New upstream version 1.6.11+dfsg (93437d2c) · Commits · Debian Med / iqtree

CMakeLists.txt

+12 −10

Original line number	Diff line number	Diff line
		@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE)
		# The version number.
		set (iqtree_VERSION_MAJOR 1)
		set (iqtree_VERSION_MINOR 6)
		set (iqtree_VERSION_PATCH "9")
		set (iqtree_VERSION_PATCH "11")

		set(BUILD_SHARED_LIBS OFF)

		@@ -277,9 +277,14 @@ if (NOT IQTREE_FLAGS MATCHES "single")
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
		elseif (CLANG)
		if (APPLE)
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xpreprocessor -fopenmp -pthread")
		set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Xpreprocessor -fopenmp -lomp")
		else()
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp=libomp -pthread")
		set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fopenmp=libomp")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
		endif()
		endif()
		else()
		message("OpenMP : NONE")
		@@ -509,12 +514,10 @@ add_library(kernelfma tree/phylokernelfma.cpp)
		endif()
		endif()

		if (IQTREE_FLAGS MATCHES "mpi")
		add_library(mympi utils/TreeCollection.cpp utils/ObjectStream.cpp)
		endif()

		if (NOT IQTREE_FLAGS MATCHES "single")
		if (BINARY32)
		if (APPLE)
		link_directories(${PROJECT_SOURCE_DIR}/libmac)
		elseif (BINARY32)
		link_directories(${PROJECT_SOURCE_DIR}/lib32)
		else()
		link_directories(${PROJECT_SOURCE_DIR}/lib)
		@@ -602,7 +605,6 @@ endif()

		# MPI libraries
		if (IQTREE_FLAGS MATCHES "mpi")
		target_link_libraries(iqtree mympi)
		if (NOT CMAKE_CXX_COMPILER MATCHES "mpi")
		target_link_libraries(iqtree ${MPI_CXX_LIBRARIES})
		endif()

alignment/alignment.cpp

+17 −5

Original line number	Diff line number	Diff line
		@@ -2943,14 +2943,23 @@ void convert_range(const char *str, int &lower, int &upper, int &step_size, char
		if (*endptr != '-') return;

		// parse the upper bound of the range
		str = endptr+1;
		endptr++;
		// skip blank chars
		for (; *endptr == ' '; endptr++) {}
		str = endptr;
		d = strtol(str, &endptr, 10);
		if ((d == 0 && endptr == str) \|\| abs(d) == HUGE_VALL) {
		if (str[0] == '.') {
		// 2019-06-03: special character '.' for whatever ending position
		d = lower-1;
		endptr++;
		} else {
		string err = "Expecting integer, but found \"";
		err += str;
		err += "\" instead";
		throw err;
		}
		}

		//lower = d_save;
		upper = d;
		@@ -2982,6 +2991,9 @@ void extractSiteID(Alignment aln, const char spec, IntVector &site_id) {
		for (; *str != 0; ) {
		int lower, upper, step;
		convert_range(str, lower, upper, step, str);
		// 2019-06-03: special '.' character
		if (upper == lower-1)
		upper = aln->getNSite();
		lower--;
		upper--;
		nchars += (upper-lower+1)/step;

alignment/superalignment.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -935,6 +935,7 @@ void SuperAlignment::createBootstrapAlignment(Alignment aln, IntVector pattern
		auto site_pattern = boot_aln->site_pattern;
		for (int j = 1; j < gene_freq[i]; j++)
		boot_aln->site_pattern.insert(boot_aln->site_pattern.end(), site_pattern.begin(), site_pattern.end());
		boot_aln->countConstSite();
		}
		partitions.push_back(boot_aln);
		}

main/main.cpp

+28 −49

Original line number	Diff line number	Diff line
		@@ -68,9 +68,6 @@
		#include "vectorclass/instrset.h"

		#include "utils/MPIHelper.h"
		#ifdef _IQTREE_MPI
		#include <mpi.h>
		#endif

		#ifdef _OPENMP
		#include <omp.h>
		@@ -1721,6 +1718,7 @@ void processNCBITree(Params &params) {
		class outstreambuf : public streambuf {
		public:
		outstreambuf* open( const char* name, ios::openmode mode = ios::out);
		bool is_open();
		outstreambuf* close();
		~outstreambuf() { close(); }
		streambuf *get_fout_buf() {
		@@ -1753,6 +1751,10 @@ outstreambuf* outstreambuf::open( const char* name, ios::openmode mode) {
		return this;
		}

		bool outstreambuf::is_open() {
		return fout.is_open();
		}

		outstreambuf* outstreambuf::close() {
		cout.rdbuf(cout_buf);
		if ( fout.is_open()) {
		@@ -1850,8 +1852,8 @@ extern "C" void startLogFile(bool append_log) {
		}

		extern "C" void endLogFile() {
		if (_out_buf.is_open())
		_out_buf.close();

		}

		void funcExit(void) {
		@@ -1862,6 +1864,7 @@ void funcExit(void) {
		}

		endLogFile();
		MPIHelper::getInstance().finalize();
		}

		extern "C" void funcAbort(int signal_number)
		@@ -2218,20 +2221,9 @@ int main(int argc, char *argv[]) {
		*/
		int instruction_set;

		#ifdef _IQTREE_MPI
		double time_initial, time_current;
		int n_tasks, task_id;
		if (MPI_Init(&argc, &argv) != MPI_SUCCESS) {
		outError("MPI initialization failed!");
		}
		MPI_Comm_size(MPI_COMM_WORLD, &n_tasks);
		MPI_Comm_rank(MPI_COMM_WORLD, &task_id);
		MPIHelper::getInstance().setNumProcesses(n_tasks);
		MPIHelper::getInstance().setProcessID(task_id);
		MPIHelper::getInstance().setNumTreeReceived(0);
		MPIHelper::getInstance().setNumTreeSent(0);
		MPIHelper::getInstance().setNumNNISearch(0);
		#endif
		MPIHelper::getInstance().init(argc, argv);

		atexit(funcExit);

		/*************************/
		{ /* local scope */
		@@ -2289,17 +2281,22 @@ int main(int argc, char *argv[]) {
		if (checkpoint->hasKey("finished")) {
		if (checkpoint->getBool("finished")) {
		if (Params::getInstance().force_unfinished) {
		if (MPIHelper::getInstance().isMaster())
		cout << "NOTE: Continue analysis although a previous run already finished" << endl;
		} else {
		delete checkpoint;
		if (MPIHelper::getInstance().isMaster())
		outError("Checkpoint (" + filename + ") indicates that a previous run successfully finished\n" +
		"Use `-redo` option if you really want to redo the analysis and overwrite all output files.");
		delete checkpoint;
		return EXIT_FAILURE;
		else
		exit(EXIT_SUCCESS);
		exit(EXIT_FAILURE);
		}
		} else {
		append_log = true;
		}
		} else {
		if (MPIHelper::getInstance().isMaster())
		outWarning("Ignore invalid checkpoint file " + filename);
		checkpoint->clear();
		}
		@@ -2318,25 +2315,9 @@ int main(int argc, char *argv[]) {
		cout << endl << "******************************************************"
		<< endl << "CHECKPOINT: Resuming analysis from " << filename << endl << endl;
		}
		#ifdef _IQTREE_MPI
		cout << "************************************************" << endl;
		cout << "* START TREE SEARCH USING MPI WITH " << MPIHelper::getInstance().getNumProcesses() << " PROCESSES *" << endl;
		cout << "************************************************" << endl;
		unsigned int rndSeed;
		if (MPIHelper::getInstance().isMaster()) {
		rndSeed = Params::getInstance().ran_seed;
		cout << "Random seed of master = " << rndSeed << endl;
		}
		// Broadcast random seed
		MPI_Bcast(&rndSeed, 1, MPI_INT, PROC_MASTER, MPI_COMM_WORLD);
		if (MPIHelper::getInstance().isWorker()) {
		// Params::getInstance().ran_seed = rndSeed + task_id * 100000;
		Params::getInstance().ran_seed = rndSeed;
		// printf("Process %d: random_seed = %d\n", task_id, Params::getInstance().ran_seed);
		}
		#endif

		atexit(funcExit);
		MPIHelper::getInstance().syncRandomSeed();

		signal(SIGABRT, &funcAbort);
		signal(SIGFPE, &funcAbort);
		signal(SIGILL, &funcAbort);
		@@ -2469,8 +2450,10 @@ int main(int argc, char *argv[]) {
		}
		#endif

		#ifdef _IQTREE_MPI
		cout << endl << "MPI: " << MPIHelper::getInstance().getNumProcesses() << " processes";
		#endif

		#ifndef _IQTREE_MPI
		int num_procs = countPhysicalCPUCores();
		#ifdef _OPENMP
		if (num_procs > 1 && Params::getInstance().num_threads == 1) {
		@@ -2480,7 +2463,6 @@ int main(int argc, char *argv[]) {
		#else
		if (num_procs > 1)
		cout << endl << endl << "NOTE: Consider using the multicore version because your CPU has " << num_procs << " cores!";
		#endif
		#endif

		//cout << "sizeof(int)=" << sizeof(int) << endl;
		@@ -2638,8 +2620,5 @@ int main(int argc, char *argv[]) {

		finish_random();

		#ifdef _IQTREE_MPI
		MPI_Finalize();
		#endif
		return EXIT_SUCCESS;
		}

model/modeldna.cpp

+8 −2

Original line number	Diff line number	Diff line
		@@ -377,8 +377,14 @@ bool ModelDNA::setRateType(string rate_str) {
		cout << rates[i] << " ";
		cout << endl;
		}
		if (param_fixed.size() == num_params + 1) {
		num_params = 0;
		for (auto p : param_fixed)
		if (!p) num_params++;
		} else {
		param_fixed.resize(num_params+1, false);
		param_fixed[0] = true; // fix the last entry
		}
		delete [] num_rates;
		delete [] avg_rates;
		return true;