[Gate-users] Hello!

Wed Jun 22 05:24:51 CEST 2011

-------- Forwarding messages --------
From: yangmeng412721 <yangmeng412721 at 126.com>
Date: 2011-06-22 09:24:10
To: wugc <wuguocheng at neusoft.com>
Subject: Hello!
I have solved the problem which has stuck for several days. But there are any question. when I execute "make" successfully, there is a "Gate" in /home/administrator/Gate5/gate_v5.0.0.p01/bin/Linux-g++. go into this directory, I perform "./Gate" in the terminal. the following is the result:
  root at ubuntu:/home/administrator/Gate5/gate_v5.0.0_p01/bin/Linux-g++# ./Gate

*************************************************************
 Geant4 version Name: geant4-09-02-patch-04    (16-September-2010)
                      Copyright : Geant4 Collaboration
                      Reference : NIM A 506 (2003), 250-303
                            WWW : http://cern.ch/geant4
*************************************************************

/home/administrator/Gate5/gate_v5.0.0_p01/Materials.xml:1: parser error : Document is empty

^
/home/administrator/Gate5/gate_v5.0.0_p01/Materials.xml:1: parser error : Start tag expected, '<' not found

^
   GateMaterialDatabase: did not find the Materials.xml file: no properties read for material 'Air'
     This is only a problem when OPTICAL PHOTONS are transported in this material.'
Visualization Manager instantiating...
Visualization Manager initialising...
Registering graphics systems...

You have successfully registered the following graphics systems.
Current available graphics systems are:
  ASCIITree (ATree)
  DAWNFILE (DAWNFILE)
  G4HepRep (HepRepXML)
  G4HepRepFile (HepRepFile)
  RayTracer (RayTracer)
  VRML1FILE (VRML1FILE)
  VRML2FILE (VRML2FILE)
  OpenGLImmediateX (OGLIX)
  OpenGLStoredX (OGLSX)

Registering model factories...

You have successfully registered the following model factories.
Registered model factories:
  generic
  drawByCharge
  drawByParticleID
  drawByOriginVolume
  drawByAttribute

Registered filter factories:
  chargeFilter
  particleFilter
  originVolumeFilter
  attributeFilter

Time set to (s) 0

**********************************************************************
 GATE version name: gate_v5.0.0  (1-May-2009)                    
                    Copyright : OpenGATE Collaboration               
                    Reference : Phys. Med. Biol. 49 (2004) 4543-4561 
                    WWW : http://opengatecollaboration.healthgrid.org/
**********************************************************************

/control/saveHistory
/run/verbose 2
/event/verbose 1
/tracking/verbose 1
/gate/timing/setTime 0. s
Time set to (s) 0
/gate/application/setTimeSlice 1. s
PreInit>

I don't know whether gate is installed successfully, because there still some errors which I write in red. Will  these errors affect my future work? How I solve this problem?

At 2011-06-21 16:47:58，wugc <wuguocheng at neusoft.com> wrote:

Hi,yangmeng412721

I can try to control, but I’m not sure to login in your computer.

2011-06-21

发件人： yangmeng412721
发送时间： 2011-06-21  16:37:48
收件人： wugc
抄送：
主题： Hello!
can you use remote control my computer to help me correct the error?

At 2011-06-21 16:15:57，wugc <wuguocheng at neusoft.com> wrote:

Hi,yangmeng412721

Your right, there need export before PATH.

2011-06-21

发件人： yangmeng412721
发送时间： 2011-06-21  16:09:20
收件人： wugc
抄送：
主题： Re:Re: Re:Fw: Re: Re:Re: Hello! (yangmeng412721)
this is the photo of my folder. Can you give me the exact LD_LIBRARY_PATH and PATH variable .  In additon, is there no need to add "export" before PATH?

At 2011-06-21 16:01:28，wugc <wuguocheng at neusoft.com> wrote:

Hi,yangmeng412721

Just like follows,but not limit to.

PATH=$PATH:$HOME/bin:/home/admin/gate_instal/gate_v5.0.0
export  LD_LIBRARY_PATH=/home/admin/gate_instal/Root/lib:$LD_LIBRARY_PATH

2011-06-21

发件人： yangmeng412721
发送时间： 2011-06-21  15:54:16
收件人： wugc
抄送：
主题： Re:Fw: Re: Re:Re: Hello! (yangmeng412721)
The following is my .bashrc.sh. How I add LD_LIBRARY_PATH and PATH into it ?

# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

# don't put duplicate lines in the history. See bash(1) for more options
# ... or force ignoredups and ignorespace
HISTCONTROL=ignoredups:ignorespace

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "$debian_chroot" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
    # We have color support; assume it's compliant with Ecma-48
    # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
    # a case would tend to support setf rather than setaf.)
    color_prompt=yes
    else
    color_prompt=
    fi
fi

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

# If this is an xterm set the title to user at host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'
fi

# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'

# Add an "alert" alias for long running commands.  Use like so:
#   sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if [ -f /etc/bash_completion ] && ! shopt -oq posix; then
    . /etc/bash_completion
fi

At 2011-06-21 15:47:23，wugc <wuguocheng at neusoft.com> wrote:

Hi,

I encounter the problem, and I solved just as I told you last week, see below.

2011-06-21

发件人： wugc
发送时间： 2011-06-17 15:45:46
收件人： yangmeng412721
抄送：
主题： Re: Re:Re: Hello! (yangmeng412721)

Hi,yangmeng412721

I think you need to add the environment variables “$ LD_LIBRARY_PATH” in your build terminal or add the variables in your bashrc file.

Hope this can helps.

wugc
2011-06-17

发件人： yangmeng412721
发送时间： 2011-06-17  15:12:29
收件人： wugc
抄送：
主题： Re:Re: Hello! (yangmeng412721)
Hi, I have just tried it again as what you say,but it no use. And a new problem came out.the following is the error:

/usr/bin/ld: cannot find -lGpad
/usr/bin/ld: cannot find -lTree
/usr/bin/ld: cannot find -lRint
/usr/bin/ld: cannot find -lPostscript
/usr/bin/ld: cannot find -lMatrix
/usr/bin/ld: cannot find -lPhysics
/usr/bin/ld: cannot find -lMathCore
/usr/bin/ld: cannot find -lThread
collect2: ld returned 1 exit status
make: *** [bin/Linux-g++/Gate] 错误 1

Have you any good advice about it? thank you advance!

At 2011-06-16 17:23:21，wugc <wuguocheng at neusoft.com> wrote:

Hi,
maybe you can re-build the geant4, when you get the following information, you should select default.

"Activates the configuration setup for allowing plugins to

analysis tools based on AIDA (Astract Interfaces for Data

Analysis). In order to use AIDA features and compliant analysis

tools, the proper environment for these tools will have to be

set (see documentation for the specific analysis tools).

[n] n "

Good Luck！
Wugc
2011-06-16

Email：wuguocheng at neusoft.com 
发件人： gate-users-request
发送时间： 2011-06-16  17:10:34
收件人： gate-users
抄送：
主题： Gate-users Digest, Vol 61, Issue 11
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Today's Topics:
   1. Hello! (yangmeng412721)
   2. Re: Calculate Trues, Randoms and Scatter coincidences
      (giuseppe iaccarino)
----------------------------------------------------------------------
Message: 1
Date: Thu, 16 Jun 2011 15:19:54 +0800 (CST)
From: yangmeng412721 <yangmeng412721 at 126.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] Hello!
Message-ID:
<7367915a.164b6.13097520a76.Coremail.yangmeng412721 at 126.com>
Content-Type: text/plain; charset=GBK
Hello!
      I am a new user of GATE. I have compiled the clhep_v2.0.4.2, geant4.9.2.p04 and root_5.24 successfully. However, when I type "make"in the terminal , I got the errors as follows. And I have tried some solutions proposed on the mailing list , but it's no use.
/home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh: In member function ?void G4RunManager::SetRandomNumberStoreDir(G4String)?:
/home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:352: warning: ignoring return value of ?int system(const char*)?, declared with attribute warn_unused_result
Compiling GateVGeometryVoxelReader.cc ...
/bin/sh: aida-config: not found
Compiling GateVGeometryVoxelReaderMessenger.cc ...
/bin/sh: aida-config: not found
Compiling GateVGeometryVoxelStore.cc ...
/bin/sh: aida-config: not found
Compiling GateVGeometryVoxelStoreMessenger.cc ...
/bin/sh: aida-config: not found
Compiling GateVGeometryVoxelTranslator.cc ...
/bin/sh: aida-config: not found
Compiling GateVoxelBoxParameterization.cc ...
/bin/sh: aida-config: not found
......
......
ompiling GateTranslationMove.cc ...
/bin/sh: aida-config: not found
Compiling GateTranslationMoveMessenger.cc ...
/bin/sh: aida-config: not found
Compiling GateUIcmdWithAnIntegerAndADouble.cc ...
/bin/sh: aida-config: not found
Compiling GateUIcmdWithTwoDouble.cc ...
/bin/sh: aida-config: not found
Compiling GateUIcontrolMessenger.cc ...
/bin/sh: aida-config: not found
Compiling GateUIterminal.cc ...
/bin/sh: aida-config: not found
Compiling GateVisAttributesMessenger.cc ...
/bin/sh: aida-config: not found
Compiling GateVisManager.cc ...
/bin/sh: aida-config: not found
Compiling GateXMLDocument.cc ...
/bin/sh: aida-config: not found
source/management finished
Creating/replacing object files in ./tmp/Linux-g++/Gate/libGate.a ...
ar: creating ./tmp/Linux-g++/Gate/libGate.a
Compiling Gate.cc ...
/bin/sh: aida-config: not found
In file included from ./source/mandatory_G4_classes/include/GateRunManager.hh:46,
                 from Gate.cc:18:
/home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh: In member function ?void G4RunManager::SetRandomNumberStoreDir(G4String)?:
/home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:352: warning: ignoring return value of ?int system(const char*)?, declared with attribute warn_unused_result
Using granular libraries ...
Linking Gate
/bin/sh: aida-config: not found
/bin/sh: aida-config: not found
/usr/bin/ld: cannot find -lLMF
/usr/bin/ld: cannot find -lCore
/usr/bin/ld: cannot find -lCint
/usr/bin/ld: cannot find -lRIO
/usr/bin/ld: cannot find -lNet
/usr/bin/ld: cannot find -lHist
/usr/bin/ld: cannot find -lGraf
/usr/bin/ld: cannot find -lGraf3d
/usr/bin/ld: cannot find -lGpad
/usr/bin/ld: cannot find -lTree
/usr/bin/ld: cannot find -lRint
/usr/bin/ld: cannot find -lPostscript
/usr/bin/ld: cannot find -lMatrix
/usr/bin/ld: cannot find -lPhysics
/usr/bin/ld: cannot find -lMathCore
/usr/bin/ld: cannot find -lThread
/usr/bin/ld: cannot find -lLMF
/usr/bin/ld: cannot find -lecat
collect2: ld returned 1 exit status
make: *** [bin/Linux-g++/Gate] ?? 1
root at ubuntu:/home/administrator/Gate5/gate_v5.0.0_p01#
Any more help for the above issue will be appreciated!
Thank you very much advance.
------------------------------

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immediately notify the sender by return e-mail, and delete the original message and all copies from
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Confidentiality Notice: The information contained in this e-mail and any accompanying attachment(s)
is intended only for the use of the intended recipient and may be confidential and/or privileged of
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is strictly prohibited, and may be unlawful.If you have received this communication in error,please
immediately notify the sender by return e-mail, and delete the original message and all copies from
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Confidentiality Notice: The information contained in this e-mail and any accompanying attachment(s)
is intended only for the use of the intended recipient and may be confidential and/or privileged of
Neusoft Corporation, its subsidiaries and/or its affiliates. If any reader of this communication is
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