Fixes #6, where the temporary results file was not written at all when the... (2d2dfc7e) · Commits · STRL / STEMsalabim

src/classes/IO.cpp

+20 −6

Original line number	Diff line number	Diff line
		@@ -929,6 +929,24 @@ string getTempFileName() {
		return output::fmt("%s/%s_%d.bin", p.tmpDir(), p.uuid(), mpi_rank);
		}

		void IO::generateTemporaryResultFile() {
		auto &mpi_env = mpi::Environment::getInstance();
		int mpi_rank = mpi_env.rank();
		auto tmpfile = std::ofstream(getTempFileName(), std::ios::binary \| std::ios::app);

		if(tmpfile.fail()) {
		output::error("Couldn't open temporary binary %s file for writing.\n", getTempFileName());
		}

		tmpfile.write(reinterpret_cast<const char *>(&mpi_rank), sizeof(mpi_rank));

		tmpfile.close();
		}

		void IO::removeTemporaryResultFile() {
		remove(getTempFileName().c_str());
		}

		void IO::writeTemporaryResult(unsigned int idefocus, unsigned int iconf, ScanPoint &point,
		shared_ptr<memory::buffer::number_buffer<float>> &ibuf,
		shared_ptr<memory::buffer::number_buffer<float>> &cbuf) {
		@@ -938,7 +956,7 @@ void IO::writeTemporaryResult(unsigned int idefocus, unsigned int iconf, ScanPoi
		auto tmpfile = std::ofstream(getTempFileName(), std::ios::binary \| std::ios::app);

		// the format is as follows:
		// int rank
		// int rank ( written in generateTemporaryResultFile)
		// for each pixel:
		// unsigned int idefocus
		// unsigned int iconf
		@@ -951,8 +969,7 @@ void IO::writeTemporaryResult(unsigned int idefocus, unsigned int iconf, ScanPoi
		}

		if(tmpfile.tellp() == 0) {
		// empty file, write rank
		tmpfile.write(reinterpret_cast<const char *>(&mpi_rank), sizeof(mpi_rank));
		output::error("File %s shouldn't be empty! Has writeTemporaryResult() been called?\n", getTempFileName());
		}

		tmpfile.write(reinterpret_cast<const char *>(&idefocus), sizeof(idefocus));
		@@ -1044,9 +1061,6 @@ void IO::copyFromTemporaryFile(const shared_ptr<GridManager> &gridman,

		nc_close(f_id);

		// remove the file, as all the data is now transferred.
		remove(getTempFileName().c_str());

		}

src/classes/IO.hpp

+10 −0

Original line number	Diff line number	Diff line
		@@ -114,6 +114,16 @@ namespace stemsalabim {
		const std::shared_ptr<GridManager> &gridman, const ScanPoint &point,
		std::shared_ptr<memory::buffer::number_buffer<float>> &cbuf, int g_id, int v_id);

		/*!
		* Generates the temporary result file and writes the header.
		*/
		static void generateTemporaryResultFile();

		/*!
		* Removes the temporary result file.
		*/
		static void removeTemporaryResultFile();

		/*!
		* Write temporary results to a binary file (custom format). This is done in MPI mode.
		* @param idefocus current defocus index

src/classes/Simulation.cpp

+3 −1

Original line number	Diff line number	Diff line
		@@ -277,6 +277,8 @@ void Simulation::run() {
		output::fmt("Finished calculation of transmission functions in %s.\n",
		output::humantime(algorithms::getTimeSince(t1))));

		_io->generateTemporaryResultFile();

		if(mpi_env.isMaster()) {
		multisliceMaster(st);
		} else {
		@@ -294,7 +296,7 @@ void Simulation::run() {
		if(rank == mpi_env.rank()) {
		auto start = high_resolution_clock::now();
		_io->copyFromTemporaryFile(_gridman, _adf_intensity_buffer, _cbed_intensity_buffer);

		_io->removeTemporaryResultFile();
		printLine(st,
		output::fmt("Finished copying pixels for %s.\n",
		output::humantime(algorithms::getTimeSince(start))));