CUDAGPUBLASTinstallreadme.docx

1、CUDAGPUBLASTinstallreadmeCUDA、GPU-BLAST的安装一、 前提条件：机器需要有GPU显卡，GPU-BLAST的安装需要有Tesla的显卡内存建议需要足够大（=4G）所以操作系统为64位比较合适，原来我在32位系统上没有装成功，不知道是不是不支持我的安装环境：机器：HPZ800, Workstation CPU: Intel(R) Xeon E5560 2.13GHz 8核 64位 内存 8G； 在硬盘中划了6G为swap区 GPU: 2块。一块是 Quadro Fx 380; 另一块是Tesla C1060OS： CentOS 6.0 64-bit驱动程序和安装

2、包：到NVIDIA的官网上下载驱动、CUDAToolkit和CUDASDKhttp:/D我下的是：Developer Drivers for Linux (270.41.19) 64-bitCUDA Toolkit for RedHat Enterprise Linux 6.0 64-bitGPU Computing SDK-Complete package including all code samples我下载的三个.run文件都放在/home/tanjun/目录下二、驱动安装离开XWindow图形界面，转到字符界面下安装#init 3#cd /home/tanjun#sh devdri

3、ver_4.0_linux_64_270.41.19.run如果之前有安装，则更新覆盖就好，一路默认安装就好完了，回到XWindow下#init 5驱动就安装完了三、CUDA Toolkit安装#cd /home/tanjun#sh cudatoolkit_4.0.17_linux_64_rhel6.0.run当需要输入安装路径的时候，可以自己制定安装路径，为了方便，我选择了默认路径/usr/local/cuda完成安装后，阅读控制台的信息，需要修改环境变量PATH和LD_LIBRARY_PATH，这个非常重要，需要慎重。设置不正确将导致CUDA不能用，甚至使系统的所有命令都用不了。1、 在/

4、etc/profile.d目录下新建一个脚本文件cuda.sh，写入export LD_LIBRARY_PATH=/usr/local/cuda/lib64export PATH=/usr/local/cuda/bin:$PATH重启、注销系统或者#source /etc/profile使设置生效2、 在/etc/profile的开头（或其他结构外的行）增加两行export PATH=$PATH:/usr/local/cuda/binexport LD_LIBRARY_PATH=$LD_LIBARARY_PATH:/usr/local/cuda/lib64重启、注销或者#source /etc

5、/profile使设置生效，普通用户也需要source3、 在/etc/ld.so.conf.d目录下新建cuda.conf，写入;/usr/local/cuda/lib64/usr/local/cuda/lib/(install path)/qtsdk-2010.03/lib （这俩在需要用QT的时候才需要，否则QT将出错）/(install path)/qtsdk-2010.03/qt/lib保存后 ldconfig一下如果安装路径有改变，则以上的路径需要和自己指定的路径一致，如果为32位机器，则以上有lib64的地方为lib完了查看PATH和LD_LIBRARY_PATH是否正确#ech

6、o $PATH，应该包含有/usr/local/cuda/lib#echo $LD_LIBRARY_PATH，应该为/usr/local/cuda/lib64否则需要重新设置，使其生效 如果出现了系统瘫痪、所有命令都不能用的情况，则是环境变量错误的问题，按以下方式解决：进入字符界面: Ctrl+Alt+F2然后用root登录，查看PATH的信息是否正确#echo $PATH如果不正确了，则修改为原来的值#PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:usr/local/sbin:/usr/bin/X11:/usr/X11R6/bin:/ro

7、ot/bin这样，命令就可以用了，然后修改环境变量，或删除之前修改的项，回到原来的值，重新设置。四、CUDA SDK的安装#cd /home/tanjun#sh gpucomputingsdk_4.0.17_linux.rn和三类似，一路默认即可，也可自己指定安装路径完了可以进入该安装目录下的子目录C下面make一下，看安装是否成功如果出现错误：1、 cannot find lglut解决：yum install *glu*2、 error:builtin_types.h:No such file or directory则是前面的环境变量/etc/profile没弄好，或者没有source

8、/etc/profile使其生效3、 cannot find Ixi(or lXmu)解决：yum install libXi-devel(libXmu-devel)其他问题可以问谷歌，比如64位和32位的问题至此，CUDA的安装环境已经安装完毕。GPU-BLAST的安装包里面有README文档，说得很清楚了，我这里只是COPY过来，我就是这么装的，不过有的时候装不上，多装几次就好了，也不知道是为什么。我的操作系统为CentOS6.0，CUDA为4.0路径与他不一样The following sequence of commands are on a CentOS 5.5 with CUDA

9、3.2.The steps cover the installation of GPU-BLAST, the formatting and sorting of adatabase and the execution of a GPU-BLAST search.The login shell is bash.1.a) Adding GPU functionality to an existing installation of NCBI-BLAST.The directory of the existing installation of NCBI-BLAST is blastpvouzise

10、ratosthenes blast$ lsncbi-blast-2.2.25+-srcpvouziseratosthenes blast$ wget http:/eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz-2010-10-19 13:02:07- http:/eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gzResolving eudoxus.cheme.cmu.edu. 128.2.55.71Connectin

11、g to eudoxus.cheme.cmu.edu|128.2.55.71|:80. connected.HTTP request sent, awaiting response. 200 OKLength: 316399 (309K) application/x-gzipSaving to: gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz100%= 316,399 -.-K/s in 0.03s2010-10-19 13:02:08 (11.2 MB/s) - gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz saved 31639

12、9/316399pvouziseratosthenes blast$ lsgpu-blast-1.0_ncbi-blast-2.2.25.tar.gz ncbi-blast-2.2.25+-srcpvouziseratosthenes blast$ tar -xzf gpu-blast-1.0_ncbi-blast-2.2.25.tar.gzpvouziseratosthenes blast$ lsgpu_blast gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz install ncbi-blast-2.2.25+-src queries READMEpvouz

13、iseratosthenes blast$ sh ./install ncbi-blast-2.2.25+-srcDo you want to install GPU-BLAST on an existing installation of blastp yes/noyes: you will be asked for the installation directory of the blastp executableno: will download and install ncbi-blast-2.2.25+-srcyesPlease input the installation dir

14、ectory of blastp of ncbi-blast-2.2.25+-src/home/pvouzis/Documents/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c+/GCC412-ReleaseMT64/binblastp version 2.2.25+ is compatibleContinuing with the installation of GPU-BLAST.Modifying NCBI-BLAST files.Compiling CUDA codeBuilding NCBI-BLAST with GPU-BLAST.(如果网络比

15、较差的话，这里会需要很久，或者换个时间再装，我昨晚一个晚上都没装好，后来今天一会儿就装好了)1.b) Downloading the NCBI-BLAST source code and adding GPU functionality.pvouziseratosthenes blast$ wget http:/eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz-2010-10-19 12:37:01- http:/eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_n

16、cbi-blast-2.2.25.tar.gzResolving eudoxus.cheme.cmu.edu. 128.2.55.71Connecting to eudoxus.cheme.cmu.edu|128.2.55.71|:80. connected.HTTP request sent, awaiting response. 200 OKLength: 316399 (309K) application/x-gzipSaving to: “gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz”100%= 316,399 -.-K/s in 0.03s2010-1

17、0-19 12:37:01 (11.3 MB/s) - “gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz” saved 316399/316399pvouziseratosthenes blast$ lsgpu-blast-1.0_ncbi-blast-2.2.25.tar.gzpvouziseratosthenes blast$ tar -xzf gpu-blast-1.0_ncbi-blast-2.2.25.tar.gzpvouziseratosthenes blast$ lsgpu_blast gpu-blast-1.0_ncbi-blast-2.2.25.

18、tar.gz install queries READMEpvouziseratosthenes blast$ sh ./install ncbi-blast-2.2.25+-srcDo you want to install GPU-BLAST on an existing installation of blastp yes/noyes: you will be asked for the installation directory of the blastp executableno: will download and install ncbi-blast-2.2.25+-srcno

19、Continuing with the downloading of ncbi-blast-2.2.25+-src.Downloading NBCI BLAST-2010-10-19 12:41:55- ftp:/ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-src.tar.gz = “ncbi-blast-2.2.25+-src.tar.gz”Resolving ftp.ncbi.nlm.nih.gov. 130.14.29.30Connecting to ftp.ncbi.nlm.nih.go

20、v|130.14.29.30|:21. connected.Logging in as anonymous . Logged in!= SYST . done. = PWD . done.= TYPE I . done. = CWD (1) /blast/executables/blast+/LATEST . done.= SIZE ncbi-blast-2.2.25+-src.tar.gz . 11482581= PASV . done. = RETR ncbi-blast-2.2.25+-src.tar.gz . done.Length: 11482581 (11M) (unauthori

21、tative)100%= 11,482,581 6.80M/s in 1.6s2010-10-19 12:41:57 (6.80 MB/s) - “ncbi-blast-2.2.25+-src.tar.gz” saved 11482581Extracting NCBI-BLAST.Configuring ncbi-blast-2.2.25+-src with options:./configure -without-debug -with-mt -without-sybase -without-ftds -without-fastcgi -without-fltk -without-wxwin

22、 -without-ncbi-c -without-sssdb -without-sss -without-geo -without-sp -without-orbacus -without-boostIf you want to change these options edit the file install, delete the directory ncbi-blast-2.2.25+-src, and rerun install.Modifying NCBI-BLAST files.Compiling CUDA codeBuilding NCBI-BLAST with GPU-BL

23、AST.pvouziseratosthenes blast$ lsconfigure.output gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz install ncbi-blast-2.2.25+-src ncbi_blast.output READMEgpu_blast gpu_blast.output modify.output ncbi-blast-2.2.25+-src.tar.gz queries2) Downloading and sorting the env_nr database.pvouziseratosthenes blast$ mkdi

24、r database/pvouziseratosthenes blast$ cd database/pvouziseratosthenes database$ wget ftp:/ftp.ncbi.nlm.nih.gov/blast/db/FASTA/env_nr.gz-2010-10-04 21:12:25- ftp:/ftp.ncbi.nlm.nih.gov/blast/db/FASTA/env_nr.gz = env_nr.gzResolving ftp.ncbi.nlm.nih.gov. 130.14.29.30Connecting to ftp.ncbi.nlm.nih.gov|13

25、0.14.29.30|:21. connected.Logging in as anonymous . Logged in!= SYST . done. = PWD . done.= TYPE I . done. = CWD /blast/db/FASTA . done.= SIZE env_nr.gz . 827145187= PASV . done. = RETR env_nr.gz . done.Length: 827145187 (789M)100%= 827,145,187 6.14M/s in 87s2010-10-04 21:13:54 (9.02 MB/s) - env_nr.

26、gz saved 827145187pvouziseratosthenes database$ gunzip env_nr.gzpvouziseratosthenes database$ cd ./ncbi-blast-2.2.25+-src/c+/GCC412-ReleaseMT64/bin/pvouziseratosthenes bin$ ./makeblastdb -in ././././database/env_nr -out ././././database/sorted_env_nr -sort_volumes -max_file_sz 500MBBuilding a new DB

27、, current time: 10/04/2010 21:16:46New DB name: ././././database/sorted_env_nrNew DB title: ././././database/env_nrSequence type: ProteinKeep Linkouts: TKeep MBits: TMaximum file size: 524288000BSorting 2676410 sequencesWriting to VolumeDone Writing to DatabaseSorting 2677316 sequencesWriting to VolumeDone Writing to DatabaseAdding sequences from FASTA; added 6031291 sequences in 267.507 seconds.Sorting 677565 sequencesWriting to Vo