Difference between revisions of "Dan's Log"

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Line 983: Line 983:
 
Tried to get things done despite it.  Naturally, things start working five minutes before our meeting.  *sigh*
 
Tried to get things done despite it.  Naturally, things start working five minutes before our meeting.  *sigh*
 
</pre>
 
</pre>
 +
 +
 +
'''Monday 14'''
 +
13:00-19:00
 +
<pre>
 +
GEMC is not running on Pumpkin.  On attempting to start it, get
 +
*************************************************************
 +
Geant4 version Name: geant4-09-01    (14-December-2007)
 +
                      Copyright : Geant4 Collaboration
 +
                      Reference : NIM A 506 (2003), 250-303
 +
                            WWW : http://cern.ch/geant4
 +
*************************************************************
 +
 +
  >>> gemc Init: >>  Retrieving gemc Detector Map...
 +
 +
  >>> gemc MySQL: >>  Connecting to database "clas12_geometry" as "clasuser".
 +
terminate called after throwing an instance of 'std::out_of_range'
 +
  what():  basic_string::substr
 +
Aborted
 +
[dan@pumpkin ~]$
 +
 +
Was working last week, and I didn't change anything.  Either a pumkpin issue, or database.  My money is on the
 +
database.  Will investigate later.
 +
 +
Working with ROOT.
 +
Found something very useful:  To spit all of the attributes of an object on a canvas to the terminal,
 +
right-click on it and click on "dump".  Alternatively, clock on "Inspect"
 +
 +
GAH!  How can I change the scale of the color palette axis?  I found a reference to fwmax. 
 +
Tweaked Kyle's phi_z.C
 +
Made edep_strip.C
 +
Sent an email to Maurizio asking for an explanation regarding the bands in phi vs. z graph.
 +
It seems as though you are not supposed to change the palette scale yourself, or at least they make it
 +
terribly difficult.  It seems always to be set automatically, and is highly sensitive to the values in one's
 +
histogram.  This coupled with the fact that ours is different from Maurizio's suggests that we are doing
 +
something differently from him.
 +
 +
I learned a lot about ROOT today.
 +
Oh, use  gStyle->SetNumberContours(255); for a nicer gradient in your color palette.
 +
 +
</pre>
 +
[[Image:Edep_strip1.jpg|Edep vs strip]]

Revision as of 22:39, 14 July 2008

Progress and Task Log for Daniel

Tasks

  • Finalize/clean-up build instructions.
  • DONE - Figure-out how to add elements to GUI
  • DONE - Steal Kyle's rather spiffy wiki formatting
  • Get rid of red lines
  • Add way to change material of target in GUI
  • Add way to change particle beam in GUI
  • Display commands issued by GUI
  • Need to be able to turn on magnetic fields
  • DONE - Need command interface
  • Ability to list/change variables
  • Need list/glossary of GEANT4 commands (linked from JLAB wiki)
  • ^Plus, need our changes
  • Document XML
  • Make simple, limited XML description
  • Model single chip
  • Make nice macros
  • Are SVT5 and SVT6 micromegas? Is Sim12 model still accurate?
  • Are material descriptions incomplete? If so, should we fill-out?
  • Get sanitized version of Sim12 source
  • Understand how SVT works
  • Write summary of how SVT works

Misc. Notes

  • nTrigger is the number of times the beam is fired.
  • Sim12/Material_HDDS.xml says that XML spec is at http://www.gluex.org/hdds, but get a 404. Maybe $HDDSROOT/HDDS-1_0.xsd is what was there?

Log

2007

October 2007

Wednesday 24 

Started working 3PM, had Freshman Physics in the middle.  Left at 6:30PM.
Experienced crash hitting Uranium target.  Start trying other materials.  Barium crashes too.  Is Barium's
(for example) small definition a problem?
Barium crash generates "Unknown Hit Type on SVT1" (for each SVT) error message.
Frustrating that GEANT4 is seemingly so specialized that google returns few people talking about it.
Read on GEANT4 site that ALL particles must be specified (seems reasonable).  Possibly the
interactions are generating undefined particles?  Should search code for error message tomorrow.
Reorganized/expanded my bits of the wiki.
Added GUI elements to Batch Guide.

Thursday 25 

Started working 12:45.  Left 13:45 for Linguistics, back at 16:00.
Searched for Magnetic Field definition.  Looks like we need to make it.
Searched for error message having to do with Unknown Hits.  Didn't find it.  Could have to do with using the
default "geantino" particle?
Looked around code for place to add handy things to menus (such as particle type) and found a reference to 
visTutor/gui.mac.  It has exactly the sorts of things I would add!  Why is it not getting read?  Maybe should
set-up breakpoints in Sim12.cc?
You can apparently run macros from within the GUI, which I tried.  At first I thought it didn't work, but it did.  
The first few lines of the macros I tried set the verbosity to 0, so I didn't see them running commands.  Further, 
the addMenu etc. commands seem not to work.  Why?  Probably something to do with pointers...
Not speaking of which, why does the source of Sim12 say that Batch Mode is the default, when it clearly is not?
Also, there's something funky with that whole area of command line parsing.
GUI mode should have ability to run commands.  Batch mode should be able to run headless, dump data.  Forget the
pictures.
Need to figure-out what the mode-selection code is actually doing.

Friday 26 

Worked from 10:00-11:00, and 15:00-18:00
Trying to understand mode code.  Think I've got pointers now, but I need to try using them.  
Thought of a way to turn on/off magnetic fields, change materials, etc. on the fly:  Can change in-memory copy of
XML file, then re-load that new copy.  With this we could add buttons to toggle fields, change target materials,
etc.  On second thought, maybe we don't care about being able to do this.
Meeting with Maurik.  Sounds like priority is getting real data out of the program on particle trajectories etc.  
Tonight should polish build guide and run through the GEANT4 Application Developer's Guide in order to understand
Sim12.

Saturday and Sunday, 26-27 

Off the clock.
Re-made build guide, building on MacOS X on Alice for hints.  Should mention that I needed to install expat,
motif, svn.  Also, EVIO Makfile hack.
Realized that GUI mode has a command line!!!  It was there all the time, but we thought it was a meaningless
box!

Tuesday, 30 

Started working through GEANT4 Application Developer's Guide:
http://geant4.web.cern.ch/geant4/G4UsersDocuments/UsersGuides/ForApplicationDeveloper/html/Examples/NoviceCodes.html

November 2007

Friday, 02 

Worked with Sam, deciphering output code.

Monday, 05 

In at 10:30, out at 12:00.
Working on getting Sim12 to log to a file.

Thursday, 15 

Trying to get GEMC to compile.
First compiled QT4, installed into ~/QT4
Installed SCons into ~/CLAS12/SCons
Copied GEMC (from Maurik's dir on Taro) to ~/CLAS12/GEMC
Tried to compile GEMC, which failed.
After many successive failures, found the following things:
Need to get qt4.py from http://www.iua.upf.es/~dgarcia/Codders/sconstools.html
and copy it to $SCONS_ROOT_DIR/lib/scons-$SCONS_version/SCons/Tool/
Need to add pyscripts dir (from SVN/Maurik's dir) to PYTHONPATH, a la:
export PYTHONPATH="/net/home/dan/CLAS12/pyscripts"
Need to add SCons bin dir to PATH, a la:
PATH="$PATH:/net/home/dan/CLAS12/SCons/bin"
Need to add directory installed QT to to environment, a la:
export QTDIR="/net/home/dan/QT4"
And add PKG_CONFIG_PATH="/net/home/dan/QT4/lib/pkgconfig" to environment
Current error message:
[dan@benfranklin GEMC]$ scons
scons: Reading SConscript files ...
Loading qt4 tool...
KeyError: 'MYSQL':
  File "/net/home/dan/CLAS12/GEMC/SConstruct", line 27:
    loadmysql(env)
  File "/net/home/dan/CLAS12/pyscripts/loadmysql.py", line 9:
    MYSQL = OSENV['MYSQL']
  File "/usr/lib/python2.3/UserDict.py", line 19:
    def __getitem__(self, key): return self.data[key]

So re-compiled QT4 with -qt-sql-mysql configure option.

Friday, 16 

Got past previous error with new QT4, but now get:

[dan@benfranklin GEMC]$ scons
scons: Reading SConscript files ...
Loading qt4 tool...
NameError: global name 'fullpath1' is not defined:
  File "/net/home/dan/CLAS12/GEMC/SConstruct", line 14:
    env = Environment(tools=['default','qt4'], options = opts)
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Environment.py", line 874:
    apply_tools(self, tools, toolpath)
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Environment.py", line 101:
    env.Tool(tool)
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Environment.py", line 1491:
    tool(self)
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Tool/__init__.py", line 175:
    apply(self.generate, ( env, ) + args, kw)
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Tool/qt4.py", line 218:
    QT4_MOC = locateQt4Command(env,'moc', env['QTDIR']),
  File "/net/home/dan/CLAS12/SCons/lib/scons-0.97.0d20070918/SCons/Tool/qt4.py", line 201:
    raise "Qt4 command '" + command + "' not found. Tried: " + fullpath1 + " and "+ fullpath2

Found that I accidentally installed into a funky directory.  Blah.
Fixed, then ran into another error message.  Realized I had to export MYSQL="/"
Ridiculous.

Also, need to add MYSQL lib dir to LD_PATH

It works!

Wednesday, 21 

GEMC thoughts:
Not all the buttons work
Text output works with ./gemc -OUTPUT="txt,blahlog"
Need command line
Is there a batch mode?
Over vacation, read through all of it, work through C++ tutorials, and GEANT4 developer's guide.
Make Glossary! (CLARA, GEMC, SIM12,

Monday, 26 

In at 10:15, out at 11:15
In at 12:00, out at 13:00
In at 15:30, out at
Got new gemc code from Maurik
Need to 
export EVIO=$EVIOROOT
Also, typo in current version of pyscripts/loadevio.py.
Change to point to something sane for include dir.
Had to further mutilate the lib section to get it to compile.
Working on adding command line to GUI
Added text box (to old version)by adding 

#include <QLineEdit>
QLineEdit *commandLineEdit = new QLineEdit();
viewLayout->addWidget(commandLineEdit);

to gui/src/gemc_MainGui.cc.

Still haven't gotten it to compile.

Monday, 26 

Trying to add a command line box.  QT Learning curve indeed!
Learning about Slots and Signals.
Didn't try to get new gemc to compile today, though Maurik got us the latest pyscripts.
How can I pass an arbitrary

Friday, 26 

MUAHAHAHAHAHAHAHAAAA!  Finally got the command box working.  Also, new gemc compiles.
Code is ugly, though.  I want to clean it up before letting others see it.  Also, must
document how to get gemc to compile (difficulty is evio, I had to hack loadevio.py).
Email Maurizio and Maurik tonight.
The thing holding-up my command box was that I was having difficulty converting the
QString I got back from the QLineEdit box into a string I could print/etc.  It seems
like it should have been so simple...

December 2007

Monday, 10 

Worked on adding command history, fixed a segfault, made layout flow

Tuesday, 11 

12:15-13:15
Polished command history, started synching with upstream.

2008

January 2008

Tuesday, 15 

13:15-17:15
Making new CLAS12 suite in /net/data/pumpkin2/taro/CLAS12
For EL5-x64, added -b 64 option during XERCESC build.  Should we add -s?

Wednesday, 16 

14:00-16:45
Worked on building CLAS12 suite.  Intending to build on Pumpkin for RHEL5-x64,
Parity/Ben Franklin for RHEL4-x32, and Corn for RHEL5-x32.
Think that Maurik is pulling the production tree of gemc, while we probably want the
development version.  Even so, new production gemc fails to build against old GEANT4.
Corn keeps going down.

Thursday, 17 

12:45-14:30, 17:00-17:30
Building things on Corn.
./configure -qt-sql-mysql --prefix=/net/data/pumpkin2/taro/CLAS12/RHEL5_x32/QT
Network storage went down.

Tuesday, 22 

13:30-16:30
./runConfigure -p linux -c gcc -x g++ -b 64 -s
Building QT on Taro with instructions from wiki, got errors

g++ -c -include .pch/release-shared/QtGui -m64 -pipe -g -fno-exceptions -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -O2 -Wall -W -D_REENTRANT -fPIC -DQT_SHARED -DQT_BUILD_GUI_LIB -DQT_NO_CAST_TO_ASCII -DQT_ASCII_CAST_WARNINGS -DQT_44_API_QSQLQUERY_FINISH -DQT_MOC_COMPAT -DQT_RASTER_IMAGEENGINE -DQT_HAVE_MMX -DQT_HAVE_SSE -DQT_HAVE_MMXEXT -DQT_HAVE_SSE2 -DQT_NO_STYLE_MAC -DQT_NO_STYLE_WINDOWSVISTA -DQT_NO_STYLE_WINDOWSXP -DQ_INTERNAL_QAPP_SRC -DQT_NO_DEBUG -DQT_CORE_LIB -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I../../mkspecs/linux-g++-64 -I. -I../../include/QtCore -I../../include/QtCore -I../../include -I../../include/QtGui -I/usr/include/freetype2 -I../3rdparty/harfbuzz/src -Idialogs -I.moc/release-shared -I/usr/X11R6/include -I.uic/release-shared -o .obj/release-shared/qstylesheetstyle.o styles/qstylesheetstyle.cpp
^C../../include/QtCore/../../src/corelib/arch/qatomic_x86_64.h: In member function `virtual QRect QStyleSheetStyle::subControlRect(QStyle::ComplexControl, const QStyleOptionComplex*, QStyle::SubControl, const QWidget*) const':
../../include/QtCore/../../src/corelib/arch/qatomic_x86_64.h:118: error: inconsistent operand constraints in an `asm'
../../include/QtCore/../../src/corelib/arch/qatomic_x86_64.h:118: error: inconsistent operand constraints in an `asm'
../../include/QtCore/../../src/corelib/arch/qatomic_x86_64.h:118: error: inconsistent operand constraints in an `asm'
../../include/QtCore/../../src/corelib/arch/qatomic_x86_64.h:118: error: inconsistent operand constraints in an `asm'
make[1]: *** Deleting file `.obj/release-shared/qstylesheetstyle.o'
make[1]: *** [.obj/release-shared/qstylesheetstyle.o] Interrupt
make: *** [sub-gui-make_default-ordered] Interrupt

Incidentally, used the following command to configure, with CLAS12ROOT set:
./configure -qt-gif -no-cups -no-qt3support -prefix $CLAS12ROOT/QT -qt-sql-mysql -no-exceptions

Friday, 25 

09:30-10:00
Googling QT build message yielded someone claiming it was due to a broken compiler.  As the change will at worse
result in slightly poorer performance, I take the suggestion at http://lists.trolltech.com/qt-interest/2007-05/thread01156-0.html
and remove the -02 optimization flag from mkspecs/common/g++.conf
Trying on Corn (which Maurik says should be stable now) and Taro.
*sigh*  Corn crashed right after I untarred QT.

~15:30
Taro finished building though!
Now try again on Corn.
Bah, Corn needs mysql!

Monday, 28 09:15-09:45 

Started compile of GEANT4 9.1, using configure script.

February 2008

Saturday, 02 

00:15-01:30, 16:45-19:05

Well, I'm sick of this.
SSH in to Parity.
Start new tree under /net/data/pumpkin2/CLAS12
Untar CLHEP to Build and run
export CLAS12ROOT=/net/data/pumpkin2/CLAS12/RHEL4_x32
./configure --prefix=/net/data/pumpkin2/CLAS12/RHEL4_x32/CLHEP --disable-shared
make
make check
make install
export CLHEP_BASE_DIR=/net/data/pumpkin2/CLAS12/RHEL4_x32/CLHEP

Now untar XERXESC to Build and run
./runConfigure -plinux -cgcc -xg++ -s
make
Build fails.  It seems it's got a really silly build process.
Move the top xercesc source dir to the intended destination, and build again.  i.e.:
./runConfigure -plinux -cgcc -xg++ -s
make

Now untar QT to Build and run
./configure -qt-gif -no-cups -no-qt3support -prefix $CLAS12ROOT/QT -qt-sql-mysql -no-exceptions -static
gmake

in qt build dir,
gmake install
export QTDIR=$CLAS12ROOT/QT
export QTLIB=/net/data/pumpkin2/CLAS12/RHEL4_x32/QT/lib
export PKG_CONFIG_PATH=/net/data/pumpkin2/CLAS12/RHEL4_x32/QT/lib/pkgconfig
export LD_LIBRARY_PATH=$QTDIR/lib:$LD_LIBRARY_PATH
export PATH=$QTDIR:$PATH

Untar Geant4 into /net/data/pumpkin2/CLAS12/RHEL4_x32/GEANT4_9.1
Unpack data, etc.
./Configure -build
And it's off!

18:45-
It finished building GEANT4.

mkdir ~/mysql
ln -s /usr/include/mysql ~/mysql/include
ln -s /usr/lib/mysql ~/mysql/lib
export MYSQL=~/mysql

Copy pyscripts, gemc, scons
export PYTHONPATH=/net/data/pumpkin2/CLAS12/pyscripts
export PATH=$PATH:/net/data/pumpkin2/CLAS12/SCons/bin
export G4INSTALL=/net/data/pumpkin2/CLAS12/RHEL4_x32/GEANT4_9.1
export EVIO=/net/data/pumpkin2/taro/CLAS12/RHEL4_x32/EVIO
scons
Get this:

[dan@parity GEMC_DEVEL]$ scons
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
Making gemc.o...
gemc.cc: In function `int main(int, char**)':
gemc.cc:176: error: `G4UIQt' has not been declared
scons: *** [gemc.o] Error 1
scons: building terminated because of errors.

*sigh*

Sunday, 03 

00:30-01:45
Continue working on RHEL4_x32.  No success.

Tuesday, 05 

09:30-10:30, 12:30-14:00
Worked with Kyle to get ANYTHING to work (in particular RHEL4_x32) and
largely failed.  Eventually decided we need to start over.  This time
with more documentation instead of waiting until things work (because they
usually don't).

Thursday, 14 

12:00-13:45
Starting over, me on RH4 (x32 on parity, x64 on Taro), Kyle on RH5.
Compiled up through QT on RHEL4_x32.  QT building on RHEL4_x64.

Friday, 15 

08:45-09:30
QT build failed on x64.  Remembered I need to remove -02 from the optimization flags
in mkspecs/common/g++.conf in the QT source directory.  Off again, with Geant building on Parity
(set env vars, then gmake in G4/source).

Monday, 18 

09:00-10:00, 15:15-16:45
To build EVIO:
untar the evio-2.0.tar.gz version
move it to destination directory (say, something/EVIO)
cd into EVIO
for 32bit build, run INSTALL_DIR=something/EVIO make install
for 64bit build, run INSTALL_DIR=something/EVIO CODA_USE64BITS make install

Finished RHEL4_x32.  Segfaults:

Tuesday,19 

09:00-10:00
Current hang-up with Taro (RHEL4_x64):

[dan@taro GEMC-RHEL4_x64]$ scons --debug=findlibs --debug=includes
scons: Reading SConscript files ...

scons: *** No tool named 'qt4': not a Zip file
File "/net/home/dan/GEMC-RHEL4_x64/SConstruct", line 14, in ?

We've had this before, but it sounds like it is an all-purpose error message,
with no useful info.  Trying to track down what is wrong.

Remember to set umask!


My current environment script (run each new session, suitable for build environment): 

#Change the mention of RHEL4_x64 and Linux_x64-x64 for other platforms.

export PLATFORM=RHEL4_x64
export GEMC=~/GEMC-$PLATFORM
export CLAS12ROOT=/net/data/pumpkin2/CLAS12

export G4SYSTEM=Linux-g++
export G4WORKDIR=$CLAS12ROOT/$PLATFORM/GEANT4.9.1
export G4ROOT=$CLAS12ROOT/$PLATFORM/GEANT4.9.1
export G4INSTALL=$G4ROOT
export G4LIB=$G4INSTALL/lib
export G4VERSION=geant4.9.1
export OGLHOME=/usr/X11R6

export CLHEP_BASE_DIR=$CLAS12ROOT/$PLATFORM/CLHEP
export XERCESCROOT=$CLAS12ROOT/$PLATFORM/XERCESC
export EVIO="$CLAS12ROOT/$PLATFORM/EVIO"
export EVIOROOT="$EVIO"

export QTDIR=$CLAS12ROOT/$PLATFORM/QT
export QTHOME=$QTDIR
export QTLIB=$QTDIR/lib

export G4UI_BUILD_QT_SESSION=1
export G4UI_USE_QT=1

export G4VIS_BUILD_OPENGLQT_DRIVER=1
export G4VIS_USE_OPENGLQT=1

export G4VIS_BUILD_OPENGLX_DRIVER=1
export G4VIS_USE_OPENGLX=1           

export G4VIS_BUILD_DAWN_DRIVER=0
export G4VIS_USE_DAWN=0

export G4UI_BUILD_OI_SESSION=0
export G4UI_USE_OI=0

export G4UI_BUILD_OIX_SESSION=0
export G4UI_USE_OIX=0
 
export G4UI_BUILD_RAYTRACERX_SESSION=1
export G4UI_USE_RAYTRACERX=1

export G4LISTS_BASE=$G4ROOT/physics_lists

export NeutronHPCrossSections=$G4ROOT/data/G4NDL       # Data for neutron scattering processes 
export G4LEVELGAMMADATA=$G4ROOT/data/PhotonEvaporation # Nuclear Photon evaporation data
export G4RADIOACTIVEDATA=$G4ROOT/data/RadioactiveDecay # Data for radioactive decay hadronic processes under data
export G4LEDATA=$G4ROOT/data/G4EMLOW                   # Data for low energy electromagnetic processes
#export G4ELASTICDATA=$G4ROOT/data/Elastic             # Data for elastic scattering processes

export PATH=$PATH:$G4INSTALL/bin/$G4SYSTEM:$GEMC:$GEMC/database_io:$QTDIR/bin
export SCONS_LIB_DIR="$CLAS12ROOT/SCons/lib"
export PKG_CONFIG_PATH="$QTLIB/pkgconfig"
export PYTHONPATH="$CLAS12ROOT/pyscripts"
export PATH="$PATH:$CLAS12ROOT/SCons/bin:$QTDIR/bin"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$EVIO/Linux-x86_64-64/lib:$QTLIB:$G4INSTALL/lib/$G4SYSTEM:/$CLHEP_BASE_DIR/lib"
export MYSQL="/"
export BMS_HOME="$CLAS12ROOT/BMS"

Friday,22 

09:00-10:00
11:00-12:30

Trying to find source of segfault on RHEL4_x32 by using GDB.  Need to re-compile GEANT4 with debugging symbols.
Prettied the wiki a bit.  Needs overhaul.

Monday,25 

16:00-17:45
Recompiled RHEL4_x32 with debugging symbols, now get the following when run:

[dan@benfranklin GEMC-RHEL4_x32]$ gemc 


  >>> gemc Init: >>  Geant4 MonteCarlo
  >>> gemc Init: >>  Setting CLHEP Random Engine...
  >>> gemc Init: >>  Instantiating Run Manager...

*************************************************************
 Geant4 version Name: geant4-09-01    (14-December-2007)
                      Copyright : Geant4 Collaboration
                      Reference : NIM A 506 (2003), 250-303
                            WWW : http://cern.ch/geant4
*************************************************************

  >>> gemc Init: >>  Building gemc Detector...
  >>> gemc MySQL: >>  Connecting to database: clasgeometry as clasuser.



  >>> gemc Init: >>  Initializing Physics List...
  >>> gemc Init: >>  Initializing Primary Generator Action...

  >>> gemc Beam Settings >>  Beam Type: e-
  >>> gemc Beam Settings >>  Beam Energy: 11 GeV
  >>> gemc Beam Settings >>  Beam Direction: (0, 0, 1)
  >>> gemc Beam Settings >>  Beam Vertex: (0, 0, 0) cm

  >>> gemc Init: >>  Initializing Event Action...
  >>> gemc Init: >>  Initializing User Interface...
  >>> gemc Init: >>  Initializing Run Manager...

  >>> gemc Construction: >>  Building Detector from Geometry STL Map...

  >>> gemc Magnetic Field: >>  Magnetic Field <ihep-solenoid> doesn't exist yet. Adding <ihep-solenoid>.
  >>> gemc Magnetic Field Constructor: >>  File sol12_map.dat could not be opened. Exiting.
[dan@benfranklin GEMC-RHEL4_x32]$

Kyle and I updated the Detailed Instructions wiki page, though I suspended most of the changes as I don't have time ATM to make them comprehensive.

Tuesday 12:30-14:00 15:40-16:15 

Re-instated the Detailed Instructions changes, and expanded.  
GEMC does not work very well.  Fixed previous error message by downloading sol12_map.dat and fsolenoid.dat
Now running "gemc -GT=svtgeometry" results in rapid scrolling of:
  >>> gemc Magnetic Field Constructor: >> 466 transverse index wrong. Map point should be 233 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 467 transverse index wrong. Map point should be 233.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 468 transverse index wrong. Map point should be 234 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 469 transverse index wrong. Map point should be 234.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 470 transverse index wrong. Map point should be 235 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 471 transverse index wrong. Map point should be 235.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 472 transverse index wrong. Map point should be 236 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 473 transverse index wrong. Map point should be 236.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 474 transverse index wrong. Map point should be 237 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 475 transverse index wrong. Map point should be 237.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 476 transverse index wrong. Map point should be 238 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 477 transverse index wrong. Map point should be 238.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 478 transverse index wrong. Map point should be 239 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 479 transverse index wrong. Map point should be 239.5 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 480 transverse index wrong. Map point should be 240 but it's  8.07098e-275 instead.
  >>> gemc Magnetic Field Constructor: >> 481 transverse index wrong.
etc...

Thursday, 28 

12:00-14:00

March 2008

Sunday 23 

14:30-17:00
Installed ROOT on Pumpkin, started playing with it.
Played with GEMC.
Helloworld windows not opening with Pumpkin ROOT.  Needs X11 libs maybe?  Installing on Parity, not waiting for compile.

Tuesday 25 

14:00-17:00

April 2008

Tuesday 1 

13:00-17:00
Collaborated with Sam and Kyle on GEMC, ROOT, etc.

Monday 7 

15:30-18:00
Trying to get ROOT to make sense of a serious GEMC run.
Run an experiment:
gemc -GT=svtgeometry -BEAM_P="proton, 1.0*GeV, 80*deg, 0*deg" -SPREAD_P="0.5*GeV, 40*deg, 360*deg" -SPREAD_V="(0.1, 0.1, 2.5)cm" -OUTPUT="evio, Test3.ev" -LUMI_P="e-, 11*GeV, 0, 0" -LUMI_V="(0, 0, -5)cm" -LUMI_EVENT="100, 124*ns, 2*ns" -USE_PHYSICSL=QGSP -HALL_MATERIAL=Vacuum -N=2500

Convert the output from evio to root:

gemc_evio2root Test3.ev Test3.root

Run ROOT (without splash):
root -l

Load the data:
TFile *g = new TFile("$GEMC/Test3.root")

Look around:
g->ls();

Yields:

root [2] g->ls();
TFile**         /net/home/dan/GEMC-RHEL5_x64/Test3.root
 TFile*         /net/home/dan/GEMC-RHEL5_x64/Test3.root
  KEY: TTree    genT;1  gemc generated infos tree
  KEY: TTree    svtT;1  gemc SVT hits infos tree
  KEY: TTree    fvtT;1  gemc FVT hits infos tree
  KEY: TTree    itofT;1 gemc Inner TOF hits infos tree
  KEY: TTree    dcT;1   gemc DC hits infos tree

Hurray!

See what's inside:

svtT->Print()
root [2] svtT->Print()
******************************************************************************
*Tree    :svtT      : gemc SVT hits infos tree                               *
*Entries :     2500 : Total =         2023753 bytes  File  Size =     885621 *
*        :          : Tree compression factor =   2.26                       *
******************************************************************************
*Br    0 :evn       : evn/I                                                  *
*Entries :     2500 : Total  Size=      10614 bytes  One basket in memory    *
*Baskets :        0 : Basket Size=      32000 bytes  Compression=   1.00     *
*............................................................................*
*Br    1 :nsvthit   : nsvthit/I                                              *
*Entries :     2500 : Total  Size=      10638 bytes  One basket in memory    *
*Baskets :        0 : Basket Size=      32000 bytes  Compression=   1.00     *
*............................................................................*
*Br    2 :layer     : layer[nsvthit]/I                                       *
*Entries :     2500 : Total  Size=     100206 bytes  File Size  =      10129 *
*Baskets :        3 : Basket Size=      32000 bytes  Compression=   8.61     *
*............................................................................*
*Br    3 :sector    : sector[nsvthit]/I                                      *
*Entries :     2500 : Total  Size=     100215 bytes  File Size  =      16966 *
*Baskets :        3 : Basket Size=      32000 bytes  Compression=   5.14     *
*............................................................................*
*Br    4 :strip     : strip[nsvthit]/I                                       *
*Entries :     2500 : Total  Size=     100206 bytes  File Size  =      35645 *
*Baskets :        3 : Basket Size=      32000 bytes  Compression=   2.45     *
*............................................................................*
*Br    5 :Edep      : Edep[nsvthit]/F                                        *
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*............................................................................*
*Br    6 :E         : E[nsvthit]/F                                           *
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*Br    7 :x         : x[nsvthit]/F                                           *
*Entries :     2500 : Total  Size=     100177 bytes  File Size  =      73498 *
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*Br    8 :y         : y[nsvthit]/F                                           *
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*Br    9 :z         : z[nsvthit]/F                                           *
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*Br   10 :lx        : lx[nsvthit]/F                                          *
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*Br   11 :ly        : ly[nsvthit]/F                                          *
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*Br   12 :lz        : lz[nsvthit]/F                                          *
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*Br   13 :t         : t[nsvthit]/F                                           *
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*Br   14 :pid       : pid[nsvthit]/I                                         *
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*Br   15 :mpid      : mpid[nsvthit]/I                                        *
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*Br   16 :vx        : vx[nsvthit]/F                                          *
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*Br   17 :vy        : vy[nsvthit]/F                                          *
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*Br   18 :vz        : vz[nsvthit]/F                                          *
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*Br   19 :mvx       : mvx[nsvthit]/F                                         *
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*Br   20 :mvy       : mvy[nsvthit]/F                                         *
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*Br   21 :mvz       : mvz[nsvthit]/F                                         *
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*............................................................................*

Tuesday 8 11:00-12:00 

I have been learning to use ROOT with a nice introduction at http://slac.stanford.edu/BFROOT/www/doc/workbook/root1/root1.html
Interesting bits:
Save a canvas like so:
c1->SaveAs("birches.png");

Making hitograms:
TH1F *myfirsthist = new TH1F("myfirsthist", "How many birches?",10,1,100);

Tuesday 15 11:15-12:00 13:30-16:15 

Okay, so what we might want to do, beginning to end, is this:
Run an experiment, outputting to EVIO format
Run evio2root
(Write a ROOT script which extracts the data we want)
Run the root script, which generates histograms, or graphs, or images, or descriptive text data.

Soeaking of, save a histogram like so:
c1->SaveAs("birches.C");

{
TFile *f = new TFile("$GEMC/Test3.root")

svtT->Draw("Edep");
#c1->SaveAs("svtT_Edep.C");
}

Sam had an idea on how to pursue one of our objectives:
We could set-up just an SVT and send particles straight at it, then vary the angle and compare the sensitivity.

Tuesday, 29 13:00-16:00 

I've been trying to figure-out if we can manually specify some geometry for the angular dependence problem.
It doesn't look like we can, but perhaps we can use the new GCARD feature to do what we want.
Compiling the last few GEMC versions has not worked for me, due to a complaint about QDomDocument not existing.
Fixed by adding "QtXml" to the loadqt pyscript.  Could not download newest pyscripts due to forgetting JLAB
password (again).  *sigh* Will check tonight if they have fixed it, and will email Maurizio if not.
For some reason my GMail account never gets the gemc_software newsletters, though I have tried to sign-up
twice.

May 2008

Tuesday 6 12:00- 

Rotation and position changes don't seem to work in GCARD yet, so we'll rotate the gun.  Which is probably
better anyway.


So we need to set-up a script which runs gemc with just the BST, and rotates gun through 1-90 degrees.
Use GCARD to translate origin close to SVT to interior.  Output to evio.  Run evio2root.
Oops, GCARD can't do this yet.

First attempt at script:

for theta in `seq 1 90`; do gemc -gcard=closeBST.gcard -OUTPUT="evio, $theta.ev" -N=1 -HALL_MATERIAL=Vacuum \
-BEAM_P="proton, 0.8GeV, "$theta"*deg, "0"*deg" -USE_QT=0 ; done 

What are reasonable values for -BEAM_P -SPREAD_P -SPREAD_V -LUMI_P -LUMI_V -LUMI_EVENT= -USE_PHYSICSL 


What does -NGENP do?

Really want to rotate through phi as well.
Attempt 2:

for phi in `seq -25 25`; do for theta in `seq -90 90`; do $GEMC/gemc -GT=BST \
-OUTPUT="evio, "theta$theta"phi"$phi".ev" -N=100 -HALL_MATERIAL=Vacuum \
-BEAM_P="proton, 0.8GeV, "$theta"*deg, "phi"*deg" -USE_QT=0 ; done; done

Should we run it?  We would be hammering the database.  Kyle's asking Maurizio.

So how will we parse this?  The end result I think we want is a graph of angle vs.hits.

June 2008

Tuesday 3 13:00-16:30 



Thursday 5
13:00-16:30





Monday 9
13:00-16:30



Right.  Must get back on top of things.  Also, record time more consistently.
Today I'm going to make a tutorial for newbies.
...
Spent a bunch of time trying to get my environment to work.  When I source my pumpkin
environment script, my shell turns unresponsive.  Doing the same thing worked last
week.
Steps to reproduce:
[dan@benfranklin ~]$ ssh -X pumpkin.unh.edu
dan@pumpkin.unh.edu's password:
Last login: Mon Jun  9 15:45:07 2008 from benfranklin.unh.edu
[dan@pumpkin ~]$source /net/data/pumpkin2/CLAS12/RHEL5_x64/env.sh
[dan@pumpkin ~]$ ls
man gcc
blah
anything

*sigh*
CTRL-C doesn't help, nor does CTRL-D.
It's the LD_LIBRARY_PATH line.
Either I am being very stupid, or something is broken.  Probably the former.
It's dying when attempting to access /net/data/taro/maurik/root/root
There is no /net/data/taro
Automount broken?
Or Taro?
Well, Taro has moved.  Changed environment script, now it works.  Bah.  Going
home, hopefully I'll get something done there....



Tuesday 10
13:00-16:00



Pumpkin was having issues, so we all went down to the computer room.
Parity was replaced.
Worked with Kyle and Sarah on getting useful things out of ROOT.
I felt like I was a little bit lost, plus the temporary lack of a computer meant that I couldn't
contribute much.  Pretty unsatisfying day.  Need to go bone-up on ROOT, GEMC, and Physics.



Wednesday 11
13:00-16:00



Most of our time today was wasted with software issues.  We changed ROOT installs due to 
/net/data/taro/maurik disappearing, and this had annoying effects.  Losing Parity and the net
access issue didn't help.  
Ran a revised 50000 event test, but could not analyze because evio2root was linked against
old ROOT.  So we pointed it at a crippled install which was still there, which let it build, but the
binary caused segmentation violations.  Left annoyed and feeling like nothing was working.
Bah!

Remotely, after hours, I built a fresh ROOT, in /net/data/pumpkin2/CLAS12/RHEL5_64/ROOT
It works, as does the evio2root I built against it.  I also installed ROOT on Alice, and set-up
the computers in our new room.  I cannot seem to compile our ROOT programs on Alice, though.





Thursday 12



14:00-16:30




Tuesday 17



13:00-14:30




Wednesday 18



14:15-17:15
Details to follow...



Thursday 19



13:15-16:30
Installed EVIO2ROOT in $CLAS12ROOT, compiled for RH5_x64.
Sarah showed us a cool logging program called elog.  I installed it and ran it with the default configuration,
but then found that I could not kill the process.  This could be a problem as we don't have administrative 
privileges, even on the workstations.  I haven't spent much time thinking about how it is possible that I
couldn't kill it.  I've never figured-out how a user can create a SUID binary (if it was).  Anyway, configuring 
that took a back seat to other things.  Also, we should probably run it on our workstations rather than
on pumpkin.
I built and installed Valgrind to find the memory leak(s) in gemc.  I don't really know what I'm doing yet, but
it sure seemed like Valgrind said that there was not much leaking happening.  It sure slows things down
though.  Of course, I also don't know anything about manually allocating/deallocating memory, as I have 
previously only used languages with garbage collection.  So at least I should learn something.
Kyle and I messed with doing some larger runs for purposes of tutorials, but it didn't come to much.
I am still behind him in terms of familiarity with root, and desperately want to catch up.  Perhaps I will be
able to this weekend.
Oh, in order to compile gemc with debugging symbols and no crazy optimizations, I couldn't find any
easier way than to manually edit the SConstruct file, adding a CCFLAGS and CPPFLAGS option to the
environment.  # ADD BETTER EXPLANATION#



Tuesday 24



13:30-15:45
Worked on getting elog to work, and valgrind.  Met with Sarah and Kyle.




Thursday 26



13:00-17:00
Got ELOG to work, though I cannot seem to access it from anywhere but a local machine.  I suspect a packet filter. Most of the time I spent on that, plus some time doing time sheets and working on my wiiki guide and tidying things in the CLAS12 directories.

PAID UNTIL HERE








July 2008


Tuesday 1
13:00-16:30







Thursday 10
11:00-14:45



Kyle and I messed around with computers in the office before giving up on them.  We went down into the Physics Lounge, and installed Ubuntu
on them on the sly.  Things were actually pretty productive, with Kyle helping me catch up on my ROOT knowledge.  Eventually talked to
Sarah a little and clarified what I should be doing on the tutorial.  In short:  Focus on new students trying to use GEMC.






Friday 11
08:00-10:30



Got here early to work on things before the meeting.  Things not working, eventually decided UNH network is down.  GAH!
Tried to get things done despite it.  Naturally, things start working five minutes before our meeting.  *sigh*





Monday 14
13:00-19:00



GEMC is not running on Pumpkin.  On attempting to start it, get 
*************************************************************
 Geant4 version Name: geant4-09-01    (14-December-2007)
                      Copyright : Geant4 Collaboration
                      Reference : NIM A 506 (2003), 250-303
                            WWW : http://cern.ch/geant4
*************************************************************

  >>> gemc Init: >>  Retrieving gemc Detector Map...

  >>> gemc MySQL: >>  Connecting to database "clas12_geometry" as "clasuser". 
terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
Aborted
[dan@pumpkin ~]$ 

Was working last week, and I didn't change anything.  Either a pumkpin issue, or database.  My money is on the
database.  Will investigate later.

Working with ROOT.
Found something very useful:  To spit all of the attributes of an object on a canvas to the terminal, 
right-click on it and click on "dump".  Alternatively, clock on "Inspect"

GAH!  How can I change the scale of the color palette axis?  I found a reference to fwmax.  
Tweaked Kyle's phi_z.C
Made edep_strip.C
Sent an email to Maurizio asking for an explanation regarding the bands in phi vs. z graph.
It seems as though you are not supposed to change the palette scale yourself, or at least they make it
terribly difficult.  It seems always to be set automatically, and is highly sensitive to the values in one's
histogram.  This coupled with the fact that ours is different from Maurizio's suggests that we are doing
something differently from him.

I learned a lot about ROOT today.
Oh, use  gStyle->SetNumberContours(255); for a nicer gradient in your color palette.




Edep vs strip






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