Re: [Seqan-dev] RazerS 3

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

Hi Sébastien,

I now moved RazerS to seqan/extras/ and cleaned it up a bit. So if you make an "svn update", follow the "Getting Started" section on trac.seqan.de, and instead of using Debug mode use the Release mode, it should compile on your system. Also I added -fomit-frame-pointer to our default CXX-Flags in Release mode. If you want to compile razers3 in Release mode with custom extra flags simply call in your build-directory:

cmake . -DCMAKE_CXX_FLAGS:STRING="-march=native" -DCMAKE_BUILD_MODE=Release
make razers3

To check which flags are actually used, call "make razers3 VERBOSE=1".

I hope that works better than the binaries. Please let me know what happened.

Cheers,
David

--
David Weese				weese@inf.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 19.08.2012 um 20:49 schrieb Sébastien Boisvert <Sebastien.Boisvert.3@ulaval.ca>
:

> Hello David,
> 
> 
> 
> [sboisver12@colosse1 ~]$ uname -a
> Linux colosse1 2.6.18-274.7.1.el5 #1 SMP Thu Oct 20 16:21:01 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
> 
> [sboisver12@colosse1 ~]$ yum list|grep glibc|grep installed
> glibc.i686                              2.5-65                        installed
> glibc.x86_64                            2.5-65                        installed
> glibc-common.x86_64                     2.5-65                        installed
> glibc-devel.i386                        2.5-65                        installed
> glibc-devel.x86_64                      2.5-65                        installed
> glibc-headers.x86_64                    2.5-65                        installed
> 
> [sboisver12@colosse1 ~]$ yum list|grep stdc++|grep installed
> compat-libstdc++-33.i386                3.2.3-61                      installed
> compat-libstdc++-33.x86_64              3.2.3-61                      installed
> libstdc++.i386                          4.1.2-51.el5                  installed
> libstdc++.x86_64                        4.1.2-51.el5                  installed
> libstdc++-devel.x86_64                  4.1.2-51.el5                  installed
> 
> [sboisver12@colosse1 ~]$ ldd /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3
> /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.10' not found (required by /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3)
> /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3)
> /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /rap/nne-790-ab/software/RazerS/v3.0-beta1/razers3.0-beta1/linux64/razers3)
> 	linux-vdso.so.1 =>  (0x00007fffbc5fd000)
> 	librt.so.1 => /lib64/librt.so.1 (0x0000003971200000)
> 	libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003972e00000)
> 	libm.so.6 => /lib64/libm.so.6 (0x000000396ea00000)
> 	libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x000000396e600000)
> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003970a00000)
> 	libpthread.so.0 => /lib64/libpthread.so.0 (0x000000396ee00000)
> 	libc.so.6 => /lib64/libc.so.6 (0x000000396e200000)
> 	/lib64/ld-linux-x86-64.so.2 (0x000000396de00000)
> 
> 
> Weese, David a écrit :
>> Mmh, maybe. What version do you have? I have the followings:
>> 
>> weese@sequoia:~$ uname -a
>> Linux sequoia 2.6.32-5-amd64 #1 SMP Sat Mar 31 04:00:05 UTC 2012 x86_64 GNU/Linux
>> 
>> weese@sequoia:~$ dpkg -l libc6
>> Desired=Unknown/Install/Remove/Purge/Hold
>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
>> ||/ Name Version Description
>> +++-========================-========================-================================================================
>> ii libc6 2.11.3-4 Embedded GNU C Library: Shared libraries
>> 
>> weese@sequoia:~$ dpkg -l libstdc++6
>> Desired=Unknown/Install/Remove/Purge/Hold
>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
>> ||/ Name Version Description
>> +++-========================-========================-================================================================
>> ii libstdc++6 4.4.5-8 The GNU Standard C++ Library v3
>> 
>> weese@sequoia:~/sandbox/seqan-trunk/build/mak3$ ldd ./sandbox/weese/apps/razers3/razers3
>> linux-vdso.so.1 => (0x00007fffdadff000)
>> librt.so.1 => /lib/librt.so.1 (0x00002ba722694000)
>> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002ba7228c8000)
>> libm.so.6 => /lib/libm.so.6 (0x00002ba722bdd000)
>> libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00002ba722e5f000)
>> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002ba72306c000)
>> libpthread.so.0 => /lib/libpthread.so.0 (0x00002ba723283000)
>> libc.so.6 => /lib/libc.so.6 (0x00002ba72349f000)
>> /lib64/ld-linux-x86-64.so.2 (0x00002ba722474000)
>> 
>> It is strange that he doesn't complain about missing/wrong libraries and instead just crashes. Weird. I attached a fresh build. Could you try this and the old one on another Linux machine?
>> 
>> Cheers,
>> Dave
>> 
>> 
>> 
>> --
>> David Weeseweese@inf.fu-berlin.de <mailto:weese@inf.fu-berlin.de>
>> Freie Universität Berlinhttp://www.inf.fu-berlin.de/
>> Institut für InformatikPhone: +49 30 838 75137
>> Takustraße 9Algorithmic Bioinformatics
>> 14195 BerlinRoom 020