Kyle and Dan Build Notes

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Kyle's Generic Notes

Typos

on http://clasweb.jlab.org/wiki/index.php/UNH_Sim12_Setup. In the second to last dashed-line box, it says $XERCESROOT rather than $XERCESCROOT

Nuances

Never ever use ~ in paths. Use absolute paths to be sure.

Sim12 Notes

Could use a redraw button, or redraw on window focus.

Kyle's Build Notes

CLHEP SETUP

  1. Download CLHEP - good (http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/distributions/clhep-2.0.3.1.tgz)
  2. tar -xzvf clhep-2.0.3.1.tgz - good
  3. changed wd to ~/CLAS12/Sim12/CLHEP/2.0.3.1/CLHEP
  4. ./configure --prefix=/net/home/kyle/Sim12/CLHEP - good
  5. make (CLHEP) - good
  6. make install (CLHEP) - good
  7. export CLHEPROOT="/net/home/kyle/CLAS12/Sim12/CLHEP" - good


XERCES-C SETUP

  1. Download XERCES-C - good (http://apache.mirror99.com/xerces/c/sources/xerces-c-src_2_8_0.tar.gz)
  2. tar -xzvf xerces-c-src_2_8_0.tar.gz - good
  3. export XERCESCROOT="/net/home/kyle/CLAS12/Sim12/XERCESC" - good
  4. cd to (XERCESCROOT)/xerces-c-src_2_8_0.tar.gz/src/xercesc
  5. ./runConfigure -plinux -cgcc -xg++ - good
  6. make (.../xercesc) - failed compiletime for Abstract DOMParser.o, several errors.

Missing header files: 

AbstractDOMParser.cpp:46:44: xercesc/dom/impl/DOMAttrImpl.hpp: No such file or directory
AbstractDOMParser.cpp:47:48: xercesc/dom/impl/DOMTypeInfoImpl.hpp: No such file or directory
AbstractDOMParser.cpp:50:44: xercesc/dom/impl/DOMTextImpl.hpp: No such file or directory
AbstractDOMParser.cpp:51:48: xercesc/dom/impl/DOMDocumentImpl.hpp: No such file or directory
AbstractDOMParser.cpp:52:52: xercesc/dom/impl/DOMDocumentTypeImpl.hpp: No such file or directory
AbstractDOMParser.cpp:54:49: xercesc/dom/impl/DOMElementNSImpl.hpp: No such file or directory
AbstractDOMParser.cpp:55:46: xercesc/dom/impl/DOMEntityImpl.hpp: No such file or directory
AbstractDOMParser.cpp:56:55: xercesc/dom/impl/DOMEntityReferenceImpl.hpp: No such file or directory
AbstractDOMParser.cpp:57:48: xercesc/dom/impl/DOMNotationImpl.hpp: No such file or directory
AbstractDOMParser.cpp:60:61: xercesc/dom/impl/DOMProcessingInstructionImpl.hpp: No such file or directory
AbstractDOMParser.cpp:61:45: xercesc/dom/impl/DOMNodeIDMap.hpp: No such file or directory
AbstractDOMParser.cpp:62:41: xercesc/dom/impl/DOMCasts.hpp: No such file or directory
AbstractDOMParser.cpp: In member function `void xercesc_2_8::AbstractDOMParser::cleanUp()':

need to export XERCESCROOT="/net/home/kyle/CLAS12/Sim12/XERCESC/xerces-c-src_2_8_0", my install directory.

  1. ./runConfigure -plinux -cgcc -xg++ - good
  2. make - good


DAWN

  1. Downloaded and extracted dawn into a directory. (http://geant4.kek.jp/%7Etanaka/DAWN/About_DAWN.html)
  2. make - good


GEANT4

  1. Downloaded and extracted geant4 and data files
  2. compiled geant4 - no problem
  3. make physics_list stuff...

had to assign many enviroment variables

make script failing

using absolute path rather than path from ~, makefile doesn't read relative paths correctly.

eg: 

CLHEPROOT=/net/home/kyle/CLAS12/Sim12/CLHEP
CLHEP_BASE_DIR=/net/home/kyle/CLAS12/Sim12/CLHEP
XERCESCROOT=/net/home/kyle/CLAS12/Sim12/XERCESC
G4WORKDIR=/net/home/kyle/CLAS12/Sim12/workDIR
CLHEP_LIB=/net/home/kyle/CLAS12/Sim12/CLHEP/lib

creating working directory:

  • export G4WORKDIR="/net/home/kyle/CLAS12/Sim12/workDIR"


Evio

Download site no longer active

  1. cp from /net/data/taro/maurik/evio
  2. make clean
  3. make - good
  4. export EVIOROOT="/net/home/kyle/CLAS12/Sim12/evio"


HDDS

  • cp maurik's HDDS files from /net/data/taro/maurik/HDDS

needs G4INSTALL defined

  1. export G4INSTALL="/net/home/kyle/CLAS12/Sim12/geant4.9.0.p01"
  2. make clean
  3. make - good!
  4. export HDDSROOT="/net/home/kyle/CLAS12/Sim12/HDDS"


JGEANT4

  1. cd to Sim12 directory
  2. svn checkout https://phys12svn.jlab.org/repos/trunk/src/JGeant4/
  3. export G4WORKDIR="/net/home/kyle/CLAS12/Sim12/JGeant4"
  4. make - good!
  5. export JGEANT4ROOT="/net/home/kyle/CLAS12/Sim12/JGeant4"
  6. export G4WORKDIR="/net/home/kyle/CLAS12/Sim12/workDIR"


Sim12

Enviroment variables: 

[kyle@parity JGeant4]$ echo $XERCESCROOT
/net/home/kyle/CLAS12/Sim12/XERCESC
[kyle@parity JGeant4]$ echo $CLHEPROOT
/net/home/kyle/CLAS12/Sim12/CLHEP
[kyle@parity JGeant4]$ echo $EVIOROOT
/net/home/kyle/CLAS12/Sim12/evio
[kyle@parity JGeant4]$ echo $HDDSROOT
/net/home/kyle/CLAS12/Sim12/HDDS
[kyle@parity JGeant4]$ echo $JGEANT4ROOT
/net/home/kyle/CLAS12/Sim12/JGeant4
[kyle@parity JGeant4]$ echo $G4WORKDIR
/net/home/kyle/CLAS12/Sim12/workDIR

make - compile time error 

Compiling Sim12.cc ...
Sim12.cc:75: error: expected class-name before '{' token
Sim12.cc: In constructor `MySession::MySession(int, char**)':
Sim12.cc:111: error: class `MySession' does not have any field named `G4UIXm'
Sim12.cc: In function `int main(int, char**)':
Sim12.cc:238: error: cannot convert `G4UIterminal*' to `MySession*' in assignment
Sim12.cc:290: error: 'class MySession' has no member named 'SessionStart'
/net/home/kyle/CLAS12/Sim12/CLHEP/include/CLHEP/Random/Randomize.h: At global scope:
/net/home/kyle/CLAS12/Sim12/CLHEP/include/CLHEP/Random/Randomize.h:67: warning: 'CLHEP::HepRandomGenActiv e' defined but not used
make: *** 
[/net/home/kyle/CLAS12/Sim12/workDIR/tmp/Linux-g++/Sim12/exe/Sim12.o] 
Error 1

solution: env.sh was NOT setting variables. Recompiled geant4 and edited env.sh as needed


linking error: 

Compiling Sim12.cc ...
Using granular libraries ...
Linking Sim12 ...
/usr/bin/ld: cannot find -l/net/home/kyle/CLAS12/Sim12/CLHEP/lib
collect2: ld returned 1 exit status
make: *** [/net/home/kyle/CLAS12/Sim12/workDIR/bin/Linux-g++/Sim12] Error 1

From make -n, our error is the the second to last thing linked by ld. The directory is in ld's path (LD_LIBRARY_PATH). Hmmmm...

solution: make was treating the variable CLHEP_LIB as an archive, but it is a directory. export CLHEP_LIB="CLHEP"

make...success!

...

Steps to make and run Sim12:

Making

Setting variables:

Not all directories will be correct in env.sh. Make sure G4 variable directories are pointing in the right place.

I needed to tag this to the end of env.sh 

export CLHEP_BASE_DIR="/net/home/kyle/CLAS12/Sim12/CLHEP"
export CLHEPROOT="/net/home/kyle/CLAS12/Sim12/CLHEP"
export CLHEP_LIB="CLHEP"
export CLHEP_LIB_DIR="/net/home/kyle/CLAS12/Sim12/CLHEP/lib"
env | grep CLHEP
export XERCESCROOT="/net/home/kyle/CLAS12/Sim12/XERCESC/xerces-c-src_2_8_0"
export EVIOROOT="/net/home/kyle/CLAS12/Sim12/evio"
export HDDSROOT="/net/home/kyle/CLAS12/Sim12/HDDS"
export JGEANT4ROOT="/net/home/kyle/CLAS12/Sim12/JGeant4"
env | grep ROOT
export G4WORKDIR="/net/home/kyle/CLAS12/Sim12/workDIR"
export G4INSTALL="/net/home/kyle/CLAS12/Sim12/geant4.9.0.p01"
export G4INCLUDE="/net/home/kyle/CLAS12/Sim12/geant4.9.0.p01/include"
export G4LIB="/net/home/kyle/CLAS12/Sim12/geant4.9.0.p01/lib"


  1. Set env variables with env.sh: 'source ...../env.sh'
  2. cd to Sim12 directory, make

Success!


Running

Make sure LD_LIBRARY_PATH is up to date. 

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$G4LIB/$G4SYSTEM:$CLHEP_LIB_DIR:$HDDSROOT/tmp/$G4SYSTEM/hdds:$JGEANT4ROOT/tmp/$G4SYSTEM/JGeant4:$XERCESROOT/lib:$EVIOROOT"

My whole path: 

LD_LIBRARY_PATH=/net/home/kyle/CLAS12/Sim12/GEANT4/lib/geant4/Linux-g++:/net/home/kyle/CLAS12/Sim12/CLHEP/lib:
/net/home/kyle/CLAS12/Sim12/geant4.9.0.p01/lib/Linux-g++:/net/home/kyle/CLAS12/Sim12/CLHEP/lib:
/net/home/kyle/CLAS12/Sim12/HDDS/tmp/Linux-g++/hdds:/net/home/kyle/CLAS12/Sim12/JGeant4/tmp/Linux-g++/JGeant4:
/lib:/net/home/kyle/CLAS12/Sim12/evio:/net/home/kyle/CLAS12/Sim12/XERCESC/xerces-c-src_2_8_0/lib


You want to be in the directory with clas12.xml...your Sim12 directory. IE on my station it's in /net/home/kyle/CLAS12/Sim12/Sim12


Now simply run $G4WORKDIR/bin/Linux-g++/Sim12


Now your sciencing!!!

Dan's Notes

Useful links I keep losing:

http://clasweb.jlab.org/wiki/index.php/UNH_Sim12_Setup http://clasweb.jlab.org/wiki/index.php/Getting_Started_with_Sim12_Offsite


The Official Sim12 Offsite wiki has you leaving stuff where you compile it most of the time, while some of the directions assume that you do not. This is extremely confusing and leads to lots of problems. Also, I think it is better to install to a separate directory, so I will do so:

NOTE: DO NOT USE PATH NAMES WITH ~ for HOME DIRECTORY! USE ABSOLUTE PATHS!

The process(will be cleaned-up):

Preliminaries:

  1. mkdir -p /net/home/dan/Sim12-build
  2. mkdir -p /net/home/dan/Sim12

CLHEP

  1. mkdir -p /net/home/dan/Sim12/CLHEP
  2. mkdir -p /net/home/dan/Sim12-build/CLHEP
  3. cd /net/home/dan/Sim12-build/CLHEP
  4. tar -zxvf /net/home/dan/Tarpit/clhep-2.0.3.1.tgz
  5. cd 2.0.3.1/CLHEP
  6. ./configure --prefix=/net/home/dan/Sim12/CLHEP
  7. make
  8. make install
  9. export CLHEPROOT="/net/home/dan/Sim12/CLHEP"

XERCESC

  1. mkdir /net/home/dan/Sim12-build/xercesc
  2. mkdir -p /net/home/dan/Sim12/XERCESC
  3. cd /net/home/dan/Sim12-build/xercesc
  4. tar -zxvf /net/home/dan/Tarpit/xerces-c-src_2_8_0.tar.gz
  5. cd xerces-c-src_2_8_0/src/xercesc
  6. export XERCESCROOT="/net/home/dan/Sim12-build/xercesc/xerces-c-src_2_8_0"
  7. ./runConfigure -p linux -c gcc -x g++ -P /net/home/dan/Sim12/XERCESC
  8. make
  9. make install

Building XERCESC fails if using ~/blah for XERCESROOT!

  1. export XERCESCROOT="/net/home/dan/Sim12/XERCESC"

DAWN

  1. mkdir /net/home/dan/Sim12/DAWN
  2. mkdir /net/home/dan/Sim12-build/dawn
  3. cd /net/home/dan/Sim12-build/dawn
  4. tar -zxvf /net/home/dan/Tarpit/dawn_3_88a.taz
  5. cd dawn_3_88a
  6. edit Makefile: Change INSTALL_DIR line to use "/net/home/dan/Sim12/DAWN"
  7. make
  8. make install

GEANT4

  1. mkdir /net/home/dan/Sim12-build/geant4
  2. cd /net/home/dan/Sim12-build/geant4
  3. tar -zxvf ~/Tarpit/geant4.9.0.p01.gtar.gz
  4. cd geant4.9.0.p01
  5. mkdir data
  6. cd data
  7. tar -zxvf /net/home/dan/Tarpit/G4EMLOW.4.3.tar.gz
  8. tar -zxvf /net/home/dan/Tarpit/G4NDL.3.11.tar.gz
  9. tar -zxvf /net/home/dan/Tarpit/G4RadioactiveDecay.3.2.tar.gz
  10. tar -zxvf /net/home/dan/Tarpit/PhotonEvaporation.2.0.tar.gz
  11. cd /net/home/dan/Sim12-build/geant4
  12. mv geant4.9.0.p01 /net/home/dan/Sim12/GEANT4
  13. cd /net/home/dan/Sim12/GEANT4
  14. ./Configure -build

GEANT4 Questions:

Definition of G4SYSTEM variable is Linux-g++. That stands for:

1) OS : Linux

2) Compiler : g++

To modify default settings, select number above (e.g. 2) [Press [Enter] for default settings]

I can set things up so that your shell scripts and binaries are more portable, at what may be a noticable cost in performance. In particular, if you ask to be portable, the following happens: 

    1) Shell scripts will rely on the PATH variable rather than using
       the paths derived above.
    2) ~username interpretations will be done at run time rather than
       by Configure.

Do you expect to run these scripts and binaries on multiple machines? [n] y

Where is Geant4 source installed? [/net/home/dan/Sim12/GEANT4]

Specify the path where Geant4 libraries and source files should be installed. [/net/home/dan/Sim12/GEANT4]

Do you want to copy all Geant4 headers in one directory? [n] y

Please, specify default directory where ALL the Geant4 data is installed: 

G4LEVELGAMMADATA:              /net/home/dan/Sim12/GEANT4/data/PhotonEvaporation2.0

G4RADIOACTIVEDATA:             /net/home/dan/Sim12/GEANT4/data/RadioactiveDecay3.2

G4LEDATA:                      /net/home/dan/Sim12/GEANT4/data/G4EMLOW4.3

G4NEUTRONHPDATA:               /net/home/dan/Sim12/GEANT4/data/G4NDL3.11

You will be asked about customizing these next. [/net/home/dan/Sim12/GEANT4/data]

Please, specify default directory where the Geant4 data is installed:

1) G4LEVELGAMMADATA: /net/home/dan/Sim12/GEANT4/data/PhotonEvaporation2.0 2) G4RADIOACTIVEDATA: /net/home/dan/Sim12/GEANT4/data/RadioactiveDecay3.2 3) G4LEDATA: /net/home/dan/Sim12/GEANT4/data/G4EMLOW4.3 4) G4NEUTRONHPDATA: /net/home/dan/Sim12/GEANT4/data/G4NDL3.11

To modify default settings, select number above (e.g. 2) [Press [Enter] for default settings]

Could not find CLHEP installed on this system! Please, specify where CLHEP is installed:

CLHEP_BASE_DIR: /net/home/dan/Sim12/CLHEP

You can customize paths and library name of you CLHEP installation:

1) CLHEP_INCLUDE_DIR: /net/home/dan/Sim12/CLHEP/include 2) CLHEP_LIB_DIR: /net/home/dan/Sim12/CLHEP/lib 3) CLHEP_LIB: CLHEP To modify default settings, select number above (e.g. 2) [Press [Enter] for default settings]

By default 'static' (.a) libraries are built. Do you want to build 'shared' (.so) libraries? [n] y

You selected to build 'shared' (.so) libraries. Do you want to build 'static' (.a) libraries too? [n] y

Do you want to build 'global' compound libraries? [n] n

Do you want to compile libraries in DEBUG mode (-g)? [n] n 

 G4UI_NONE

If this variable is set, no UI sessions nor any UI libraries are built. This can be useful when running a pure batch job or in a user framework having its own UI system. Do you want to set this variable ? [n] 

 G4UI_BUILD_XAW_SESSION
 G4UI_USE_XAW

 Specifies to include and use the XAW interfaces in the
 application to be built.
 The XAW (X11 Athena Widget set) extensions are required to activate 
 and build this driver.

[n] y

You have selected to use the XAW based user interfaces. Specify the correct path where XAW is installed in your system. It was found in /usr/X11R6. Press [Enter] to set this path or type the correct one.

You can set '-' (without quotation) to CANCEL the XAW flag at all: [/usr/X11R6] 

 G4UI_BUILD_XM_SESSION
 G4UI_USE_XM

 Specifies to include and use the XM Motif based user interfaces.
 The XM Motif extensions are required to activate and build this
 driver.

[n] y

You have selected to use the XM Motif based user interfaces. Specify the correct path where Xm is installed in your system. It was found in /usr/X11R6. Press [Enter] to set this path or type the correct one.

You can set '-' (without quotation) to CANCEL the XM flag at all: [/usr/X11R6] 

 G4VIS_NONE

If this variable is set, no visualization drivers will be built or used. Do you want to set this variable ? [n] 

 G4VIS_BUILD_OPENGLX_DRIVER
 G4VIS_USE_OPENGLX

It is an interface to the de facto standard 3D graphics library, OpenGL. It is well suited for real-time fast visualization and prototyping. The X11 version of the OpenGL libraries is required. [n] y 

 G4VIS_BUILD_OPENGLXM_DRIVER
 G4VIS_USE_OPENGLXM

It is an interface to the de facto standard 3D graphics library, OpenGL. It is well suited for real-time fast visualization and prototyping. The X11 version of the OpenGL libraries and the Motif Xm extension is required. [n] y 

 G4VIS_BUILD_DAWN_DRIVER
 G4VIS_USE_DAWN

DAWN drivers are interfaces to the Fukui Renderer DAWN. DAWN is a vectorized 3D PostScript processor suited to prepare technical high quality outputs for presentation and/or documentation. [n] y 

 G4VIS_BUILD_OIX_DRIVER
 G4VIS_USE_OIX

The OpenInventor driver is based on OpenInventor technology for scientific visualization. The X11 version of OpenInventor is required. [n] n 

 G4VIS_BUILD_RAYTRACERX_DRIVER
 G4VIS_USE_RAYTRACERX

Allows for interactive ray-tracing graphics through X11. The X11 package is required. [n] y 

 G4VIS_BUILD_VRML_DRIVER
 G4VIS_USE_VRML

These driver generate VRML files, which describe 3D scenes to be visualized with a proper VRML viewer. [n] y 

 OGLHOME/include
 OGLHOME/lib

You have selected to use OpenGL driver. Specify the correct path (OGLHOME) where OpenGL is installed in your system. It was found in /usr. Press [Enter] to set this path or type the correct one.

You can set '-' (without quotation) to CANCEL the OpenGL flag at all: [/usr] 

 G4LIB_BUILD_G3TOG4

The utility module 'g3tog4' will be built by setting this variable. NOTE: it requires a valid FORTRAN compiler to be installed on your system and the 'cernlib' command in the path, in order to build the ancillary tools! Do you want to build 'g3tog4' ?

[n] y 

 G4LIB_BUILD_ZLIB

Do you want to activate compression for output files generated by the HepRep visualization driver?

[n] y 

 G4ANALYSIS_USE

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]

End of configuration phase."


source /net/home/dan/Sim12/GEANT4/.config/bin/Linux-g++/env.sh mkdir /net/home/dan/Sim12/workDir export G4WORKDIR="/net/home/dan/Sim12/workDir" cd /net/home/dan/Sim12/GEANT4/source/physics_lists make

EVIO

  1. mkdir /net/home/dan/Sim12-build/evio
  2. mkdir /net/home/dan/Sim12/EVIO
  3. cd /net/home/dan/Sim12-build/evio
  4. tar -zxvf ~/Tarpit/evio-2.0-source.tar.gz
  5. cd evio
  6. export G4WORKDIR="/net/home/dan/Sim12/workDir"

Current focus: Exploring Sim12

Notes:

  1. Get rid of red lines
  2. Add way to find out material of target
  3. Display commands issued by GUI
  4. Need to be able to turn on magnetic fields
  5. Need command interface
  6. Ability to list/change variables
  7. Need list/glossary of GEANT4 commands (linked from JLAB wiki)
  8. ^Plus, need our changes
  9. Document XML
  10. Make simple, limited XML description
  11. Model single chip
  12. Make nice macros
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