[Bioclusters] RE: mpiblast 1.3 on Mac Xserve G5

Ian Yi-Feng Chang d49228002 at ym.edu.tw
Thu Dec 23 04:49:42 EST 2004


 
Thanks for your help~
It seems works while compiling mpiblast
Now I'm trying to use it~
Wish me luck and thank you again.

ian
-----Original Message-----
From: bioclusters-bounces at bioinformatics.org
[mailto:bioclusters-bounces at bioinformatics.org] On Behalf Of Aaron Darling
Sent: Wednesday, December 22, 2004 1:52 PM
To: Clustering, compute farming & distributed computing in life science
informatics
Subject: Re: [Bioclusters] RE: mpiblast 1.3 on Mac Xserve G5

Ian, the compiler errors you report signify that mpiBLAST is being compiled
against an unpatched toolbox. Although it appears you patched and built the
toolbox you should verify that the path you are giving to ./configure
--with-ncbi is the same as the path to the patched and compiled toolbox. (It
would seem that /usr/local/ncbi is unpatched)

Also, all of the command line arguments to ./configure should be given in a
single ./configure command, rather than the three successive commands you
list below...

Hope that helps,
-Aaron


Ian Yi-Feng Chang wrote:

> Dear All:
> Did anyone had successfuly install mpiblast 1.3 on mac os x (Xserve G5)?
> I've some problem to install it
> I've compiled NCBI toolkit without error messages $patch -p1 < 
> ../mpiblast-1.3.0/ncbi_Oct2004_evalue.patch (within the 'ncbi' 
> directory) $ncbi/make/makedis.csh $./configure with the 
> --disable-dependency-tracking $./configure 
> --disable-dependency-tracking $./configure --with-ncbi=/usr/local/ncbi 
> $./configure --prefix=/usr/local/mpiblast but when I build mpiblast, 
> it response following messages I also had check previous discussion 
> about mpiblast 1.2.1, the they seems sort of diffent could anyone help 
> me ?
> ian chang
> mpiBlast 1.3
> NCBI Toolkit 200410 installed
> gcc (GCC) 3.3 20030304
> $make
> make all-am
> if mpicc -DHAVE_CONFIG_H -I. -I. -I. -I../include/ 
> -I/usr/local/ncbi/include/ -DUSING_MPI 
> -DINSTALL_PREFIX="\"/usr/local/mpiblast\"" -g -O2 -MT 
> mpiblast-blast_hooks.o -MD -MP -MF ".deps/mpiblast-blast_hooks.Tpo" -c 
> -o mpiblast-blast_hooks.o `test -f 'blast_hooks.c' || echo 
> './'`blast_hooks.c; \ then mv -f ".deps/mpiblast-blast_hooks.Tpo"
> ".deps/mpiblast-blast_hooks.Po"; else rm -f 
> ".deps/mpiblast-blast_hooks.Tpo"; exit 1; fi
> blast_hooks.c: In function `initBLAST':
> blast_hooks.c:695: error: structure has no member named 
> `query_adjustments'
> blast_hooks.c:696: error: structure has no member named 
> `effective_db_lengths'
> blast_hooks.c: In function `getQuery':
> blast_hooks.c:747: error: structure has no member named `current_queryI'
> blast_hooks.c: In function `runBLAST':
> blast_hooks.c:1455: error: structure has no member named 
> `calculate_statistics_and_exit'
> blast_hooks.c:1457: error: structure has no member named 
> `calculate_statistics_and_exit'
> blast_hooks.c:1478: error: structure has no member named `current_queryI'
> blast_hooks.c: In function `outputResults':
> blast_hooks.c:1573: error: structure has no member named 
> `calculate_statistics_and_exit'
> mpicc: No such file or directory
> make[1]: *** [mpiblast-blast_hooks.o] Error 1
> make: *** [all] Error 2
>
>-----------------------------------------------------------------------
>-
>
>_______________________________________________
>Bioclusters maillist  -  Bioclusters at bioinformatics.org 
>https://bioinformatics.org/mailman/listinfo/bioclusters
>  
>
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https://bioinformatics.org/mailman/listinfo/bioclusters



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