Merge pull request #303 from PDoakORNL/fix_legacy_hdf5_read (33ced5f9) · Commits · NDIP / Tool Sources / Direct-Geometry Spectroscopy / DCA / DCA Main

include/dca/io/hdf5/hdf5_reader.hpp

+13 −6

Original line number	Diff line number	Diff line
		// Copyright (C) 2018 ETH Zurich
		// Copyright (C) 2018 UT-Battelle, LLC
		// Copyright (C) 2023 ETH Zurich
		// Copyright (C) 2023 UT-Battelle, LLC
		// All rights reserved.
		//
		// See LICENSE for terms of usage.
		// See CITATION.md for citation guidelines, if DCA++ is used for scientific publications.
		//
		// Author: Peter Staar (taa@zurich.ibm.com)
		// Peter W. Doak (doakpw@ornl.gov)
		//
		// HDF5 reader.

		@@ -18,6 +19,9 @@

		#include "H5Cpp.h"

		#include "dca/config/haves_defines.hpp"
		#include "dca/platform/dca_gpu.h"

		#include "dca/io/buffer.hpp"
		#include "dca/function/domains.hpp"
		#include "dca/function/function.hpp"
		@@ -62,7 +66,7 @@ public:
		void begin_step();
		void end_step();

		std::string get_path();
		std::string get_path() const;

		std::size_t getStepCount();

		@@ -113,6 +117,7 @@ public:
		}

		private:
		bool buildCheckedFullName(const std::string& name, std::string& full_name) const;
		bool exists(const std::string& name) const;

		void read(const std::string& name, H5::DataType type, void* data) const;
		@@ -123,6 +128,9 @@ private:

		bool verbose_;

		/// work around for Legacy hdf5
		bool is_legacy_ = false;

		int step_ = 0;
		bool in_step_ = false;
		};
		@@ -138,9 +146,8 @@ void HDF5Reader::from_file(arbitrary_struct_t& arbitrary_struct, std::string fil

		template <typename Scalar>
		bool HDF5Reader::execute(const std::string& name, Scalar& value) {
		std::string full_name = get_path() + "/" + name;

		if (!exists(full_name)) {
		std::string full_name;
		if (!buildCheckedFullName(name, full_name)) {
		return false;
		}

include/dca/io/hdf5/hdf5_writer.hpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -22,6 +22,7 @@

		#include <H5Cpp.h>

		#include "dca/platform/dca_gpu.h"
		#include "dca/function/domains.hpp"
		#include "dca/io/buffer.hpp"
		#include "dca/function/function.hpp"

include/dca/io/reader.hpp

+3 −0

Original line number	Diff line number	Diff line
		@@ -17,6 +17,9 @@
		#include <string>
		#include <variant>

		#include "dca/config/haves_defines.hpp"
		#include "dca/platform/dca_gpu.h"

		#include "dca/io/io_types.hpp"
		#include "dca/io/hdf5/hdf5_reader.hpp"
		#include "dca/io/json/json_reader.hpp"

include/dca/io/writer.hpp

+6 −0

Original line number	Diff line number	Diff line
		@@ -89,6 +89,10 @@ public:
		}
		#endif

		bool isHDF5() {
		return std::holds_alternative<io::HDF5Writer>(writer_);
		}

		bool isOpen() { return is_open_; }

		void begin_step() {
		@@ -172,6 +176,8 @@ public:
		std::visit([&](auto& var) { var.set_verbose(verbose); }, writer_);
		}

		Concurrency& get_concurrency() { return concurrency_; }

		dca::parallel::thread_traits::mutex_type& get_mutex() { return mutex_; }
		private:
		dca::parallel::thread_traits::mutex_type mutex_;

include/dca/phys/dca_data/dca_data.hpp

+29 −8

Original line number	Diff line number	Diff line
		@@ -615,25 +615,45 @@ void DcaData<Parameters, DT>::initializeSigma(adios2::ADIOS& adios [[maybe_unuse
		reader.end_step();
		}
		readSigmaFile(reader);
		reader.close_file();
		}
		concurrency_.broadcast(parameters_.get_chemical_potential());
		concurrency_.broadcast(Sigma);
		}
		#endif

		// Strong assumption here that this only gets called for HDF5 input.
		template <class Parameters, DistType DT>
		void DcaData<Parameters, DT>::initializeSigma(const std::string& filename) {
		if (concurrency_.id() == concurrency_.first()) {
		std::cout << "reading Sigma File\n";
		io::IOType sigma_file_io = io::extensionToIOType(filename);
		io::Reader reader(concurrency_, sigma_file_io);
		int hdf5_last_iteration = -1;
		reader.open_file(filename);
		std::size_t step_count = reader.getStepCount();
		// Work around odd way hdf5 steps get written
		int completed_iteration = 0;
		find_step:
		for (std::size_t i = 0; i < step_count; ++i) {
		reader.begin_step();
		std::cerr << "current step " << i << '\n';
		bool has_iteration =
		reader.execute("DCA-loop-functions/completed-iteration", completed_iteration);
		std::cerr << "completed_iteration " << completed_iteration << '\n';
		if (has_iteration && (i >= completed_iteration)) {
		std::cerr << "past complete iterations " << completed_iteration << "at step " << i << '\n';
		hdf5_last_iteration = completed_iteration;
		reader.close_file();
		reader.open_file(filename);
		step_count = hdf5_last_iteration;
		goto find_step;
		}
		reader.end_step();
		}
		reader.begin_step();
		readSigmaFile(reader);
		reader.close_file();
		}
		concurrency_.broadcast(parameters_.get_chemical_potential());
		concurrency_.broadcast(Sigma);
		@@ -648,7 +668,8 @@ void DcaData<Parameters, DT>::readSigmaFile(io::Reader<Concurrency>& reader) {
		bool has_iteration = reader.execute("completed-iteration", completed_iteration);

		if (chemical_potential_present && has_iteration) {
		std::cout << "chemical-potential from Sigma file: " << chemical_potentials[completed_iteration] << '\n';
		std::cout << "chemical-potential from Sigma file: " << chemical_potentials[completed_iteration]
		<< '\n';
		parameters_.get_chemical_potential() = chemical_potentials[completed_iteration];
		}
		else {