李继飞做的GATE安装指南

1、为了使用pet仿真平台，我装了大约一周，主要是中间出现各种问题，幸好可以借助google，baidu，以及那些先贤们的blog，终于历尽千辛万苦，成功攻克这一难题，仅以此文帮助那些后来者，本文包括如何安装clhep，安装geant4，安装root等等。其中geant4部分主要借鉴了这样一篇文章在ubuntu10.04.1下安装geant4作者陶仕达等。总体来说pet仿真平台的安装更需要以下几篇文章基于 gate 的 pet 仿真环境的实现与应用-张斌以及官网下载的gateinstallation guide。另外文中很多问题是我遇到的，希望可以帮助你们！2012.07.19上海大学430实验室

2、-李继飞我开始是用的ubtuntu10.04.1版本，把仿真平台装好后又升级到unbuntu12.04 lts版本，我升级后发现一个问题，新版本的新立得包管理器竟然找不到从哪里用，恕我不才，至今不会用。所以老老实实的按照在ubuntu10.04.1下安装geant4来做就可以，等一切ok之后，再升级到ubuntu 12.04 lts版本。有的地方需要用管理员权限#来安装，否则会因权限不够，导致出现错误，到时候用命令sudo-i进入root#第一、安装gate运行所必须的支撑库文件即安装基本编译环境：1. 安装基本编译环境sudo apt-get install build-essential2

3、.安裝 opengl librarysudo apt-get install libgl1-mesa-dev3. 安裝 opengl utilitiessudo apt-get install libglu1-mesa-dev4. 安装 sudo apt-get install libxt-dev不装这个包在编译 geant4 时会报 error: x11/intrinsic.h: no such file or directory 的错误。5. 安装 libxmu。打开新立得软件包管理器,查找 libxmu。把找到的七项全装上。（这里ubuntu10.04.1就有新立得包管理器，而12.04

4、就不能用，不知道为什么？）6. 安装 sudo apt-get install libxi-dev7. 确认系统已经安装了gcc：（ubuntu默认是已经安装的，我们这里只是确认一下它是哪个版本的，不太低就好）gcc -v第二、配置root运行的相关文件库，尤其是系统字体库，否则后面运行root时会出现：couldnt find font -adobe-helvetica-medium-r-*-*-10-*-*-*-*-*-iso8859-1,trying fixed. please fix your system so helvetica can be found,this font typ

5、ically is in the rpm (or pkg equivalent) packagexfree86-75,100dpi-fonts or fonts-xorg-75,100dpi，这个问题我可是费了好大功夫才解决，这里特别感谢远在海外的邵立晶博士的指导！1. install xfs and xfstt:命令为 sudo apt-get install xfs xfstt2. install the following fonts: 命令为sudo apt-get install t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-n

6、onfree-syriac xfonts-75dpi xfonts-100dpi 也就是下面四个系统字体 t1-xfree86-nonfree 即- non-free postscript type 1 fonts from xfree86 ttf-xfree86-nonfree 即- non-free truetype fonts from xfree86 ttf-xfree86-nonfree-syriac 即- non-free syriac opentype fonts from xfree86 xfonts-75dpi 即- 75 dpi fonts for x xfonts-100

7、dpi 即- 100 dpi fonts for x第三、安装clhep，血淋淋的教训呀！一定要一开始就把它装在geant4（我自己新建的文件夹）这个文件夹下到以下网站下载 clhep 数据包。http:/proj-clhep.web.cern.ch/proj-clhep/distribution/clhep.html，我下载的是版本1把下载的数据包放到某个文件夹例如home/fei/geant42解压clhep-.tgzcd /home/fei/geant4tar -zxvf clhep-.tgz成功安装会显示/clhep/vector

8、/configure/clhep/config.guess/clhep/config.sub/clhep/makefile.in/clhep/configure3 进入你解压出来的文件夹配置环境。命令如下:首先获取权限，因为是make和make install需要权限sudo -icd /home/fei/geant4//clhep./configure -prefix=/home/fei/geant4/clhep（这个地方要根据你想把clhep所装的位置来设置,这里的clhep是运行命令后自动产生的新目录，也就是我们的cl

9、hep安装目录，一会会用到该目录,注意绝对不能是//clhep，否则会出错）,大约一分钟成功安装会显示config.status: creating test/exctest4.shconfig.status: creating test/exctestnothrow.shconfig.status: creating test/excdblthrow.shconfig.status: creating exceptions/defs.hconfig.status: executing depfiles commands4 编译clhepmake大约三分钟，成功编译会显示rm -

10、f libclhep-.aliblist=./getobjectlist -static units vector evaluator genericfunctions geometry random matrix randomobjects cast refcount exceptions; ar cru libclhep-.a $liblist; ranlib libclhep-.arm -f libclhep-.soliblist=./getobjectlist -shared units vector evaluator gene

11、ricfunctions geometry random matrix randomobjects cast refcount exceptions; g+ -o -ansi -pedantic -wall -d_gnu_source -g -o2 -o libclhep-.so -shared -wl,-no-undefined -wl,-soname,libclhep-.so $liblist -o libclhep-.so./build-headermake1:正在离开目录 /home/fei/geant4//clhep5 安装cl

12、hepmake install成功安装会显示test -z /home/fei/geant4/clhep/include/clhep | mkdir -p - /home/fei/geant4/clhep/include/clhepif test -f clhepversion.h; then echo /usr/bin/install -c -m 644 clhepversion.h /home/fei/geant4/clhep/include/clhep/clhepversion.h; /usr/bin/install -c -m 644 clhepversion.h /home/fei/

13、geant4/clhep/include/clhep/clhepversion.h; else :; fi /usr/bin/install -c -m 644 clhepversion.h /home/fei/geant4/clhep/include/clhep/clhepversion.hmake2: 没有什么可以做的为 install-data-am。（这一句没有关系，呵呵，看到也不要担心）make2:正在离开目录 /home/fei/geant4//clhepmake1:正在离开目录 /home/fei/geant4//clhep这样，我在/home/fei

14、/geant4/clhep目录里看到include和lib两个目录，表示clhep安装成功。那么我的clhep安装路径就是/home/fei/geant4/clhep，到时我们会用到这个路径注意用命令exit退出终端第四、下载安装geant4重新进入终端1. 到以下网站下载你所需的数据包 。http:/geant4.web.cern.ch/geant4/，在soucefiles选择所需版本2. 解压 geant4.9.3.p02.tar.gz。把下载的压缩包解压到某一个文件夹。cd /home/fei/geant4tar -zxvf geant4.9.3.p02.tar.gz成功解压会显示ge

15、ant4.9.3.p02/source/visualization/modeling/src/g4trajectoryparticlefilter.ccgeant4.9.3.p02/source/visualization/modeling/src/g4vmodel.ccgeant4.9.3.p02/source/visualization/modeling/src/g4vtrajectorymodel.ccgeant4.9.3.p02/source/visualization/modeling/src/g4vistrajcontext.cc3. 另外在data里下载各种data files（

16、我是下载了所有的data files ，管它是干什么用的呢），在你 geant4.9.3.p02 文件夹里新建一个名为data 的文件夹,把下载的 g4emlow.6.9.tar.gz等数据包（我下载了7个包）放进去,逐个解压(其他数据包同理)。解压命令如下:cd /geant4.9.3.p02/datatar -zxvf g4emlow.6.9.tar.gz然后重复，一直把这七个包都解压完。成功解压会显示g4emlow6.9/tripdata/pp-trip-cs-95.datg4emlow6.9/tripdata/pp-trip-cs-96.datg4emlow6.9/tripdata/p

17、p-trip-cs-97.datg4emlow6.9/tripdata/pp-trip-cs-98.datg4emlow6.9/tripdata/pp-trip-cs-99.dat接着逐个解压其他的data文件4. 配置环境：进入 geant4.9.3.p02 文件夹配置环境。命令如下:cd /home/fei/geant4/geant4.9.3.p02./configure -build回答问题。输入以上两条命令按回车后,你将在终端被问一系列问题,除以下两个问题外,全部采用默认设置。问题一:when it asks:enable building of the x11 opengl visu

18、alization driver? nenter: ythis tells geant4 that you want to include the optional opengl visualizationdriver.问题二:when it asks:enable building of the x11 raytracer visualization driver? nenter: ythis tells geant4 that you want to include the optional raytracerx visualizationdriver.如果问找不到clhep，则手动输入为

19、/home/fei/geant4/clhep,也就是包括lib和inclde文件的那个目录其他的就一顿enter就可以，只要出问题答案不对，它会提示你的，而且就自动停止，直到你解决问题。问题回答完后,终端将显示如下内容press enter to start installation or use a shell escape to editconfig.sh:5. 安装geant4 按下回车，开始安装，这时在终端可以看到now starting geant4 libraries build.当你看到以下内容的时候,我又要恭喜你,你的编译已经成功开始了。内容如下:compiling g4all

20、ocatorpool.cc .即使看到一大堆warning也不要紧，它是由gcc编译器本身引起的，直接忽视，不会有影响的！6. 安装成功，继续等上个 40 分钟左右,如果你看到以下内容的话,恭喜你,你的 geant4 至此已经安装成功了。当然你不必坐在电脑前干等,插上电源线,趁机去洗个衣服或吃个饭什么的都行。大爷的，我怎么没早看到，白白坐了半天。另外务必注意，不要随便动终端，血的教训呀，我装了大概30分钟时，切换qq，不知怎么回事鼠标切到终端里了，结果悲剧呀编译暂停，害我又重新装了40分钟！安装成功会显示：# your geant4 installation seems to be succe

21、ssful! # to be sure please have a look into the log file: # /home/fei/geant4/geant4.9.3.p02/.config/bin/linux-g+/g4make.log #第五、运行应用程序1. 创建geant4脚本，命令如下./configure会看到以下内容 - geant4 toolkit installation - (setting environments for user )-the geant4 toolkit installation was found.the files env.csh will

22、 be copied to your current directory.for setting geant4 environments you should make:source env.cshor. env.shit will also check g4workdir setting and set it toyour home if needed.you can use these files also for further modifications(adding your own environments).-这样,你将在home/fei/geant4/geant4.9.3.p0

23、2目录下看到两个文件env.sh 和 env.csh 两个文件2. 创建geant4工作目录：首先创建一个文件夹命名为g4work,注意不要放在geant4的安装目录geant4.9.3.p02里。g4work将作为我们geant4的工作目录，这样做是为了防止破坏原始geant4的安装目录。在终端命令如下export g4workdir=/home/fei/geant4/g4work3. 把应用程序复制到工作目录：这里选择a01，直接在终端敲入命令如下cp -r /home/fei/geant4/geant4.9.3.p02/examples/extended/analysis/a01 $g4

24、workdir/a01，这里务必要注意$前面有一个空格，否则会出现cp: 在/home/fei/geant4/geant4.9.3.p02/examples/extended/analysis/a01/home/fei/g4work/a01 后缺少了要操作的目标文件请尝试执行cp -help来获取更多信息。完成以后，我们在/home/fei/g4work就可以看到复制的应用文件a01.4. 配置应用程序运行环境。注意,每次在一个新终端运行应用程序时你都应该做这一步。命令如下:export g4workdir=/home/fei/geant4/g4workexport ld_library_pa

25、th=/home/fei/geant4/clhep/lib/:$ld_library_pathsource /home/fei/geant4/geant4.9.3.p02/env.sh备注（我们装geatn4其实是为了一会装应用gate-v6.1，所以配置环境变量这一步以后用gate的时候不用每次在终端输入，到时有专门的环境配置文件来做，一会就会讲到。不过这里我们来检验geatn4是否安装成功的时候，还是需要每次都这样做的。）it will respond:on this machine the g4system=linux-g+on this machine the g4install=/h

26、ome/fei/geant4/geant4.9.3.p02on this machine the g4lib=/home/fei/geant4/geant4.9.3.p02/libon this machine the g4levelgammadata=/home/fei/geant4/geant4.9.3.p02/data/photonevaporation2.0on this machine the g4radioactivedata=/home/fei/geant4/geant4.9.3.p02/data/radioactivedecay3.2on this machine the g4

27、ledata=/home/fei/geant4/geant4.9.3.p02/data/g4emlow6.9on this machine the g4neutronhpdata=/home/fei/geant4/geant4.9.3.p02/data/g4ndl3.13on this machine the g4abladata=/home/fei/geant4/geant4.9.3.p02/data/g4abla3.0on this machine the g4realsurfacedata=/home/fei/geant4/geant4.9.3.p02/data/realsurface1

28、.0on this machine the clhep_base_dir=/home/fei/geant4/clhepon this machine the clhep_include_dir=/home/fei/geant4/clhep/includeon this machine the clhep_lib_dir=/home/fei/geant4/clhep/libon this machine the clhep_lib=clhepon this machine the g4ui_use_tcsh=1on this machine the g4vis_build_openglx_dri

29、ver=1on this machine the g4vis_build_raytracerx_driver=1on this machine the g4vis_use_openglx=1on this machine the g4vis_use_raytracerx=1on this machine the xmflags=on this machine the xmlibs=on this machine the xmflags=on this machine the xawflags=on this machine the xawlibs=on this machine the g4l

30、ib_build_shared=15. 编译程序，进入你的应用程序文件夹编译程序，终端输入命令cd $g4workdir/a01make如果成功则显示creating shared library /home/fei/geant4/g4work/tmp/linux-g+/a01app/liba01app.so .compiling a01app.cc .using global libraries .linking a01app. done!6. 运行生成的可执行文件。命令如下:$g4workdir/bin/linux-g+/a01app你将在终端看到如下内容:chamber2physical

31、0 chamber2logical 1 argongas wireplane2physical0 wireplane2logical 0 argongas /chamber2 chamber2physical1 chamber2logical 1 argongas wireplane2physical0 wireplane2logical 0 argongas /chamber2 chamber2physical2 chamber2logical 1 argongas wireplane2physical0 wireplane2logical 0 argongas /chamber2 cham

32、ber2physical3 chamber2logical 1 argongas wireplane2physical0 wireplane2logical 0 argongas /chamber2 chamber2physical4 chamber2logical 1 argongas wireplane2physical0 wireplane2logical 0 argongas /chamber2 emcalorimeterphysical0 emcalorimeterlogical 1 csi cellphysical-1 celllogical 0 csi /emcalorimete

33、r hadcalorimeterphysical0 hadcalorimeterlogical 1 lead hadcalcolumnphysical-1 hadcalcolumnlogical 1 lead hadcalcellphysical-1 hadcalcelllogical 1 lead hadcallayerphysical-1 hadcallayerlogical 1 lead hadcalscintiphysical0 hadcalscintilogical 0 scintillator /hadcalorimeteridle 7. 打开视窗,查看你定义的几何模型。即在“id

34、le”后输入以下命令:/vis/open oglix/vis/drawvolume你将在一个新窗口看到如下图形,这里省略了。8. 查看粒子径迹和粒子碰撞过程。即在终端继续输入如下命令:/vis/scene/add/trajectories/vis/scene/add/hits/run/beamon 1图略9. 运行完毕退出,命令：exit第六、安装root(这几个是我在root网张上看得，说是安装root需要的一些基本编译环境，所以我就安装了，具体什么用我也不清楚，貌似没多大用处，因为本身ubuntu里已经默认安装好了大部分)sudo apt-get install subversionsud

35、o apt-get install libx11-devsudo apt-get install libxpm-devsudo apt-get install libxft-devsudo apt-get install libxext-dev1. 到下述网站下载root安装包http:/root.cern.ch/drupal/，我下载的是root_v5.34.01.source.tar.gz，而并不用binary版本一是因为太大，二是因为安装好像不太方便。把安装包放到/home/fei/geant4中2. 打开终端输入，并解压文件cd /home/fei/geant4tar -xvzf ro

36、ot_v5.34.01.source.tar.gz3. 编译获取权限sudo -icd /home/fei/geant4/root_v5.34.01(这里我把解压后产生的文件夹root重命名为root_v5.34.01，这是为了下一步预编译产生一个新的root安装目录)./configure -prefix=/home/fei/geant4/root（注意这里为什么更改root为root_v5.34.01呢？原因是安装目录和解压后的文件目录如果放在一块，会发生错误库文件调用，引起很大的麻烦）成功会显示enabled support for asimage, astiff, builtin_af

37、terimage, builtin_ftgl, builtin_glew, builtin_pcre, builtin_lzma, cintex, explicitlink, genvector, memstat, opengl, reflex, shadowpw, shared, tmva, x11, xft, xml.to build root type: make make install4. make大约30分钟，如顺利则显示cp /home/fei/geant4/root_v5.34.01/cint/reflex/python/genreflex/genrootmap.py lib/

38、python/genreflex/genrootmap.pycp /home/fei/geant4/root_v5.34.01/cint/reflex/python/genreflex/selclass.py lib/python/genreflex/selclass.py = = root build successful. = = run make install now. = =5. make install成功会显示 = = root build successful. = = run make install now. = =installing binaries in /home/

39、fei/geant4/root/bininstalling libraries in /home/fei/geant4/root/lib/rootinstalling headers in /home/fei/geant4/root/include/rootinstalling /home/fei/geant4/root_v5.34.01/main/src/rmain.cxx in /home/fei/geant4/root/include/rootinstalling cint/cint/include cint/cint/lib and cint/cint/stl in /home/fei

40、/geant4/root/lib/root/cintinstalling icons in /home/fei/geant4/root/share/root/iconsinstalling fonts in /home/fei/geant4/root/share/root/fontsinstalling misc docs in /home/fei/geant4/root/share/doc/rootinstalling tutorials in /home/fei/geant4/root/share/doc/root/tutorialsinstalling tests in /home/fe

41、i/geant4/root/share/doc/root/testinstalling macros in /home/fei/geant4/root/share/root/macrosinstalling man(1) pages in /home/fei/geant4/root/share/man/man1installing config files in /etc/rootinstalling autoconf macro in /home/fei/geant4/root/share/aclocalinstalling emacs lisp library in /home/fei/g

42、eant4/root/share/emacs/site-lispinstalling gdml conversion scripts in /home/fei/geant4/root/lib/root6. 配置root环境变量add bin/ to path and lib/ to ld_library_path.即添加路径，直接在终端输入下列命令:. bin/thisroot.sh(注意是. bin/thisroot.sh,里面有个点)退出终端重新进入7. 运行root看是否成功安装source /home/fei/geant4/root/bin/thisroot.shroot会看到 fei

43、ubuntu:$ source /home/fei/geant4/root/bin/thisroot.shfeiubuntu:$ root * * * * w e l c o m e to r o o t * * * * version 5.34/01 13 july 2012 * * * * you are welcome to visit our web site * * http:/root.cern.ch * * * *root 5.34/01 (tags/v5-34-0145048, jul 13 2012, 15:31:31 on linux)cint/root c/c+ inte

44、rpreter version 5.18.00, july 2, 2010type ? for help. commands must be c+ statements.enclose multiple statements between .root 0 强制关掉终端开始下一步第七、安装gate1.首先安装ecat和lmf（什么用处，目前我还不知道），下载/installinggate放到文件夹geant4中后，解压缩，命令：cd /home/fei/geant4tar -xvzf ecat.tar.gzsudu -icd

45、 /home/fei/geant4/ecatmake会看到 ar r libecat.a crash.o make3dfilter.o makefilter.o matpkg.o matrix_extra.o matrix.o matrix_xdr.o sino_dets.o machine_indep.o matrix_64.o convert_64.o convert_70.o rts_cmd.o rfa_xdr.o matrix_slice.o ecat_model.o plandefs.o interfile.o analyze.o num_sort.o save_volume7.o

46、load_volume7.oar: creating libecat.a然后命令：make install 会看到chmod -r 700 ./ecat_7mkdir -p ./ecat_7/lib/linux-g+mkdir -p ./ecat_7/includerm -rf ./ecat_7/lib/linux-g+/*rm -rf ./ecat_7/include/*cp *.a ./ecat_7/lib/linux-g+/cp *.h ./ecat_7/include/chmod -r 555 ./ecat_72. 安装lmf,（好像也是从上面ecat那个网站下载的，反正，这个包很容易

47、找的，具体哪个版本不做要求）解压,命令：cd /home/fei/geant4tar -zvxf lmf_v3.0.tar.gzsudu -i获取权限cd /home/fei/geant4/lmf_v3.0./configure会显示#ifndef _format_for_lmf_#define _format_for_lmf_typedef char i8;typedef unsigned char u8;typedef short i16;typedef unsigned short u16;typedef long i32;typedef unsigned long u32;typede

48、f unsigned long long int u64;typedef long long int i64;#endif命令：make为什么显示etags src/*.c,cc includes/*.h,hh/bin/sh: etags: not foundmake: * tags 错误 127？（对后面好像没什么影响）命令：make install 会显示chmod -r 700 ./lmf_3.0mkdir -p ./lmf_3.0/libmkdir -p ./lmf_3.0/includesrm -rf ./lmf_3.0/./lib/liblmf.a rm -rf ./lmf_3.0

49、/includes/*cp ./lib/liblmf.a ./lmf_3.0/./lib/liblmf.a cp includes/* ./lmf_3.0/includes/chmod -r 555 ./lmf_3.03. 安装gate：从该网站下载安装包gate_v6.1/2.把它放到目录/home/fei/geant4中，解压cd /home/fei/geant4tar -xvzf gate_v6_1_tar_gz_98524.gz4. 设置安装前的环境变量：用文本编辑器打开目录gate_v6.1里的env_gate.s

50、h文件在该文件头部粘贴export g4workdir=/home/fei/geant4/g4work（注意这个文件夹是我自己新建的用来当作gate的工作目录）export gatehome=/home/fei/geant4/gate_v6.1（注意这个地址是gate的安装地址）export g4install=/home/fei/geant4/geant4.9.3.p02（这个是geant4的安装地址）export g4version=9.3（这个版本号要看你装得是哪个版本，必须跟你安装的版本一致，我装的是geant4.933.p02,所以用写9.3就可以，目前最新的geant4版本是9.5

51、）export rootsys=/home/fei/geant4/root（注意不是解压产生的那个目录root5.34.01（就是被我重命名的那个文件夹），而是我安装的root目录）export ld_library_path=$ld_library_path:$rootsys/lib:/home/fei/geant4/clhep/lib(它是指定动态链接库，指向clhep和root的安装目录文件库)export path=$path:$rootsys/lib:$gatehome/bin/$g4system(它可以使我们从终端的任意目录下运行gate和root)保存后，退出5. 然后在终端里运

52、行source /home/fei/geant4/gate_v6.1/env_gate.sh会显示checking your path variable. = ok: /home/fei/geant4/gate_v6.1/bin/linux-g+ added to your path variablechecking your ld_library_path variable. = ok: /home/fei/geant4/gate_v6.1/tmp/linux-g+/gate added to your path variableg4version9_3 is set: gate is co

53、mpatible with the geant4 version 9.3 and 9.4done6. 安装cd /home/fei/geant4/gate_v6.1make成功会显示source/physics finishedcreating shared library tmp/linux-g+/gate/libgate.so .compiling gate.cc .using global libraries .linking gate. done!第八、运行gate1. source /home/fei/geant4/root/bin/thisroot.sh(这个是配置root运行的环境变量，如果不配置，gate也不能用，会出现gate: error while loading shared libraries: libcore.so: cannot open shared object file: no such file or directory)2. source /home/fei/geant4