CUDAGPUBLASTinstallreadme.docx

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CUDAGPUBLASTinstallreadme.docx

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CUDAGPUBLASTinstallreadme.docx

CUDAGPUBLASTinstallreadme

CUDA、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@2.13GHz8核64位

内存8G；在硬盘中划了6G为swap区

GPU:

2块。

一块是QuadroFx380;另一块是TeslaC1060

OS：

CentOS6.064-bit

驱动程序和安装包：

到NVIDIA的官网上下载驱动、CUDAToolkit和CUDASDK

http:

//D

我下的是：

DeveloperDriversforLinux（270.41.19）64-bit

CUDAToolkitforRedHatEnterpriseLinux6.064-bit

GPUComputingSDK-Completepackageincludingallcodesamples

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

#init3

#cd/home/tanjun

#shdevdriver_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

#init5

驱动就安装完了

三、CUDAToolkit安装

#cd/home/tanjun

#shcudatoolkit_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/etc/profile.d目录下新建一个脚本文件cuda.sh，写入

exportLD_LIBRARY_PATH=/usr/local/cuda/lib64

exportPATH=/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

exportPATH=$PATH:

/usr/local/cuda/bin

exportLD_LIBRARY_PATH=$LD_LIBARARY_PATH:

/usr/local/cuda/lib64

重启、注销或者#source/etc/profile使设置生效，普通用户也需要source

3、在/etc/ld.so.conf.d目录下新建cuda.conf，写入;

/usr/local/cuda/lib64

/usr/local/cuda/lib

/（installpath）/qtsdk-2010.03/lib（这俩在需要用QT的时候才需要，否则QT将出错）

/（installpath）/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

#echo$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:

/root/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、CUDASDK的安装

#cd/home/tanjun

#shgpucomputingsdk_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、cannotfind–lglut

解决：

yuminstall*glu*

2、error:

builtin_types.h:

Nosuchfileordirectory

则是前面的环境变量/etc/profile没弄好，或者没有source/etc/profile使其生效

3、cannotfind–Ixi（orlXmu）

解决：

yuminstalllibXi-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

ThefollowingsequenceofcommandsareonaCentOS5.5withCUDA3.2.

ThestepscovertheinstallationofGPU-BLAST,theformattingandsortingofa

databaseandtheexecutionofaGPU-BLASTsearch.

Theloginshellisbash.

1.a）AddingGPUfunctionalitytoanexistinginstallationofNCBI-BLAST.

ThedirectoryoftheexistinginstallationofNCBI-BLASTis"blast"

[pvouzis@eratosthenesblast]$ls

ncbi-blast-2.2.25+-src

[pvouzis@eratosthenesblast]$wgethttp:

//eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

--2010-10-1913:

02:

07--http:

//eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

Resolvingeudoxus.cheme.cmu.edu...128.2.55.71

Connectingtoeudoxus.cheme.cmu.edu|128.2.55.71|:

80...connected.

HTTPrequestsent,awaitingresponse...200OK

Length:

316399（309K）[application/x-gzip]

Savingto:

`gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz'

100%[====================================================================================================================>]316,399--.-K/sin0.03s

2010-10-1913:

02:

08（11.2MB/s）-`gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz'saved[316399/316399]

[pvouzis@eratosthenesblast]$ls

gpu-blast-1.0_ncbi-blast-2.2.25.tar.gzncbi-blast-2.2.25+-src

[pvouzis@eratosthenesblast]$tar-xzfgpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

[pvouzis@eratosthenesblast]$ls

gpu_blastgpu-blast-1.0_ncbi-blast-2.2.25.tar.gzinstallncbi-blast-2.2.25+-srcqueriesREADME

[pvouzis@eratosthenesblast]$sh./installncbi-blast-2.2.25+-src

DoyouwanttoinstallGPU-BLASTonanexistinginstallationof"blastp"[yes/no]

yes:

youwillbeaskedfortheinstallationdirectoryofthe"blastp"executable

no:

willdownloadandinstall"ncbi-blast-2.2.25+-src"

yes

Pleaseinputtheinstallationdirectoryof"blastp"of"ncbi-blast-2.2.25+-src"

/home/pvouzis/Documents/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin

"blastp"version2.2.25+iscompatible

ContinuingwiththeinstallationofGPU-BLAST...

ModifyingNCBI-BLASTfiles

CompilingCUDAcode

BuildingNCBI-BLASTwithGPU-BLAST

........................................................................................................................................................................................................................................................................（如果网络比较差的话，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）DownloadingtheNCBI-BLASTsourcecodeandaddingGPUfunctionality.

[pvouzis@eratosthenesblast]$wgethttp:

//eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

--2010-10-1912:

37:

01--http:

//eudoxus.cheme.cmu.edu/gpublast/gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

Resolvingeudoxus.cheme.cmu.edu...128.2.55.71

Connectingtoeudoxus.cheme.cmu.edu|128.2.55.71|:

80...connected.

HTTPrequestsent,awaitingresponse...200OK

Length:

316399（309K）[application/x-gzip]

Savingto:

“gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz”

100%[=====================================================================================================================================================>]316,399--.-K/sin0.03s

2010-10-1912:

37:

01（11.3MB/s）-“gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz”saved[316399/316399]

[pvouzis@eratosthenesblast]$ls

gpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

[pvouzis@eratosthenesblast]$tar-xzfgpu-blast-1.0_ncbi-blast-2.2.25.tar.gz

[pvouzis@eratosthenesblast]$ls

gpu_blastgpu-blast-1.0_ncbi-blast-2.2.25.tar.gzinstallqueriesREADME

[pvouzis@eratosthenesblast]$sh./installncbi-blast-2.2.25+-src

DoyouwanttoinstallGPU-BLASTonanexistinginstallationof"blastp"[yes/no]

yes:

youwillbeaskedfortheinstallationdirectoryofthe"blastp"executable

no:

willdownloadandinstall"ncbi-blast-2.2.25+-src"

Continuingwiththedownloadingofncbi-blast-2.2.25+-src...

DownloadingNBCIBLAST

--2010-10-1912:

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”

Resolvingftp.ncbi.nlm.nih.gov...130.14.29.30

Connectingtoftp.ncbi.nlm.nih.gov|130.14.29.30|:

21...connected.

Logginginasanonymous...Loggedin!

==>SYST...done.==>PWD...done.

==>TYPEI...done.==>CWD

（1）/blast/executables/blast+/LATEST...done.

==>SIZEncbi-blast-2.2.25+-src.tar.gz...11482581

==>PASV...done.==>RETRncbi-blast-2.2.25+-src.tar.gz...done.

Length:

11482581（11M）（unauthoritative）

100%[=====================================================================================================================================================>]11,482,5816.80M/sin1.6s

2010-10-1912:

41:

57（6.80MB/s）-“ncbi-blast-2.2.25+-src.tar.gz”saved[11482581]

ExtractingNCBI-BLAST

...

Configuringncbi-blast-2.2.25+-srcwithoptions:

./configure--without-debug--with-mt--without-sybase--without-ftds--without-fastcgi--without-fltk--without-wxwin--without-ncbi-c--without-sssdb--without-sss--without-geo--without-sp--without-orbacus--without-boost

Ifyouwanttochangetheseoptionseditthefile"install",deletethedirectoryncbi-blast-2.2.25+-src,andreruninstall

....................

ModifyingNCBI-BLASTfiles

CompilingCUDAcode

BuildingNCBI-BLASTwithGPU-BLAST

[pvouzis@eratosthenesblast]$ls

configure.outputgpu-blast-1.0_ncbi-blast-2.2.25.tar.gzinstallncbi-blast-2.2.25+-srcncbi_blast.outputREADME

gpu_blastgpu_blast.outputmodify.outputncbi-blast-2.2.25+-src.tar.gzqueries

2）Downloadingandsortingtheenv_nrdatabase.

[pvouzis@eratosthenesblast]$mkdirdatabase/

[pvouzis@eratosthenesblast]$cddatabase/

[pvouzis@eratosthenesdatabase]$wgetftp:

//ftp.ncbi.nlm.nih.gov/blast/db/FASTA/env_nr.gz

--2010-10-0421:

12:

25--ftp:

//ftp.ncbi.nlm.nih.gov/blast/db/FASTA/env_nr.gz

=>`env_nr.gz'

Resolvingftp.ncbi.nlm.nih.gov...130.14.29.30

Connectingtoftp.ncbi.nlm.nih.gov|130.14.29.30|:

21...connected.

Logginginasanonymous...Loggedin!

==>SYST...done.==>PWD...done.

==>TYPEI...done.==>CWD/blast/db/FASTA...done.

==>SIZEenv_nr.gz...827145187

==>PASV...done.==>RETRenv_nr.gz...done.

Length:

827145187（789M）

100%[====================================================================================================================>]827,145,1876.14M/sin87s

2010-10-0421:

13:

54（9.02MB/s）-`env_nr.gz'saved[827145187]

[pvouzis@eratosthenesdatabase]$gunzipenv_nr.gz

[pvouzis@eratosthenesdatabase]$cd../ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin/

[pvouzis@eratosthenesbin]$./makeblastdb-in../../../../database/env_nr-out../../../../database/sorted_env_nr-sort_volumes-max_file_sz500MB

BuildinganewDB,currenttime:

10/04/201021:

16:

NewDBname:

../../../../database/sorted_env_nr

NewDBtitle:

../../../../database/env_nr

Sequencetype:

Protein

KeepLinkouts:

KeepMBits:

Maximumfilesize:

524288000B

Sorting2676410sequences

WritingtoVolume

DoneWritingtoDatabase

Sorting2677316sequences

WritingtoVolume

DoneWritingtoDatabase

AddingsequencesfromFASTA;added6031291sequencesin267.507seconds.

Sorting677565sequences

WritingtoVo

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