Chuming, mpiblast-pio 1.4.0 uses the same mpiformatdb as mpiblast-1.4.0 does, so you can reuse the database fragments created by mpiblast 1.4.0. One thing you might want to know is that if you are using NFS, make sure to add "--use-master-write" option to run mpiblast. You can also look at the README file in the mpiblast-pio package for more information about the mpiblast-pio specific options.
Thanks, Heshan On Tue, 2006-03-21 at 13:43 -0500, Chuming Chen wrote: > Heshan, > > Thank you very much. > > I have successfully compiled mpiblast-pio 1.4.0 with Oct 2004 NCBI > toolbox. > > Do I still need to run mpiformatdb of mpiblast-pio first, then run > mpiblast? > > Chuming > > On 3/20/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > Chuming, > > The current release of mpiBLAST-pio only supports the Oct2004 > NCBI > toolbox. Could you give it a try and let me know what is > happening? Sorry > about the inconvenience. We are working on it and will > integrate the > newest version of NCBI toolbox in the next release. > > Thanks, > Heshan > > > I followed the compilation order you mentioned, still no > luck. By the way, > > I > > am compiling mpiBLAST-pio 1.4.0 instead of mpiBLAST 1.4.0. > > > > myblastool.c: In function `BLASTOptionNewEx': > > myblastool.c:1462: error: structure has no member named > `no_check_score' > > myblastool.c:1486: error: structure has no member named > `no_check_score' > > > > The errors above happend for the structure > "BLAST_OptionsBlkPtr options". > > > > Do you know where is this structure defined? > > > > Thanks, > > > > -Chuming > > > > On 3/20/06, Anoop Rajendra <[EMAIL PROTECTED]> wrote: > >> > >> Did you compile the NCBI source tree first? You'll need to > do that > >> before > >> you compile mpiblast. > >> The order of compiling is > >> > >> 1. Patch NCBI Blast with the patch supplied by mpiblast > >> 2. Compile NCBI Blast > >> 3. Compile MPI-Blast and during configure point to the NCBI > source tree > >> that you just compiled. > >> > >> -Anoop > >> > >> On Mar 20, 2006, at 2:06 PM, Chuming Chen wrote: > >> > >> I did apply the ncbi_Dec2005_evalue.patch. But I still got > the same > >> error > >> messages. > >> > >> On 3/20/06, Anoop Rajendra < [EMAIL PROTECTED]> > wrote: > >> > > >> > If you're compiling with the latest NCBI source tree, you > will want > >> > to use ncbi_Dec2005_evalue.patch > >> > rather than the june 2005 patch. > >> > > >> > -Anoop > >> > > >> > On Mar 20, 2006, at 1:18 PM, Chuming Chen wrote: > >> > > >> > > Hi all, > >> > > > >> > > I failed to compile mpiblast-pio-1.4.0 on Rocks cluster > 4.1. > >> > > > >> > > Here is the error messages I got: > >> > > > >> > > myblastool.c: In function `BLASTOptionNewEx': > >> > > myblastool.c:1462: error: structure has no member named > >> > > `no_check_score' > >> > > myblastool.c :1486: error: structure has no member > named > >> > > `no_check_score' > >> > > myblastool.c: In function `BLASTPostSearchLogic': > >> > > myblastool.c:6263: error: structure has no member > named > >> > > `original_expect_value' > >> > > myblastool.c:6269: warning: assignment from > incompatible pointer > >> type > >> > > make[2]: *** [myblastool.o] Error 1 > >> > > make[2]: Leaving directory `/home/chen/src/mpiblast- > 1.4.0-pio/src' > >> > > make[1]: *** [all] Error 2 > >> > > make[1]: Leaving directory > `/home/chen/src/mpiblast-1.4.0-pio/src' > >> > > make: *** [all-recursive] Error 1 > >> > > > >> > > Am I missing anything? I have NCBI src tree and have > applied the > >> > > ncbi_Jun2005_evalue_patch. > >> > > > >> > > Thank you for your help. > >> > > > >> > > Chuming Chen > >> > > >> > > >> > > >> > ------------------------------------------------------- > >> > This SF.Net email is sponsored by xPML, a groundbreaking > scripting > >> > language > >> > that extends applications into web and mobile media. > Attend the live > >> > webcast > >> > and join the prime developer group breaking into this new > coding > >> > territory! > >> > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > >> > _______________________________________________ > >> > Mpiblast-users mailing list > >> > [email protected] > >> > > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > >> > > >> > >> > >> > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking > scripting language > that extends applications into web and mobile media. Attend > the live webcast > and join the prime developer group breaking into this new > coding territory! > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 > _______________________________________________ > Mpiblast-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
