mpiBlast安装详解以及使用说明

Gettingmpiblast

现在下载包文件：

wget
'target='_blank'>http://www.mpiblast.org/downloads/files/mpiBLAST-1.6.0-pio.tgz[/code]

解压包文件：
tarxvzfmpiBLAST*.tgz
然后下载ncbi：
wget'target='_blank'>ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20061015/ncbi.tar.gz[/code]
解压包
tarxvzfncbi.tar.gz
Buildingmpiblast
将ncbi文件move:mvncbimpiblast/ncbi/make/前进至mpiblast目录：cdmpiblast
./ncbi/make/makedis.csh
(Note:IfyoureceiveanerroraboutCSH,youdon'thavetheCshellinstalled,butthat'seasytofixwith
apt-getinstallcsh
.)Theabovecommand(makedis.csh)needstoberunthreetimes.Thefirsttimeyourun,itwillfinishwithanerror:
make:***Noruletomaketarget`ncbimain.o',neededby`libncbi.a'.Stop.FatalerrorbuildingNCBIcorelibraries.
PleasebesurethatyouhaveX11andMotiflibrariesinstalled.
TheNCBItoolkitFAQatftp://ftp.ncbi.nih.gov/toolbox/FAQ.htmlmaybehelpful.

Runthesamecommandagain,
./ncbi/make/makedis.csh

eventhoughitfinishedwithanerror.Thistime,itwilltakequiteabitlonger,anditwillfinishwithadifferenterror:
make:***Noruletomaketarget`ni_debug.o',neededby`libnetcli.a'.Stop.
FAILUREprimarymakestatus=0,demo=0,threaded_demo=0,net=2
#######
####################
#########
#############
##################
#########
#################

Run
./ncbi/make/makedis.csh

onelasttime,anditshouldfinishsuccessfully:
Putthedatestamptothefile../VERSION
*********************************************************
*Thenewbinariesarelocatedin./ncbi/build/directory*
*********************************************************

Thenit'ssafetocontinueontobuildingmpiblastitself.安装mpiblast(安装在/usr/bin)：
./configure--prefix=/usr/--with-ncbi=
`pwd`/ncbi
--host=x86_64makemakeinstall
检查是否安装成功：
whichmpiblast
更新一下：
updatedb
locatempiblast|grep-vsrc
进入当前用户的home路径（如果是一root进入，则进入/root，否则进入home）编辑.ncbirc：
[code]
[code][mpiBLAST]
Shared=/usr/bin/mpiblast
Local=/usr/bin/mpiblast

GettingDatabases:

wget'target='_blank'>ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/drosoph.nt.gz[/code]Thenyou'llneedtountarorjustungzipthem.Iftheyendin
.tg.gz
,usetotartountarthefile:
tarxvzfyourfile.tg.gz

Iftheyjustendin
.gz
,they'reonlygzipped,sounzipthemwith
gunzipyourfile.gz

安装1)下载openmpi2)tar-xzvfopenmpi-1.4.3.tar.gz3)cdopenmpi-1.4.34)./configure--prefix=/usr/|tee../install.log5)makeall|tee../make.log6)makeinstall|tee../install2.log配置环境7)vi/etc/ld.so.conf最后增加一行/usr/bin保存退出8）/sbin/ldconfig回车等待。9）vi/etc/profile，最后增加一行：PATH=${PATH}:/usr//bin保存退出10）执行./etc/profile测试10）cdexamples11)make12)mpirun-np4./hello_f90可以得到类似ppt中的输出mpi多机时，需要有machines文件。文件内容如下：tp11/home/pact/mpich/examples/basic/cpitp21/home/pact/mpich/examples/basic/cpitp31/home/pact/mpich/examples/basic/cpi分别表示机器名/ip，进程个数，进程名（进程名可以没有）；当使用机器名时，则需要架设DNS服务器。mpirun-machinefile./machine.linux-np4./hello_f90OK:
使者运行一下：
mpiformatdb-idrosoph.nt--nfrags=4-pF
-i
specifiesmyinputfile,drosoph.nt
--nfrags=4
tellsittomakefourfragments
-p
specifieswhetherthefileisaproteinfileornot.IputFforfalse,sincethisisanucleotidefile,notanaminoacidfile.Mpiblastwillberunjustusing
mpirun
or
mpiexec
,butthereareafewimportantcommandlinearguments.Theseinclude
-d
-thedatabasetobequeriedagainst
-i
-theinputfile
-p
-thetypeofblastquerytorun,including
blastn
fornucleotides
blastp
forproteins
-o
-thenameofthefiletosavetheoutputinThecommandruninitscompletestateshouldlooksomethinglikethis:
mpiexec-np4/shared/bin/mpiblast-ddrosoph.nt-itest.in-pblastn-oresults.txt

Ofcourse,ifyou'reusingthe
versionofmpiexecwithTorquefunctionality,you'llneedtowrapthisina
qsubscript.Whenit'sfinishedrunning,youshouldhaveanew
results.txt
filethatlookssomethinglikethis: