From 6424f1dae0e71c9a292638cc739c82b3dc9cf79e Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Mon, 7 Nov 2022 21:01:55 -0500 Subject: [PATCH 1/4] re-hack release build --- build-tools/CMakeLists.txt | 52 +++++++++++++++++++++++++++++++++++++- build-tools/makeBinRelease | 7 ++++- 2 files changed, 57 insertions(+), 2 deletions(-) diff --git a/build-tools/CMakeLists.txt b/build-tools/CMakeLists.txt index 87ee3d2..39d818a 100644 --- a/build-tools/CMakeLists.txt +++ b/build-tools/CMakeLists.txt @@ -35,7 +35,38 @@ endif() set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") add_library(handlegraph_objs OBJECT - src/handle.cpp + src/deletable_handle_graph.cpp + src/handle_graph.cpp + src/mutable_handle_graph.cpp + src/path_metadata.cpp + src/mutable_path_metadata.cpp + src/path_handle_graph.cpp + src/path_position_handle_graph.cpp + src/mutable_path_handle_graph.cpp + src/ranked_handle_graph.cpp + src/serializable.cpp + src/snarl_decomposition.cpp + src/trivially_serializable.cpp + src/types.cpp + src/copy_graph.cpp + src/append_graph.cpp + src/are_equivalent.cpp + src/find_tips.cpp + src/topological_sort.cpp + src/apply_orientations.cpp + src/is_single_stranded.cpp + src/count_walks.cpp + src/eades_algorithm.cpp + src/dagify.cpp + src/strongly_connected_components.cpp + src/find_shortest_paths.cpp + src/dijkstra.cpp + src/is_acyclic.cpp + src/reverse_complement.cpp + src/split_strands.cpp + src/chop.cpp + src/weakly_connected_components.cpp + src/extend.cpp src/include/handlegraph/handle_graph.hpp src/include/handlegraph/mutable_handle_graph.hpp src/include/handlegraph/deletable_handle_graph.hpp @@ -48,6 +79,25 @@ add_library(handlegraph_objs OBJECT src/include/handlegraph/util.hpp src/include/handlegraph/types.hpp src/include/handlegraph/iteratee.hpp + src/include/handlegraph/algorithms/copy_graph.hpp + src/include/handlegraph/algorithms/append_graph.hpp + src/include/handlegraph/algorithms/are_equivalent.hpp + src/include/handlegraph/algorithms/find_tips.hpp + src/include/handlegraph/algorithms/topological_sort.hpp + src/include/handlegraph/algorithms/apply_orientations.hpp + src/include/handlegraph/algorithms/is_single_stranded.hpp + src/include/handlegraph/algorithms/count_walks.hpp + src/include/handlegraph/algorithms/eades_algorithm.hpp + src/include/handlegraph/algorithms/dagify.hpp + src/include/handlegraph/algorithms/strongly_connected_components.hpp + src/include/handlegraph/algorithms/find_shortest_paths.hpp + src/include/handlegraph/algorithms/dijkstra.hpp + src/include/handlegraph/algorithms/reverse_complement.hpp + src/include/handlegraph/algorithms/is_acyclic.hpp + src/include/handlegraph/algorithms/split_strands.hpp + src/include/handlegraph/algorithms/chop.hpp + src/include/handlegraph/algorithms/weakly_connected_components.hpp + src/include/handlegraph/algorithms/extend.hpp ) # Use the include directory when building the objects. diff --git a/build-tools/makeBinRelease b/build-tools/makeBinRelease index d5b71e3..7405a34 100755 --- a/build-tools/makeBinRelease +++ b/build-tools/makeBinRelease @@ -20,7 +20,7 @@ set -x rm -rf ${binBuildDir} mkdir -p ${binBuildDir} cd ${binBuildDir} -git clone --recursive https://github.com/ComparativeGenomicsToolkit/hal2vg.git +git clone https://github.com/ComparativeGenomicsToolkit/hal2vg.git cd hal2vg git fetch --tags origin @@ -34,8 +34,13 @@ cp ./build-tools/CMakeLists.txt ./deps/libbdsg-easy/deps/libhandlegraph/CMakeLis if [ $(man gcc | grep nehalem | wc -l) -ge 1 ] then # attempt to increase portability by using older architecture + # this make/sed/make thing is a hack to get around a linking error that just cropped up + CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static -j 8 || true + sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g" CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make check-static else + make static || true + sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g" make check-static fi From af885528e4c4d3af08b61e33a68928de0468b58a Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Mon, 7 Nov 2022 21:01:55 -0500 Subject: [PATCH 2/4] re-hack release build --- build-tools/CMakeLists.txt | 52 +++++++++++++++++++++++++++++++++++++- build-tools/makeBinRelease | 7 ++++- 2 files changed, 57 insertions(+), 2 deletions(-) diff --git a/build-tools/CMakeLists.txt b/build-tools/CMakeLists.txt index 87ee3d2..39d818a 100644 --- a/build-tools/CMakeLists.txt +++ b/build-tools/CMakeLists.txt @@ -35,7 +35,38 @@ endif() set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") add_library(handlegraph_objs OBJECT - src/handle.cpp + src/deletable_handle_graph.cpp + src/handle_graph.cpp + src/mutable_handle_graph.cpp + src/path_metadata.cpp + src/mutable_path_metadata.cpp + src/path_handle_graph.cpp + src/path_position_handle_graph.cpp + src/mutable_path_handle_graph.cpp + src/ranked_handle_graph.cpp + src/serializable.cpp + src/snarl_decomposition.cpp + src/trivially_serializable.cpp + src/types.cpp + src/copy_graph.cpp + src/append_graph.cpp + src/are_equivalent.cpp + src/find_tips.cpp + src/topological_sort.cpp + src/apply_orientations.cpp + src/is_single_stranded.cpp + src/count_walks.cpp + src/eades_algorithm.cpp + src/dagify.cpp + src/strongly_connected_components.cpp + src/find_shortest_paths.cpp + src/dijkstra.cpp + src/is_acyclic.cpp + src/reverse_complement.cpp + src/split_strands.cpp + src/chop.cpp + src/weakly_connected_components.cpp + src/extend.cpp src/include/handlegraph/handle_graph.hpp src/include/handlegraph/mutable_handle_graph.hpp src/include/handlegraph/deletable_handle_graph.hpp @@ -48,6 +79,25 @@ add_library(handlegraph_objs OBJECT src/include/handlegraph/util.hpp src/include/handlegraph/types.hpp src/include/handlegraph/iteratee.hpp + src/include/handlegraph/algorithms/copy_graph.hpp + src/include/handlegraph/algorithms/append_graph.hpp + src/include/handlegraph/algorithms/are_equivalent.hpp + src/include/handlegraph/algorithms/find_tips.hpp + src/include/handlegraph/algorithms/topological_sort.hpp + src/include/handlegraph/algorithms/apply_orientations.hpp + src/include/handlegraph/algorithms/is_single_stranded.hpp + src/include/handlegraph/algorithms/count_walks.hpp + src/include/handlegraph/algorithms/eades_algorithm.hpp + src/include/handlegraph/algorithms/dagify.hpp + src/include/handlegraph/algorithms/strongly_connected_components.hpp + src/include/handlegraph/algorithms/find_shortest_paths.hpp + src/include/handlegraph/algorithms/dijkstra.hpp + src/include/handlegraph/algorithms/reverse_complement.hpp + src/include/handlegraph/algorithms/is_acyclic.hpp + src/include/handlegraph/algorithms/split_strands.hpp + src/include/handlegraph/algorithms/chop.hpp + src/include/handlegraph/algorithms/weakly_connected_components.hpp + src/include/handlegraph/algorithms/extend.hpp ) # Use the include directory when building the objects. diff --git a/build-tools/makeBinRelease b/build-tools/makeBinRelease index d5b71e3..7405a34 100755 --- a/build-tools/makeBinRelease +++ b/build-tools/makeBinRelease @@ -20,7 +20,7 @@ set -x rm -rf ${binBuildDir} mkdir -p ${binBuildDir} cd ${binBuildDir} -git clone --recursive https://github.com/ComparativeGenomicsToolkit/hal2vg.git +git clone https://github.com/ComparativeGenomicsToolkit/hal2vg.git cd hal2vg git fetch --tags origin @@ -34,8 +34,13 @@ cp ./build-tools/CMakeLists.txt ./deps/libbdsg-easy/deps/libhandlegraph/CMakeLis if [ $(man gcc | grep nehalem | wc -l) -ge 1 ] then # attempt to increase portability by using older architecture + # this make/sed/make thing is a hack to get around a linking error that just cropped up + CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static -j 8 || true + sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g" CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make check-static else + make static || true + sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g" make check-static fi From 3ec151a4eaf2ee9c100132b66059ecd9cde2e9a3 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 9 Nov 2022 14:55:13 -0500 Subject: [PATCH 3/4] update libbdsg-easy --- deps/libbdsg-easy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/libbdsg-easy b/deps/libbdsg-easy index 2e5211b..629fc5a 160000 --- a/deps/libbdsg-easy +++ b/deps/libbdsg-easy @@ -1 +1 @@ -Subproject commit 2e5211bfa830399e011dddfaf5e827ddff5a4213 +Subproject commit 629fc5a664bd3fdcb9daadc19c093eb3999e432a From d826d83cd6945009e547a1334477e3a2835784cf Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Wed, 9 Nov 2022 14:57:26 -0500 Subject: [PATCH 4/4] take away -j --- build-tools/makeBinRelease | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build-tools/makeBinRelease b/build-tools/makeBinRelease index 7405a34..b37de1b 100755 --- a/build-tools/makeBinRelease +++ b/build-tools/makeBinRelease @@ -35,7 +35,7 @@ if [ $(man gcc | grep nehalem | wc -l) -ge 1 ] then # attempt to increase portability by using older architecture # this make/sed/make thing is a hack to get around a linking error that just cropped up - CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static -j 8 || true + CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static || true sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g" CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make check-static else