Re: [Seqan-dev] RazerS 3

[Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>]

Hi David,

After a 'svn up', razers3 appeared ;-)


[sboisver12@colosse1 seqan]$ ./razers3 
razers3 - Fast Read Mapping with Sensitivity Control
====================================================
    razers3 [OPTIONS] <GENOME FILE> <READS FILE>
    razers3 [OPTIONS] <GENOME FILE> <PE-READS FILE1> <PE-READS FILE2>
    Try 'razers3 --help' for more information.

VERSION
    razers3 version: 3.1 [12646]
    Last update 2012-08-27


Thank you !

On 20/08/12 02:43 PM, Weese, David wrote:
> 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
>