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:
