[Bioclusters] blat and hmmer on some architectures?

Vsevolod (Simon) Ilyushchenko simonf at cshl.edu
Tue Oct 25 11:42:54 EDT 2005


The reason I said only i686 is supported is that the available machine 
types I saw in the lib directory did not include x86_64. Of course, I'll 
compile it there anyway using the appropriate flags, I just wanted to 
see if other architectures are included out of the box.


Jason Stajich wrote on 10/25/2005 08:05 AM:
> re: blat
> Now that is not really fair about changing all the makefiles, you  only 
> need to edit inc/common.mk to set the CFLAGS/COPT and CC  options.  I 
> built blast with icc on i686 and gcc on x86_64 with no  problems.
> I don't understand why you think i686 is only supported.  just set  the 
> $MACHTYPE variable.
> echo "MACHTYPE is: '$$MACHTYPE'" ; \
>                 echo "it should be something simple: i386 i686 sparc  
> alpha x86_64 ppc, etc..." ;
> So just edit the inc/common.mk to specify your compiler flags and set  
> the MACHTYPE environment variable to uname -m
> -jason
> On Oct 25, 2005, at 5:11 AM, Tim Cutts wrote:
>> On 24 Oct 2005, at 7:44 pm, Vsevolod (Simon) Ilyushchenko wrote:
>>> Hi,
>>> Our lab is starting to test several server architectures by  
>>> compiling and timing programs like blast, blat and hmmer. The  setups 
>>> are Darwin, regular i686, Intel's and AMD's X86_64 and  IBM's ppc64.
>>> I've found that blat only has the i686 machine type as a  compilation 
>>> option - not x86_64, and of course not Darwin or  ppc64. Hmmer is 
>>> smarter better - it only lacks support for ppc64  (it has plain ppc 
>>> though). Does anyone know if it's possible to  compile blat and hmmer 
>>> on these architectures?
>> I don't see why not, as long as you're using a suitable compiler.   
>> You'll just need to work out what the appropriate compiler options  
>> are.  HMMER will probably work fine on ppc64, since it already  
>> supports other 64-bit architectures fine.  The same goes for BLAT -  
>> it works fine on Alpha for us, so I see no reason why it shouldn't  
>> compile OK on other 64-bit architectures.
>> You'll have fun finding the bazillion places in Jim Kent's  makefiles 
>> that you need to make the changes though.
>> Tim
>> -- 
>> Dr Tim Cutts
>> Informatics Systems Group, Wellcome Trust Sanger Institute
>> GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
> -- 
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters


Simon (Vsevolod ILyushchenko)   simonf at cshl.edu

"Think like a man of action, act like a man of thought."

		         Henri Bergson

More information about the Bioclusters mailing list