Re: [Seqan-dev] RazerS 3 compilation issue

["Weese, David" <weese@campus.fu-berlin.de>]

Mmh. Difficult to say. You could check that there are no limitations to the amount of memory your processes are allowed to allocate (see ulimit) or try to use cmake with another compiler "CXX=g++-4.7 cmake ...".

Cheers
Dave

--
David Weese, Ph.D.              david.weese@fu-berlin.de
Freie Universität Berlin        http://www.inf.fu-berlin.de/
Institut für Informatik         Phone: +49 30 838 75137
Takustraße 9                    Algorithmic Bioinformatics
14195 Berlin                    Room 020

Am 27.02.2014 um 10:25 schrieb Tran Ngoc Hieu (Dr) <NHTran@ntu.edu.sg>:

> Dear David,
> 
> Thank you for your prompt reply. I run on a Linux server with more than 20GB free memory available. Is there any other possible reasons? Any requirement about gcc version?
> 
> Cheers,
> Hieu
> 
> -----Original Message-----
> From: Weese, David [mailto:weese@campus.fu-berlin.de] 
> Sent: Thursday, 27 February, 2014 4:23 PM
> To: SeqAn Development
> Subject: Re: [Seqan-dev] RazerS 3 compilation issue
> 
> Hi,
> 
> the "internal compiler error" in correlation with the heavy templating in RazerS3 is usually an indicator for insufficient memory of your build machine. If you compile using the gcc make sure you have at least 4GB of free memory available.
> 
> Cheers,
> David
> 
> --
> David Weese, Ph.D.              david.weese@fu-berlin.de
> Freie Universität Berlin        http://www.inf.fu-berlin.de/
> Institut für Informatik         Phone: +49 30 838 75137
> Takustraße 9                    Algorithmic Bioinformatics
> 14195 Berlin                    Room 020
> 
> Am 27.02.2014 um 06:23 schrieb Tran Ngoc Hieu (Dr) <NHTran@ntu.edu.sg>:
> 
>> Dear All,
>> 
>> I encountered the following errors when trying to compile RazerS 3 (everything was fine when I tried other tools such as Mason, Masai). Could anyone please help with some advice? Thank you very much!
>> 
>> $ make razers3
>> [  0%] Built target seqan_extras
>> [  0%] Built target seqan_core
>> 
>> [100%] Building CXX object 
>> extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o
>> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/basic/test_system.h:
>> 73: warning: âclass seqan::Testâ has virtual functions but non-virtual 
>> destructor
>> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h
>> :197: warning: âclass seqan::ToolDocPrinter_â has virtual functions 
>> but non-virtual destructor
>> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h
>> :210: warning: âclass seqan::ManToolDocPrinter_â has virtual functions 
>> but non-virtual destructor
>> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h
>> :223: warning: âclass seqan::HtmlToolDocPrinter_â has virtual 
>> functions but non-virtual destructor
>> /home/nhtran/SeqAn/seqan-trunk/core/include/seqan/arg_parse/tool_doc.h
>> :318: warning: âclass seqan::TextToolDocPrinter_â has virtual 
>> functions but non-virtual destructor
>> 
>> /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_parallel.h: In function âvoid seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String<seqan::ThreadLocalStorage<seqan::MapPairedReads<seqan::String<seqan::MatchRecord<long unsigned int>, seqan::Alloc<void> >, seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >, seqan::Finder<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Finder<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Pattern<seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::OpenAddressing_> > >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >, seqan::String<seqan::String<short unsigned int, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSMode<seqan::RazerSGlobal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::NMatchesNone_> > >, seqan::Alloc<void> >, TFragmentStore = seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >, TSplitters = seqan::String<unsigned int, seqan::Alloc<void> >, TShape = const seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, TOptions = seqan::RazerSOptions<seqan::RazerSSpec<false, false> >]â:
>> 
>> /home/nhtran/SeqAn/seqan-trunk/extras/apps/razers3/razers_matepairs_pa
>> rallel.h:338: internal compiler error: in single_succ_edge, at 
>> basic-block.h:620 Please submit a full bug report, with preprocessed source if appropriate.
>> See <URL:http://bugzilla.redhat.com/bugzilla> for instructions.
>> Preprocessed source stored into /tmp/ccHRTako.out file, please attach this to your bugreport.
>> make[3]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] 
>> Error 1
>> make[2]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/all] Error 2
>> make[1]: *** [extras/apps/razers3/CMakeFiles/razers3.dir/rule] Error 2
>> make: *** [razers3] Error 2
>> 
>> 
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