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Removing OpenMP from amrfinder #265

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Merged
andrewdavidsmith merged 4 commits into from
Jun 11, 2025
Merged

Removing OpenMP from amrfinder #265

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b0babd3
src/amrfinder/amrfinder.cpp: converted omp parallel for loops into lo…
andrewdavidsmith Jun 11, 2025
5131b32
src/abismal: updated submodule
andrewdavidsmith Jun 11, 2025
8331273
m4/ads_openmp.m4: removing
andrewdavidsmith Jun 11, 2025
a856e9f
Removing all things OpenMP
andrewdavidsmith Jun 11, 2025
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3 changes: 1 addition & 2 deletions Makefile.am
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,7 @@ SUBDIRS := src/smithlab_cpp src/abismal
install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx

AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
AM_CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
CXXFLAGS += -O3 -DNDEBUG # default has optimization on

EXTRA_DIST = \
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10 changes: 0 additions & 10 deletions configure.ac
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Expand Up @@ -26,16 +26,6 @@ AC_PROG_CXX
AX_CXX_COMPILE_STDCXX_17([noext], [mandatory])
AC_PROG_RANLIB

dnl OpenMP happens here
AC_OPENMP([C++])
AS_VAR_IF(OPENMP_CXXFLAGS, [], [
dnl check for the OpenMP library; can't be later
AC_SEARCH_LIBS([omp_get_num_threads], [gomp omp], [],
[AC_MSG_FAILURE([OpenMP library not found])])
dnl now we get setup for the right OpenMP flags
ADS_OPENMP([], [AC_MSG_FAILURE([OpenMP must be installed to build dnmtools])])
])dnl end of OpenMP stuff

dnl recursively configure abismal and smithlab_cpp
AC_CONFIG_SUBDIRS([src/abismal])
AC_CONFIG_SUBDIRS([src/smithlab_cpp])
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2 changes: 1 addition & 1 deletion docs/content/abismal.md
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Expand Up @@ -195,7 +195,7 @@ even longer. It usually take quite a long time to map reads from a
single large file with tens of millions of reads. If you have access
to a cluster, one strategy is to launch multiple jobs, each working on
a subset of reads simultaneously, and finally combine their output.
`abismal` takes advantage of OpenMP to parallelize the process of
`abismal` uses standard c++ threads to parallelize the process of
mapping reads using the shared index.

If each node can only access its local storage, dividing the set of
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159 changes: 0 additions & 159 deletions m4/ads_openmp.m4
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This file was deleted.

2 changes: 1 addition & 1 deletion src/abismal
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Submodule abismal updated 22 files
+34 −0 .clang-format
+32 −13 .gitignore
+1 −2 Makefile.am
+4 −7 README.md
+0 −12 configure.ac
+0 −159 m4/ads_openmp.m4
+0 −123 m4/ax_openmp.m4
+42 −34 src/AbismalAlign.hpp
+728 −593 src/AbismalIndex.cpp
+131 −92 src/AbismalIndex.hpp
+709 −596 src/abismal.cpp
+6 −4 src/abismal_cigar_utils.hpp
+19 −1 src/abismal_main.cpp
+35 −60 src/abismalidx.cpp
+24 −4 src/abismalidx.hpp
+19 −1 src/abismalidx_main.cpp
+1 −1 src/bamxx
+9 −5 src/dna_four_bit_bisulfite.hpp
+37 −18 src/simreads.cpp
+24 −4 src/simreads.hpp
+19 −1 src/simreads_main.cpp
+1 −1 src/smithlab_cpp
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