mpiBlast安装详解以及使用说明

Getting mpiblast

现在下载包文件：

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

解压包文件：

tar xvzf mpiBLAST*.tgz

然后下载ncbi：

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

解压包

tar xvzf ncbi.tar.gz

Building mpiblast

将ncbi文件move:

mv ncbi mpiblast/ncbi/make/

前进至mpiblast目录：

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.

安装mpiblast(安装在/usr/bin)：

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

make

make install

检查是否安装成功：

which mpiblast

更新一下：

updatedb

locate mpiblast | grep -v src

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：

[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

安装
1) 下载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）cd examples
11) make

12) mpirun -np 4 ./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：

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 -np 4 ./hello_f90

OK:

使者运行一下：

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: