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Fix lack of optimisation for SHAPEIT4 v4.1.3 #12206

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9 changes: 5 additions & 4 deletions easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.1.3-foss-2019b.eb
Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,15 @@ SHAPEIT4 is a fast and accurate method for estimation of haplotypes
"""

toolchain = {'name': 'foss', 'version': '2019b'}
toolchainopts = {'opt': True, 'cstd': 'std=c++11'}
toolchainopts = {'opt': True, 'cstd': 'c++11'}

github_account = 'odelaneau'
source_urls = [GITHUB_SOURCE]
sources = ['v%(version)s.tar.gz']
patches = ['SHAPEIT4_use_EB_settings.patch']
patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch']
checksums = [
'd209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8', # v4.1.3.tar.gz
'a10cd98b61eae90228ab2e7a9b6071803037f7e7dcdc7ad47b91bf1a1a102743', # SHAPEIT4_use_EB_settings.patch
'4e021d9cd685462b691a2e42f4d61470cf8c9c9b74d636712fe77ec9bc800291', # SHAPEIT4_4.1.3_use_EB_settings.patch
]

dependencies = [
Expand All @@ -30,7 +30,8 @@ dependencies = [
]

buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts '
buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options'
buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options '
buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS"'

files_to_copy = [(['bin/shapeit4'], 'bin'), 'maps']

Expand Down
Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
Disable hard-coded library and flag settings

Adam Huffman

--- shapeit4-4.1.3/makefile 2020-02-26 15:58:58.000000000 +0000
+++ shapeit4-4.1.3.new/makefile 2021-02-19 17:35:46.902449694 +0000
@@ -1,14 +1,14 @@
#COMPILER MODE C++11
-CXX=g++ -std=c++11
+#CXX=g++ -std=c++11

#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
-HTSLIB_INC=$(HOME)/Tools/htslib-1.9
-HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a
+#HTSLIB_INC=$(HOME)/Tools/htslib-1.9
+#HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a

#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
-BOOST_INC=/usr/include
-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+#BOOST_INC=/usr/include
+#BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+#BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a

#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
#HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include
@@ -23,10 +23,10 @@
#Best performance is achieved with this. Use it if running on the same plateform you're compiling, it's definitely worth it!
#CXXFLAG=-O3 -march=native
#Good performance and portable on most intel CPUs
-CXXFLAG=-O3 -mavx2 -mfma
+#CXXFLAG=-O3 -mavx2 -mfma
#Portable version without avx2 (much slower)
#CXXFLAG=-O3
-LDFLAG=-O3
+#LDFLAG=-O3

#DYNAMIC LIBRARIES
DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma