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author | t-karatsu <49965247+t-karatsu@users.noreply.github.com> | 2019-09-29 03:44:02 +0900 |
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committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-09-28 13:44:02 -0500 |
commit | c065c25a4ccb2e29f56d7b5c534e615cec531135 (patch) | |
tree | 1030d38340bf560027fa04676b1f57304f06547a /var | |
parent | 4cebc68f064838393efe9928d867a0e3d1547542 (diff) | |
download | spack-c065c25a4ccb2e29f56d7b5c534e615cec531135.tar.gz spack-c065c25a4ccb2e29f56d7b5c534e615cec531135.tar.bz2 spack-c065c25a4ccb2e29f56d7b5c534e615cec531135.tar.xz spack-c065c25a4ccb2e29f56d7b5c534e615cec531135.zip |
bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953)
Diffstat (limited to 'var')
3 files changed, 86 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch new file mode 100644 index 0000000000..ca4895dff0 --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie/fix_narrowing_err.patch @@ -0,0 +1,11 @@ +--- bowtie-1.2.3.org/alphabet.cpp 2019-09-26 12:14:35.508558749 +0900 ++++ bowtie-1.2.3/alphabet.cpp 2019-09-26 14:15:56.960009461 +0900 +@@ -274,7 +274,7 @@ + const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn"; + + char mask2iupac[16] = { +- -1, ++ static_cast<char>(-1), + 'A', // 0001 + 'C', // 0010 + 'M', // 0011 diff --git a/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch b/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch new file mode 100644 index 0000000000..4dafbaaf20 --- /dev/null +++ b/var/spack/repos/builtin/packages/bowtie/for_aarch64.patch @@ -0,0 +1,68 @@ +diff -ur bowtie-1.2.3.org/Makefile bowtie-1.2.3/Makefile +--- bowtie-1.2.3.org/Makefile 2019-09-26 12:14:35.498557693 +0900 ++++ bowtie-1.2.3/Makefile 2019-09-26 12:15:17.262960932 +0900 +@@ -174,14 +174,22 @@ + ifeq (x86_64, $(shell uname -p)) + BITS=64 + endif ++ ifeq (aarch64, $(shell uname -p)) ++ BITS=64 ++ endif + endif + + ifeq (32,$(BITS)) + $(error bowtie2 compilation requires a 64-bit platform ) + endif + +-DEBUG_FLAGS = -O0 -g3 -m64 +-RELEASE_FLAGS = -O3 -m64 ++ifeq (aarch64, $(shell uname -p)) ++ DEBUG_FLAGS = -O0 -g3 ++ RELEASE_FLAGS = -O3 ++else ++ DEBUG_FLAGS = -O0 -g3 -m64 ++ RELEASE_FLAGS = -O3 -m64 ++endif + NOASSERT_FLAGS = -DNDEBUG + FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE + +diff -ur bowtie-1.2.3.org/ebwt.h bowtie-1.2.3/ebwt.h +--- bowtie-1.2.3.org/ebwt.h 2019-09-26 12:14:35.518559804 +0900 ++++ bowtie-1.2.3/ebwt.h 2019-09-26 14:13:12.142637470 +0900 +@@ -1957,7 +1957,11 @@ + struct USE_POPCNT_INSTRUCTION { + inline static int pop64(uint64_t x) { + int64_t count; ++#ifdef __aarch64__ ++ count = __builtin_popcount(x); ++#else + asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x)); ++#endif + return count; + } + }; +diff -ur bowtie-1.2.3.org/third_party/cpuid.h bowtie-1.2.3/third_party/cpuid.h +--- bowtie-1.2.3.org/third_party/cpuid.h 2019-09-26 12:14:35.548562971 +0900 ++++ bowtie-1.2.3/third_party/cpuid.h 2019-09-26 12:17:41.677842567 +0900 +@@ -65,6 +65,7 @@ + #define bit_FSGSBASE (1 << 0) + #define bit_BMI (1 << 3) + ++#ifndef __aarch64__ + #if defined(__i386__) && defined(__PIC__) + /* %ebx may be the PIC register. */ + #if __GNUC__ >= 3 +@@ -185,3 +186,13 @@ + __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); + return 1; + } ++#endif ++#ifdef __aarch64__ ++static __inline int ++__get_cpuid (unsigned int __level, ++ unsigned int *__eax, unsigned int *__ebx, ++ unsigned int *__ecx, unsigned int *__edx) ++{ ++ return 1; ++} ++#endif diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py index 50c02c9825..c89f8f4081 100644 --- a/var/spack/repos/builtin/packages/bowtie/package.py +++ b/var/spack/repos/builtin/packages/bowtie/package.py @@ -45,6 +45,13 @@ class Bowtie(MakefilePackage): # https://svnweb.freebsd.org/ports?view=revision&revision=483954 patch('issue-87.patch', when='@:1.2.2 %gcc@8.0.0:') + # correspond to 'aarch64' architecture + # reference: https://github.com/BenLangmead/bowtie/pull/13 + patch('for_aarch64.patch', when='target=aarch64:') + + # measures for narrowing error + patch('fix_narrowing_err.patch') + def edit(self, spec, prefix): makefile = FileFilter('Makefile') makefile.filter('CC = .*', 'CC = ' + env['CC']) |