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Old 03-12-2016, 02:15 AM   #1
Luis
Junior Member
 
Location: Spain

Join Date: Oct 2015
Posts: 2
Default Bowtie2 and TBB compilation

Hi all,

Because Bowtie2 with "-p xx" option don't make multithreading, I tried to build from source with TBB (make WITH_TBB=1), but "make" reports 6 errors.

Versions are:
MacOSX version: 10.10.5 (Yosemite)
Bowtie2 src version: 2.2.8
TBB version: 4.4-20160128

Someone has experienced the same problem and has a solution?

The trace begin with:

$ make WITH_TBB=1
c++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS=""-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB"" -DPOPCNT_CAPABILITY -DWITH_TBB \
-fno-strict-aliasing -DBOWTIE2_VERSION=""`cat VERSION`"" -DBUILD_HOST=""`hostname`"" -DBUILD_TIME=""`date`"" -DCOMPILER_VERSION=""`c++ -v 2>&1 | tail -1`"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o bowtie2-build-s bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
-lpthread -ltbb -ltbbmalloc_proxy
In file included from bt2_build.cpp:27:
In file included from ./bt2_idx.h:42:
In file included from ./blockwise_sa.h:24:
In file included from /usr/local/include/tbb/tbb.h:53:
In file included from /usr/local/include/tbb/flow_graph.h:30:
/usr/local/include/tbb/task.h:913:13: error: no matching function for call to object of type 'const VSorting_worker<SString<char> >'
my_func();
^~~~~~~
/usr/local/include/tbb/task.h:917:9: note: in instantiation of member function 'tbb::internal::function_task<VSorting_worker<SString<char> > >::execute'
requested here
function_task( const F& f ) : my_func(f) {}
^
/usr/local/include/tbb/task_group.h:100:79: note: in instantiation of member function 'tbb::internal::function_task<VSorting_worker<SString<char> >
>::function_task' requested here
owner().spawn( *new( owner().allocate_additional_child_of(*my_root) ) Task(f) );
^
/usr/local/include/tbb/task_group.h:179:9: note: in instantiation of function template specialization 'tbb::internal::task_group_base::internal_run<const
VSorting_worker<SString<char> >, tbb::internal::function_task<VSorting_worker<SString<char> > > >' requested here
internal_run< const F, internal::function_task<F> >( f );
^
./diff_sample.h:832:12: note: in instantiation of function template specialization 'tbb::task_group::run<VSorting_worker<SString<char> > >' requested here
tbb_grp.run(VSorting_worker<TStr>(((void*)&tparams[tid])));
^
./blockwise_sa.h:422:24: note: in instantiation of member function 'DifferenceCoverSample<SString<char> >::build' requested here
_dc.get()->build(this->_nthreads);
^
./blockwise_sa.h:401:4: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
build();
^
./blockwise_sa.h:216:32: note: in instantiation of member function 'KarkkainenBlockwiseSA<SString<char> >::reset' requested here
{ _randomSrc.init(__seed); reset(); _done = new bool[_nthreads]; }
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Old 03-12-2016, 03:14 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,884
Default

Is there a reason you are compiling this on your own? Have you tried the compiled binary provided for OS X?
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Old 03-12-2016, 10:38 PM   #3
Luis
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Location: Spain

Join Date: Oct 2015
Posts: 2
Default

Yes. I try to compile with TBB becasuse the MacOSX binary only launch one thread and the source version compiled without TBB also only launch one thread. So, my last option was compilation with TBB.
Thank you for your answer.
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Old 03-13-2016, 08:31 PM   #4
yueluo
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Location: Guangzhou China

Join Date: Aug 2013
Posts: 82
Default

I had problems compiling bowtie2 with TBB support too. My OS was Centos 6.6. Bowtie2 source and TBB versions were the same as yours.
My 'fix' was to compile with LDFLAGS=-L/pathto/lib(or LD_RUN_PATH=/pathto/lib) but not CPPFLAGS=-I/pathto/include(or INC=/pathto/include). Sounds weird but it did work for me...
Hope this helps.
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