Update genesis for faster thread pool

lczech · Jul 16, 2024 · 5bc391e · 5bc391e
1 parent de372c0
commit 5bc391e
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Showing 6 changed files with 8 additions and 7 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -168,7 +168,7 @@ include( "${CMAKE_CURRENT_LIST_DIR}/tools/cmake/DownloadDependency.cmake" )
 # These are replaced by tools/cmake/update_dependencies.sh to the hashes that are currently checked out.
 # Thus, do not replace the hashes manually!
 SET( CLI11_COMMIT_HASH "5cb3efabce007c3a0230e4cc2e27da491c646b6c" ) #CLI11_COMMIT_HASH#
-SET( genesis_COMMIT_HASH "76b24dde721eacea3ec8186dd7a9a79915011dd6" ) #genesis_COMMIT_HASH#
+SET( genesis_COMMIT_HASH "ca0afb161a540ce2eebda24e3f511cde86dbeaf0" ) #genesis_COMMIT_HASH#
 
 # Call the github download function, which takes four arguments:
 #  - LIBPATH    : Path to the libracy dir where dependencies are stored.

diff --git a/libs/genesis b/libs/genesis
diff --git a/src/commands/analyze/fst_cathedral.cpp b/src/commands/analyze/fst_cathedral.cpp
@@ -43,8 +43,8 @@
 #include "genesis/utils/core/fs.hpp"
 #include "genesis/utils/core/logging.hpp"
 #include "genesis/utils/core/std.hpp"
-#include "genesis/utils/core/thread_functions.hpp"
-#include "genesis/utils/core/thread_pool.hpp"
+#include "genesis/utils/threading/thread_functions.hpp"
+#include "genesis/utils/threading/thread_pool.hpp"
 #include "genesis/utils/formats/json/document.hpp"
 #include "genesis/utils/text/convert.hpp"
 #include "genesis/utils/text/string.hpp"

diff --git a/src/commands/tools/version.cpp b/src/commands/tools/version.cpp
@@ -78,7 +78,8 @@ void run_version( VersionOptions const& options )
     LOG_BOLD;
     LOG_BOLD << "grenedalf version: " << grenedalf_version();
     LOG_BOLD;
-    LOG_BOLD << genesis::utils::Options::get().info_compile_time();
+    LOG_BOLD << genesis::utils::info_print_compiler();
+    LOG_BOLD << genesis::utils::info_print_hardware();
     LOG_BOLD;
     LOG_BOLD << "For citation information, call  `grenedalf tools citation`";
     LOG_BOLD << "For license information, call  `grenedalf tools license`";

diff --git a/src/options/global.hpp b/src/options/global.hpp
@@ -31,7 +31,7 @@
 
 #include "genesis/utils/core/logging.hpp"
 #include "genesis/utils/core/options.hpp"
-#include "genesis/utils/core/thread_pool.hpp"
+#include "genesis/utils/threading/thread_pool.hpp"
 
 #include <string>
 #include <vector>

diff --git a/src/options/variant_input.cpp b/src/options/variant_input.cpp
@@ -321,7 +321,7 @@ void VariantInputOptions::prepare_stream_() const
 
     // Get and check the number of input files provided.
     size_t const file_count = get_input_file_count();
-    size_t const max_file_count = genesis::utils::info_max_file_count();
+    size_t const max_file_count = genesis::utils::info_process_max_file_count();
     size_t const file_count_margin = 10;
     if( max_file_count > 0 && file_count > max_file_count - file_count_margin ) {
         LOG_WARN << "In total, " <<  file_count << " input files are provided. However, the system "
+349 −116		.github/workflows/ci.yaml
+82 −0		doc/manual/supplement/acknowledgements.md
+81 −0		doc/manual/supplement/acknowledgements/c_07_concurrent_queue.inc
+2 −2		lib/genesis/population/function/diversity_pool_processor.hpp
+2 −2		lib/genesis/population/function/fst_pool_processor.hpp
+1 −0		lib/genesis/sequence.hpp
+119 −70		lib/genesis/sequence/formats/fastq_writer.cpp
+22 −19		lib/genesis/sequence/formats/fastq_writer.hpp
+4 −1		lib/genesis/sequence/formats/fastx_input_stream.hpp
+537 −0		lib/genesis/sequence/formats/fastx_input_view_stream.hpp
+32 −3		lib/genesis/sequence/formats/fastx_output_stream.hpp
+152 −36		lib/genesis/tree/drawing/functions.cpp
+74 −5		lib/genesis/tree/drawing/functions.hpp
+3 −3		lib/genesis/tree/drawing/layout_base.hpp
+4 −38		lib/genesis/tree/function/operators.cpp
+4 −9		lib/genesis/tree/function/operators.hpp
+8 −4		lib/genesis/utils.hpp
+4 −4		lib/genesis/utils/color/map.hpp
+4 −4		lib/genesis/utils/containers/generic_input_stream.hpp
+1,788 −258		lib/genesis/utils/core/info.cpp
+315 −90		lib/genesis/utils/core/info.hpp
+0 −175		lib/genesis/utils/core/options.cpp
+130 −107		lib/genesis/utils/core/options.hpp
+0 −587		lib/genesis/utils/core/thread_pool.hpp
+5 −3		lib/genesis/utils/formats/bmp/writer.cpp
+7 −7		lib/genesis/utils/formats/svg/color_bar.cpp
+2 −1		lib/genesis/utils/formats/svg/color_bar.hpp
+7 −2		lib/genesis/utils/formats/svg/document.cpp
+28 −4		lib/genesis/utils/io/base_input_source.hpp
+13 −5		lib/genesis/utils/io/file_output_target.hpp
+5 −2		lib/genesis/utils/io/gzip_block_ostream.cpp
+1 −1		lib/genesis/utils/io/gzip_block_ostream.hpp
+15 −1		lib/genesis/utils/io/gzip_input_source.hpp
+1 −3		lib/genesis/utils/io/input_buffer.hpp
+79 −33		lib/genesis/utils/io/input_reader.hpp
+10 −6		lib/genesis/utils/io/input_stream.cpp
+637 −0		lib/genesis/utils/threading/blocking_concurrent_queue.hpp
+3,946 −0		lib/genesis/utils/threading/concurrent_queue.hpp
+475 −0		lib/genesis/utils/threading/lightweight_semaphore.hpp
+3 −3		lib/genesis/utils/threading/multi_future.hpp
+435 −0		lib/genesis/utils/threading/sequential_output_buffer.hpp
+5 −5		lib/genesis/utils/threading/thread_functions.hpp
+776 −0		lib/genesis/utils/threading/thread_pool.hpp
+5 −5		lib/genesis/utils/threading/threadsafe_queue.hpp
+20 −0		test/data/sequence/dna_10_single.fasta
+24 −0		test/src/sequence/fasta.cpp
+33 −1		test/src/sequence/fastq.cpp
+2 −2		test/src/utils/containers/iterators.cpp
+1 −1		test/src/utils/containers/mru_cache.cpp
+97 −11		test/src/utils/core/info.cpp
+8 −1		test/src/utils/math/regression.cpp
+192 −0		test/src/utils/threading/sequential_output_buffer.cpp
+5 −5		test/src/utils/threading/thread_pool.cpp
+1 −1		test/src/utils/threading/threadsafe_queue.cpp
+2 −2		tools/cmake/GTestDownload.cmake
+1 −1		tools/cmake/IncludeHtslib.cmake