- update pipeline runner config

      - make clean && PATH=/opt/intel/oneapi/compiler/latest/bin:$PATH BUILDDIR=$PWD/../build_ifort-icpx CXX=icpx FC=ifort FCFLAGS="-O3 -diag-disable=10448" make -j

      - echo "Running make with Intel ifx and Intel icpx..."

      - make clean && LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/lib PATH=/opt/intel/oneapi/compiler/latest/bin:$PATH BUILDDIR=$PWD/../build_ifx-icpx CXX=icpx FC=ifx FCFLAGS=-O3 make -j

      - echo "Running make with default MPI compilers"

      - make clean && BUILDDIR=$PWD/../build_mpi CXX=mpicxx FC=mpif90 USE_MPI=1 make -j

building_stage:

   stage: build

RUN DEBIAN_FRONTEND=noninteractive apt -y install intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-dpcpp-cpp

# install lapacke and its dependencies, both standard and the version with 64 bit integers

RUN DEBIAN_FRONTEND=noninteractive apt -y install liblapacke-dev liblapacke64-dev libopenblas-dev libopenblas-openmp-dev libopenblas64-dev libopenblas64-openmp-dev

# install MPI stack

RUN DEBIAN_FRONTEND=noninteractive apt -y install mpi-default-dev mpi-default-bin

# install packages needed to run python scripts for checks

RUN DEBIAN_FRONTEND=noninteractive apt -y install python3 python-is-python3 python3-regex

# install packages needed to run doxygen to create html docs

WORKDIR /root

# install the strictly needed runtime libraries needed to run the executables

# and the python check scripts

RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 liblapacke64 libopenblas64-0-openmp python3 python-is-python3 python3-regex hdf5-tools && rm -rf /var/lib/apt/lists/*

RUN DEBIAN_FRONTEND=noninteractive apt update && DEBIAN_FRONTEND=noninteractive apt upgrade && DEBIAN_FRONTEND=noninteractive apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 liblapacke64 libopenblas64-0-openmp python3 python-is-python3 python3-regex hdf5-tools mpi-default-bin && rm -rf /var/lib/apt/lists/*

COPY --from=np-tmcode-run-dev /root /root

# remove everything which is not needed to run the codes

RUN cd /root/np-tmcode && find build -name "*.o" -exec rm -v \{\} \; && find build -name "*.gcno" -exec rm -v \{\} \; && cd src && rm -rvf cluster libnptm trapping include sphere Makefile make.inc README.md && cd .. && rm -rvf containers && cd doc && rm -rvf src && cd build/latex && rm -rvf *.tex *.out *.sty *.ind *.log *.toc *.ilg *.idx *.aux *.eps Makefile class*.pdf

// I would like to put it all in a struct, but then I'd have to write a constructor for it, due to members defined as references, creating a worse nightmare than the one I'd like to simplify...

int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan, Logger *logger);

int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan);

/*! \brief C++ implementation of CLU

 *

	// do the first iteration on jxi488 separately, since it seems to be different from the others

	int jxi488 = 1;

	chrono::time_point<chrono::high_resolution_clock> start_iter_1 = chrono::high_resolution_clock::now();

	int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid, output, output_path, tppoan, logger);

	int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid, output, output_path, tppoan);

	chrono::time_point<chrono::high_resolution_clock> end_iter_1 = chrono::high_resolution_clock::now();

	elapsed = start_iter_1 - t_start;

	message = "INFO: Calculation setup took " + to_string(elapsed.count()) + "s.\n";

	  // ok, now I can actually start the parallel calculations

#pragma omp for

	  for (jxi488 = cid_2->firstxi; jxi488 <= cid_2->lastxi; jxi488++) {

	    int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2, logger);

	    int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2);

	  }

#pragma omp barrier

      // ok, now I can actually start the parallel calculations

#pragma omp for

      for (int jxi488 = cid_2->firstxi; jxi488 <= cid_2->lastxi; jxi488++) {

	int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2, logger);

	int jer = cluster_jxi488_cycle(jxi488, sconf, gconf, p_scattering_angles, cid_2, output_2, output_path, *tppoanp_2);

      }

#pragma omp barrier

  delete logger;

}

int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan, Logger *logger)

int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConfiguration *gconf, ScatteringAngles *sa, ClusterIterationData *cid, FILE *output, const string& output_path, fstream& tppoan)

{

  int nxi = sconf->number_of_scales;

  string message = "INFO: running scale iteration " + to_string(jxi488) + " of " + to_string(nxi) + ".\n";

  Logger *logger = new Logger(LOG_INFO);

  logger->log(message);

  chrono::duration<double> elapsed;

  chrono::time_point<chrono::high_resolution_clock> interval_start, interval_end;

  logger->log("INFO: finished scale iteration " + to_string(jxi488) + " of " + to_string(nxi) + ".\n");

  delete logger;

  return jer;

}