mpiBlast安装详解以及使用说明

mpiBlast安装详解以及使用说明

Getting mpiblast

​​现在下载包文件：​​

​​ wget 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 with​​apt-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:

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