity check for output classes"

      - chmod +x test_outputs

      - rm valgrind.log

      - valgrind --leak-check=full --log-file=valgrind.log ./test_outputs

      - grep "0 errors from 0 contexts" valgrind.log

      - rm -rf c_OCLU_24

      

running_stage:

   stage: run
@@ -215,7 +223,9 @@ running_stage: 
      - hostname

      - echo $CI_COMMIT_SHA

      - echo $CI_COMMIT_BRANCH

      - cd build/sphere

      - cd build/libnptm

      - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"

      - cd ../sphere

      - echo "Running np_sphere"

      - chmod +x np_sphere

      - ./np_sphere
@@ -240,7 +250,7 @@ testing_stage: 
      - running_stage

   artifacts:

      paths:

         - build/cluster/pycompare.html

         - build/cluster/pycompare_*.html

         - build/inclusion/pycompare.html

         - build/sphere/pycompare.html

      exclude:
@@ -253,7 +263,9 @@ testing_stage: 
      - hostname

      - echo $CI_COMMIT_SHA

      - echo $CI_COMMIT_BRANCH

      - cd build/sphere

      - cd build/libnptm

      - export LD_LIBRARY_PATH="$LD_LIBRARY_PATH;$PWD"

      - cd ../sphere

      - export FFILE=../../test_data/sphere/OSPH

      - echo "Comparing output of SPHERE"

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OSPH --html
@@ -266,13 +278,26 @@ testing_stage: 
      - cd ../cluster

      - echo "Comparing output of CLUSTER"

      - export FFILE=../../test_data/cluster/OCLU

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_dev.html

      - echo "Testing cluster with 24 spheres"

      - OMP_NUM_THREADS=1 OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 mpirun -n 2 ./np_cluster ../../test_data/cluster/DEDFB_24 ../../test_data/cluster/DCLU_24 .

      - echo "Comparing output of CLUSTER with 24 spheres"

      - export FFILE=../../test_data/cluster/OCLU_24

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_24.html

      - echo "Checking consistency among legacy and HDF5 configuration files"

      - ../testing/test_TEDF ../../test_data/cluster/DEDFB_24 c_TEDF c_TEDF.hd5

      - echo "Checking consistency among legacy and HDF5 TM files"

      - ../testing/test_TTMS c_TTMS c_TTMS.hd5

      - echo "Testing cluster with 48 spheres"

      - OMP_NUM_THREADS=5 ./np_cluster ../../test_data/cluster/DEDFB_48 ../../test_data/cluster/DCLU_48 .

      - echo "Comparing output of CLUSTER with 48 spheres"

      - export FFILE=../../test_data/cluster/OCLU_48

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU --html=pycompare_48.html

      - cd ../testing

      - echo "Checking consistency of HDF5 output"

      - chmod u+x test_outputs

      - ./test_outputs

      - export FFILE=../../test_data/cluster/OCLU_24

      - python3 ../../src/scripts/pycompare.py --no-progress --ffile $FFILE --cfile c_OCLU_24

      - rm -rf c_OCLU_24

      
 No newline at end of file

build/Makefile

+16 −4
Original line number Diff line number Diff line
@@ -14,21 +14,29 @@ else 
	NPTM_LIB=libnptm/libnptm.a

	CXXFLAGSLIB=-static

endif # LIBMODE

NP_LIBNPTM_SRCS=../src/libnptm/algebraic.cpp ../src/libnptm/clu_subs.cpp ../src/libnptm/Commons.cpp ../src/libnptm/Configuration.cpp ../src/libnptm/cublas_calls.cpp ../src/libnptm/file_io.cpp ../src/libnptm/inclu_subs.cpp ../src/libnptm/logging.cpp ../src/libnptm/lapack_calls.cpp ../src/libnptm/magma_calls.cpp ../src/libnptm/Parsers.cpp ../src/libnptm/sph_subs.cpp ../src/libnptm/tfrfme.cpp ../src/libnptm/tra_subs.cpp ../src/libnptm/TransitionMatrix.cpp ../src/libnptm/utils.cpp

NP_LIBNPTM_OBJS=../src/libnptm/algebraic.o ../src/libnptm/clu_subs.o ../src/libnptm/Commons.o ../src/libnptm/Configuration.o ../src/libnptm/cublas_calls.o ../src/libnptm/file_io.o ../src/libnptm/inclu_subs.o ../src/libnptm/logging.o ../src/libnptm/lapack_calls.o ../src/libnptm/magma_calls.o ../src/libnptm/Parsers.o ../src/libnptm/sph_subs.o ../src/libnptm/tfrfme.o ../src/libnptm/tra_subs.o ../src/libnptm/TransitionMatrix.o ../src/libnptm/utils.o

NP_DOC_SRCS=../doc/src/config.dox

NP_LIBNPTM_SRCS=../src/libnptm/algebraic.cpp ../src/libnptm/clu_subs.cpp ../src/libnptm/Commons.cpp ../src/libnptm/Configuration.cpp ../src/libnptm/cublas_calls.cpp ../src/libnptm/file_io.cpp ../src/libnptm/inclu_subs.cpp ../src/libnptm/logging.cpp ../src/libnptm/lapack_calls.cpp ../src/libnptm/magma_calls.cpp ../src/libnptm/outputs.cpp ../src/libnptm/Parsers.cpp ../src/libnptm/sph_subs.cpp ../src/libnptm/tfrfme.cpp ../src/libnptm/tra_subs.cpp ../src/libnptm/TransitionMatrix.cpp ../src/libnptm/utils.cpp

NP_LIBNPTM_OBJS=../src/libnptm/algebraic.o ../src/libnptm/clu_subs.o ../src/libnptm/Commons.o ../src/libnptm/Configuration.o ../src/libnptm/cublas_calls.o ../src/libnptm/file_io.o ../src/libnptm/inclu_subs.o ../src/libnptm/logging.o ../src/libnptm/lapack_calls.o ../src/libnptm/magma_calls.o ../src/libnptm/outputs.o ../src/libnptm/Parsers.o ../src/libnptm/sph_subs.o ../src/libnptm/tfrfme.o ../src/libnptm/tra_subs.o ../src/libnptm/TransitionMatrix.o ../src/libnptm/utils.o

NP_CLUSTER_SRCS=../src/cluster/np_cluster.cpp ../src/cluster/cluster.cpp

NP_CLUSTER_OBJS=../src/cluster/np_cluster.o ../src/cluster/cluster.o

NP_CLUSTER_BINS=cluster/np_cluster

NP_INCLUSION_SRCS=../src/inclusion/np_inclusion.cpp ../src/inclusion/inclusion.cpp

NP_INCLUSION_OBJS=../src/inclusion/np_inclusion.o ../src/inclusion/inclusion.o

NP_INCLUSION_BINS=inclusion/np_inclusion

NP_SPHERE_SRCS=../src/sphere/np_sphere.cpp ../src/sphere/sphere.cpp

NP_SPHERE_OBJS=../src/sphere/np_sphere.o ../src/sphere/sphere.o

NP_SPHERE_BINS=sphere/np_sphere

NP_TRAPPING_SRCS=../src/trapping/np_trapping.cpp ../src/trapping/cfrfme.cpp ../src/trapping/clffft.cpp

NP_TRAPPING_OBJS=../src/trapping/np_trapping.o ../src/trapping/cfrfme.o ../src/trapping/clffft.o

NP_TRAPPING_BINS=trapping/np_trapping

NP_TESTING_OBJS=../src/testing/test_ParticleDescriptor.o ../src/testing/test_TEDF.o ../src/testing/test_TTMS.o

NP_TESTING_BINS=testing/test_ParticleDescriptor testing/test_TEDF testing/test_TTMS

NP_TESTING_OBJS=../src/testing/test_outputs.o ../src/testing/test_ParticleDescriptor.o ../src/testing/test_TEDF.o ../src/testing/test_TTMS.o

NP_TESTING_BINS=testing/test_outputs testing/test_ParticleDescriptor testing/test_TEDF testing/test_TTMS



all: $(NPTM_LIB) $(FORTRAN_BINS) $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)



docs: $(NP_LIBNPTM_SRCS) $(NP_CLUSTER_SRCS) $(NP_DOC_SRCS) $(NP_INCLUSION_SRCS) $(NP_SPHERE_SRCS) $(NP_TRAPPING_SRCS)

	cd ../doc/src; doxygen config.dox



libnptm/libnptm.a: $(NP_LIBNPTM_OBJS)

	$(AR) $(ARFLAGS) $@ $(NP_LIBNPTM_OBJS)
@@ -75,6 +83,9 @@ trapping/np_trapping: $(NPTM_LIB) $(NP_TRAPPING_OBJS) 
testing/test_ParticleDescriptor: $(NPTM_LIB) ../src/testing/test_ParticleDescriptor.o

	$(CXX) $(CXXFLAGS) ../src/testing/test_ParticleDescriptor.o -o $@ $(CXXLDFLAGS)



testing/test_outputs: $(NPTM_LIB) ../src/testing/test_outputs.o

	$(CXX) $(CXXFLAGS) ../src/testing/test_outputs.o -o $@ $(CXXLDFLAGS)



testing/test_TEDF: $(NPTM_LIB) ../src/testing/test_TEDF.o

	$(CXX) $(CXXFLAGS) ../src/testing/test_TEDF.o -o $@ $(CXXLDFLAGS)
@@ -146,3 +157,4 @@ clean: 
wipe:

	rm -rf $(FORTRAN_OBJS) $(NP_LIBNPTM_OBJS) $(NP_CLUSTER_OBJS) $(NP_INCLUSION_OBJS) $(NP_SPHERE_OBJS) $(NP_TRAPPING_OBJS) $(NP_TESTING_OBJS)

	rm -rf $(FORTRAN_BINS) libnptm/libnptm.a libnptm/libnptm.so $(NP_CLUSTER_BINS) $(NP_INCLUSION_BINS) $(NP_SPHERE_BINS) $(NP_TRAPPING_BINS) $(NP_TESTING_BINS)

	rm -rf ../doc/build

src/cluster/cluster.cpp

+329 −421

File changed.

Preview size limit exceeded, changes collapsed.

src/cluster/np_cluster.cpp

+6 −0
Original line number Diff line number Diff line
@@ -35,6 +35,12 @@ 
#include <cstdio>

#include <string>



#ifdef USE_MPI

#ifndef MPI_VERSION

#include <mpi.h>

#endif

#endif



#ifndef INCLUDE_TYPES_H_

#include "../include/types.h"

#endif

src/include/Commons.h

+73 −15
Original line number Diff line number Diff line
@@ -33,10 +33,6 @@ 
#ifndef INCLUDE_COMMONS_H_

#define INCLUDE_COMMONS_H_



#ifdef USE_MPI

#include <mpi.h>

#endif



class ParticleDescriptor;



/*! \brief Structure with essential MPI data.
@@ -78,58 +74,103 @@ public: 
  ParticleDescriptor *c1;

  //! \brief Vector of geometric asymmetry factors.

  double *gaps;

  //! \brief Components of extinction contribution to radiation torque on a single sphere along k.

  double **tqse;

  //! \brief Components of polarized extinction contribution to radiation torque on a single sphere along k.

  dcomplex **tqspe;

  //! \brief Components of scattering contribution to radiation torque on a single sphere along k.

  double **tqss;

  //! \brief Components of polarized scattering contribution to radiation torque on a single sphere along k.

  dcomplex **tqsps;

  //! \brief L-dependent coefficients of the geometric asymmetry parameter.

  double ****zpv;

  //! \brief Mean geometric asymmetry parameters.

  double **gapm;

  //! \brief Mean geometric asymmetry parameters referred to polarization plane.

  dcomplex **gappm;

  //! \brief Imaginary part of the harmonic functions argument.

  double *argi;

  //! \brief Argument of the harmonic functions referred to the scattering plane.

  double *args;

  //! \brief Geometric asymmetry parameters.

  double **gap;

  //! \brief Geometric asymmetry parameters referred to polarization plane.

  dcomplex **gapp;

  //! \brief Components of extinction contribution to radiation torque on the cluster along k.

  double **tqce;

  //! \brief Components of extinction contribution to radiation torque on the cluster along k referred to polarization plane.

  dcomplex **tqcpe;

  //! \brief Components of scattering contribution to radiation torque on the cluster along k.

  double **tqcs;

  //! \brief Components of scattering contribution to radiation torque on the cluster along k referred to polarization plane.

  dcomplex **tqcps;

  //! \brief Variation of unitary radiation vector. QUESTION: correct?

  double *duk;

  //! \brief Cluster extinction cross-section components referred to scattering plane.

  double **cextlr;

  //! \brief Cluster extinction cross-section components referred to meridional plane.

  double **cext;

  //! \brief Cluster Mueller Transformation Matrix components referred to scattering plane.

  double **cmullr;

  //! \brief Cluster Mueller Transformation Matrix components referred to meridional plane.

  double **cmul;

  //! \brief Geometric asymmetry parameter components.

  double *gapv;

  //! \brief Radiation extinction torque components.

  double *tqev;

  //! \brief Radiation scattering torque components.

  double *tqsv;

  //! \brief Incident unitary vector components.

  double *u;

  //! \brief Scattered unitary vector components.

  double *us;

  //! \brief Normal unitary vector components.

  double *un;

  //! \brief Normal scattered unitary vector components.

  double *uns;

  //! \brief Incident unitary vector components on polarization plane.

  double *up;

  //! \brief Scattered unitary vector components on polarization plane.

  double *ups;

  //! \brief Mean unitary vector components normal to polarization plane.

  double *unmp;

  //! \brief Mean scattered unitary vector components normal to polarization plane.

  double *unsmp;

  //! \brief Mean incident unitary vector components on polarization plane.

  double *upmp;

  //! \brief Mean scattered unitary vector components on polarization plane.

  double *upsmp;

  //! \brief Scattering angle.

  double scan;

  //! \brief Control parameter on incidence direction referred to meridional plane.

  double cfmp;

  //! \brief Control parameter on scattering direction referred to meridional plane.

  double sfmp;

  //! \brief Control parameter on incidence direction referred to scattering plane.

  double cfsp;

  //! \brief Control parameter on scattering direction referred to scattering plane.

  double sfsp;

  double qsfi;

  //! \brief SQSFI = XI^-2

  double sqsfi;

  //! \brief Vectorized scattering coefficient matrix.

  dcomplex *am_vector;

  //! \brief Scattering coefficient matrix.

  dcomplex **am;

  //! \brief Argument of harmonic functions. QUESTION: correct?

  dcomplex arg;

  //! \brief Vacuum magnitude of wave vector.

  double vk;

  //! \brief Wave number.

  double wn;

  //! \brief Normalization scale. QUESTION: correct?

  double xip;

  //! \brief Number of scales (wavelengths) to be computed.

  int number_of_scales;

  //! \brief Size of the block of scales handled by the current process.

  int xiblock;

  //! \brief Index of the first scale handled by the current process.

  int firstxi;

  //! \brief Index of the last scale handled by the current process.

  int lastxi;

  //! \brief ID of the GPU used by one MPI process.

  int proc_device;
@@ -140,11 +181,27 @@ public: 
  //! \brief Required accuracy level.

  double accuracygoal;



  /*! \brief `ClusterIterationData` default instance constructor.

   *

   * \param gconf: `GeometryConfiguration *` Pointer to a `GeometryConfiguration` object.

   * \param sconf: `ScattererConfiguration *` Pointer to a `ScattererConfiguration` object.

   * \param mpidata: `mixMPI *` Pointer to a `mixMPI` object.

   * \param device_count: `const int` Number of offload devices available on the system.

   */

  ClusterIterationData(GeometryConfiguration *gconf, ScattererConfiguration *sconf, const mixMPI *mpidata, const int device_count);

  

  /*! \brief `ClusterIterationData` copy constructor.

   *

   * \param rhs: `const ClusterIterationData &` Reference to the `ClusterIterationData` object to be copied.

   */

  ClusterIterationData(const ClusterIterationData& rhs);



#ifdef MPI_VERSION

  /*! \brief `ClusterIterationData` MPI constructor.

   *

   * \param mpidata: `const mixMPI *` Pointer to a `mixMPI` instance.

   * \param device_count: `const int` Number of offload devices available on the system.

   */

  ClusterIterationData(const mixMPI *mpidata, const int device_count);



  /*! \brief Broadcast over MPI the ClusterIterationData instance from MPI process 0 to all others.
@@ -157,10 +214,11 @@ public: 
   * \param mpidata: `mixMPI *` Pointer to the mpi structure used to do the MPI broadcast.

   */

  void mpibcast(const mixMPI *mpidata);

#endif

#endif // MPI_VERSION



  /*! \brief `ClusterIterationData` instance destroyer.

   */

  ~ClusterIterationData();



};



/*! \brief Basic data structure describing the particle model and its interaction with fields.
@@ -322,7 +380,7 @@ public: 
  dcomplex *dlri;

  //! \brief Vector of dielectric constants.

  dcomplex *dc0;

  //! \brief TBD

  //! \brief Vector of complex refractive indices.

  dcomplex *vkt;

  //! \brief Vector of sizes in units of 2*PI/LAMBDA

  double *vsz;
@@ -352,23 +410,23 @@ public: 
  // >>> END OF SECTION NEEDED BY SPHERE AND CLUSTER <<< //



  // >>> NEEDED BY CLUSTER <<<

  // \brief Vector of field intensity components.

  //! \brief Vector of field intensity components.

  dcomplex *vintt;

  //! \brief Total forward scattering amplitude.

  //! \brief Total forward scattering amplitude of the spheres.

  dcomplex tfsas;

  //! \brief Total scattering amplitude.

  //! \brief Total scattering amplitude of the spheres.

  dcomplex **tsas;

  //! \brief Total scattering cross-section.

  //! \brief Sphere scattering cross-section.

  double scs;

  //! \brief Total extinction cross-section.

  //! \brief Sphere extinction cross-section.

  double ecs;

  //! \brief Total absorption cross-section.

  //! \brief Sphere absorption cross-section.

  double acs;

  //! \brief TBD.

  dcomplex **gis;

  //! \brief TBD.

  dcomplex **gls;

  //! \brief TBD.

  //! \brief Mean scattering amplitude components.

  dcomplex **sam;

  // >>> END OF SECTION NEEDED BY CLUSTER <<< //