Getting mpiblast

? 現(xiàn)在下載包文件：

?wget http://www.mpiblast.org/downloads/files/mpiBLAST-1.6.0-pio.tgz

?解壓包文件：

?tar xvzf mpiBLAST*.tgz

?然后下載ncbi：

? wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20061015/ncbi.tar.gz

? 解壓包

? tar xvzf ncbi.tar.gz

Building mpiblast

?? 將ncbi文件move:

?? mv ncbi mpiblast/ncbi/make/

?? 前進(jìn)至mpiblast目錄：

?? cd mpiblast

? ./ncbi/make/makedis.csh

?

(Note: If you receive an error about CSH, you don't have the C shell installed, but that's easy to fix withapt-get install csh.)

The above command (makedis.csh) needs to be run three times. The first time you run, it will finish with an error:

make: *** No rule to make target `ncbimain.o', needed by `libncbi.a'. Stop.Fatal error building NCBI core libraries. Please be sure that you have X11 and Motif libraries installed. The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful.

Run the same command again,

./ncbi/make/makedis.csh

even though it finished with an error. This time, it will take quite a bit longer, and it will finish with a different error:

make: *** No rule to make target `ni_debug.o', needed by `libnetcli.a'. Stop. FAILURE primary make status = 0, demo = 0, threaded_demo = 0, net = 2 ####### # ##### ##### #### ##### # # # # # # # # # ##### # # # # # # # # # ##### ##### # # ##### # # # # # # # # # ####### # # # # #### # #

Run

./ncbi/make/makedis.csh

one last time, and it should finish successfully:

Put the date stamp to the file ../VERSION ********************************************************* *The new binaries are located in ./ncbi/build/ directory* *********************************************************

Then it's safe to continue on to building mpiblast itself.

安裝mpiblast(安裝在/usr/bin)：

?./configure --prefix=/usr/ --with-ncbi=`pwd`/ncbi --host=x86_64

?make

?make install

?檢查是否安裝成功：

?which mpiblast

更新一下：

updatedb

locate mpiblast | grep -v src

進(jìn)入當(dāng)前用戶的home路徑（如果是一root進(jìn)入，則進(jìn)入/root，否則進(jìn)入home）編輯.ncbirc：

[mpiBLAST] Shared=/usr/bin/mpiblast Local=/usr/bin/mpiblast

Getting Databases:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/drosoph.nt.gz

Then you'll need to untar or just ungzip them. If they end in .tg.gz, use to tar to untar the file:

tar xvzf yourfile.tg.gz

If they just end in .gz, they're only gzipped, so unzip them with

gunzip yourfile.gz

安裝
1) 下載openmpi
2) tar -xzvf openmpi-1.4.3.tar.gz
3) cd openmpi-1.4.3
4) ./configure --prefix=/usr/ | tee ../install.log
5) make all | tee ../make.log
6) make install | tee ../install2.log

?

配置環(huán)境
7) vi /etc/ld.so.conf? 最后增加一行
/usr/bin
保存退出
8） /sbin/ldconfig?? 回車(chē)等待。
9） vi /etc/profile， 最后 增加一行：
PATH=${PATH}:/usr//bin
保存退出

10）執(zhí)行
. /etc/profile

測(cè)試
10）cd examples
11) make

12) mpirun? -np 4 ./hello_f90????????????? 可以得到類(lèi)似ppt中的輸出

?mpi多機(jī)時(shí)， 需要有machines文件。文件內(nèi)容如下：

tp1 1 /home/pact/mpich/examples/basic/cpi
tp2 1 /home/pact/mpich/examples/basic/cpi
tp3 1 /home/pact/mpich/examples/basic/cpi

分別表示機(jī)器名/ip，? 進(jìn)程個(gè)數(shù)， 進(jìn)程名（進(jìn)程名可以沒(méi)有）； 當(dāng)使用機(jī)器名時(shí)， 則需要架設(shè)DNS服務(wù)器。

mpirun -machinefile ./machine.linux -np 4 ./hello_f90

?

OK:

使者運(yùn)行一下：

mpiformatdb -i drosoph.nt --nfrags=4 -pF

• -i specifies my input file, drosoph.nt
• --nfrags=4 tells it to make four fragments
• -p specifies whether the file is a protein file or not. I put F for false, since this is a nucleotide file, not an amino acid file.

Mpiblast will be run just using mpirun or mpiexec, but there are a few important command line arguments. These include

• -d - the database to be queried against
• -i - the input file
• -p - the type of blast query to run, including
  • blastn for nucleotides
  • blastp for proteins
• -o - the name of the file to save the output in

The command run in its complete state should look something like this:

mpiexec -np 4 /shared/bin/mpiblast -d drosoph.nt -i test.in -p blastn -o results.txt

Of course, if you're using the version of mpiexec with Torque functionality, you'll need to wrap this in a qsub script.

When it's finished running, you should have a new results.txt file that looks something like this:

?

??

總結(jié)

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