Difference between revisions of "Dan's Log"

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==Tasks==
 
==Tasks==
−
*Finalize/clean-up build instructions.
+
 
−
*DONE - Figure-out how to add elements to GUI
+
* Play with the user-modifiable database and get ADC output all the way through to ROOT.
−
*DONE - Steal Kyle's rather spiffy wiki formatting
+
* Add capability to add electronic noise to the SVT's raw data
−
*Get rid of red lines
+
* -> Create noise, and figure-out how to filter it out
−
*Add way to change material of target in GUI
+
 
−
*Add way to change particle beam in GUI
+
* Ability to list/change variables
−
*Display commands issued by GUI
+
* Understand how SVT works
−
*Need to be able to turn on magnetic fields
+
* Write summary of how SVT works
−
*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==
 
==Misc. Notes==
Line 29: Line 16:
  
 
==Log==
 
==Log==
−
====October 2007====
 
−
'''Wednesday 24'''
 
−
<pre>
 
−
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.
 
−
</pre>
 
  
−
'''Thursday 25'''
+
[[Dan's Old Logs]]
 +
 
 +
====June 2008====
 +
'''Tuesday 3'''
 +
13:00-16:30
 
<pre>
 
<pre>
−
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.
 
 
</pre>
 
</pre>
  
−
'''Friday 26'''
+
'''Thursday 5'''
 +
13:00-16:30
 
<pre>
 
<pre>
−
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.
 
 
</pre>
 
</pre>
  
−
'''Saturday and Sunday, 26-27'''
+
'''Monday 9'''
 +
13:00-16:30
 
<pre>
 
<pre>
−
Off the clock.
+
Right. Must get back on top of things.  Also, record time more consistently.
−
Re-made build guide, building on MacOS X on Alice for hints.  Should mention that I needed to install expat,
+
Today I'm going to make a tutorial for newbies.
−
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
+
Spent a bunch of time trying to get my environment to work.  When I source my pumpkin
−
box!
+
environment script, my shell turns unresponsive.  Doing the same thing worked last
−
</pre>
+
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
  
−
'''Tuesday, 30'''
+
*sigh*
−
<pre>
+
CTRL-C doesn't help, nor does CTRL-D.
−
Started working through GEANT4 Application Developer's Guide:
+
It's the LD_LIBRARY_PATH line.
−
http://geant4.web.cern.ch/geant4/G4UsersDocuments/UsersGuides/ForApplicationDeveloper/html/Examples/NoviceCodes.html
+
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....
 
</pre>
 
</pre>
  
−
====November 2007====
+
'''Tuesday 10'''
−
'''Friday, 02'''
+
13:00-16:00
 
<pre>
 
<pre>
−
Worked with Sam, deciphering output code.
+
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.
 
</pre>
 
</pre>
  
−
'''Monday, 05'''
+
'''Wednesday 11'''
 +
13:00-16:00
 
<pre>
 
<pre>
−
In at 10:30, out at 12:00.
+
Most of our time today was wasted with software issues.  We changed ROOT installs due to
−
Working on getting Sim12 to log to a file.
+
/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.
 
</pre>
 
</pre>
  
−
'''Thursday, 15'''
 
−
<pre>
 
−
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.
 
−
 
−
</pre>
 
  
−
'''Friday, 16'''
+
'''Thursday 12'''
 
<pre>
 
<pre>
−
Got past previous error with new QT4, but now get:
+
14:00-16:30
−
 
 
−
[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!
 
−
 
 
−
</pre>
 
  
−
'''Wednesday, 21'''
 
−
<pre>
 
−
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,
 
 
</pre>
 
</pre>
  
−
'''Monday, 26'''
+
'''Tuesday 17'''
 
<pre>
 
<pre>
−
In at 10:15, out at 11:15
+
13:00-14:30
−
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.
 
−
 
 
−
</pre>
 
  
−
'''Monday, 26'''
 
−
<pre>
 
−
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
 
 
</pre>
 
</pre>
  
−
'''Friday, 26'''
+
'''Wednesday 18'''
 
<pre>
 
<pre>
−
MUAHAHAHAHAHAHAHAAAA!  Finally got the command box working.  Also, new gemc compiles.
+
14:15-17:15
−
Code is ugly, though.  I want to clean it up before letting others see it.  Also, must
+
Details to follow...
−
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...
 
 
</pre>
 
</pre>
  
−
====December 2007====
+
'''Thursday 19'''
−
'''Monday, 10'''
 
 
<pre>
 
<pre>
−
Worked on adding command history, fixed a segfault, made layout flow
+
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#
 
</pre>
 
</pre>
  
−
'''Tuesday, 11'''
+
'''Tuesday 24'''
 
<pre>
 
<pre>
−
12:15-13:15
+
13:30-15:45
−
Polished command history, started synching with upstream.
+
Worked on getting elog to work, and valgrind.  Met with Sarah and Kyle.
−
</pre>
 
  
−
====January 2008====
 
−
'''Tuesday, 15'''
 
−
<pre>
 
−
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?
 
 
</pre>
 
</pre>
  
−
'''Wednesday, 16'''
+
'''Thursday 26'''
 
<pre>
 
<pre>
−
14:00-16:45
+
13:00-17:00
−
Worked on building CLAS12 suite.  Intending to build on Pumpkin for RHEL5-x64,
+
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.
−
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.
 
−
 
 
−
</pre>
 
  
−
'''Thursday, 17'''
+
PAID UNTIL HERE
−
<pre>
 
−
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.
 
 
</pre>
 
</pre>
  
−
'''Tuesday, 22'''
 
−
<pre>
 
−
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:
+
====July 2008====
−
./configure -qt-gif -no-cups -no-qt3support -prefix $CLAS12ROOT/QT -qt-sql-mysql -no-exceptions
 
−
</pre>
 
  
−
'''Friday, 25'''
+
'''Tuesday 1'''
 +
13:00-16:30
 
<pre>
 
<pre>
−
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!
 
−
</pre>
 
  
−
'''Monday, 28'''
 
−
09:15-09:45
 
−
<pre>
 
−
Started compile of GEANT4 9.1, using configure script.
 
 
</pre>
 
</pre>
  
−
====February 2008====
+
'''Thursday 10'''
−
'''Saturday, 02'''
+
11:00-14:45
 
<pre>
 
<pre>
−
00:15-01:30, 16:45-19:05
+
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
−
Well, I'm sick of this.
+
Sarah a little and clarified what I should be doing on the tutorial.  In short: Focus on new students trying to use GEMC.
−
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*
 
 
</pre>
 
</pre>
  
−
'''Sunday, 03'''
 
−
<pre>
 
−
00:30-01:45
 
−
Continue working on RHEL4_x32.  No success.
 
−
</pre>
 
  
−
'''Tuesday, 05'''
+
'''Friday 11'''
 +
08:00-10:30
 
<pre>
 
<pre>
−
09:30-10:30, 12:30-14:00
+
Got here early to work on things before the meeting.  Things not working, eventually decided UNH network is down.  GAH!
−
Worked with Kyle to get ANYTHING to work (in particular RHEL4_x32) and
+
Tried to get things done despite it.  Naturally, things start working five minutes before our meeting. *sigh*
−
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).
 
 
</pre>
 
</pre>
  
−
'''Thursday, 14'''
 
−
<pre>
 
−
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.
 
−
</pre>
 
  
−
'''Friday, 15'''
+
'''Monday 14'''
 +
13:00-19:00
 
<pre>
 
<pre>
−
08:45-09:30
+
GEMC is not running on Pumpkin.  On attempting to start it, get
−
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).
 
−
</pre>
 
  
−
'''Monday, 18'''
+
*************************************************************
−
<pre>
+
Geant4 version Name: geant4-09-01    (14-December-2007)
−
09:00-10:00, 15:15-16:45
+
                      Copyright : Geant4 Collaboration
−
To build EVIO:
+
                      Reference : NIM A 506 (2003), 250-303
−
untar the evio-2.0.tar.gz version
+
                            WWW : http://cern.ch/geant4
−
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:
+
  >>> gemc Init: >>  Retrieving gemc Detector Map...
  
−
</pre>
+
  >>> 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 ~]$
  
−
'''Tuesday,19'''
+
Was working last week, and I didn't change anything.  Either a pumkpin issue, or database.  My money is on the
−
<pre>
+
database.  Will investigate later.
−
09:00-10:00
 
−
Current hang-up with Taro (RHEL4_x64):
 
  
−
[dan@taro GEMC-RHEL4_x64]$ scons --debug=findlibs --debug=includes
+
Working with ROOT.
−
scons: Reading SConscript files ...
+
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"
  
−
scons: *** No tool named 'qt4': not a Zip file
+
GAH!  How can I change the scale of the color palette axis?  I found a reference to fwmax. 
−
File "/net/home/dan/GEMC-RHEL4_x64/SConstruct", line 14, in ?
+
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.
  
−
We've had this before, but it sounds like it is an all-purpose error message,
+
I learned a lot about ROOT today.
−
with no useful info. Trying to track down what is wrong.
+
Oh, use  gStyle->SetNumberContours(255); for a nicer gradient in your color palette.
 +
Also, I don't think Maurizio cut the data for phi=0 from his phi_z graph, as "0" appears as the lower bound.
 +
If he had set it higher, 0 would not have appeared, based on my experience.  But hopefully he will say.
 +
Oh, some database info:  http://clasweb.jlab.org/wiki/index.php/12/10/2007_hands_on
 
</pre>
 
</pre>
 +
[[Image:Edep_strip1.jpg|Edep vs strip]]
  
−
Remember to set umask!
+
'''Tuesday 15'''
−
 
+
13:00-14:45, 15:45-17:00
−
 
 
−
My current environment script (run each new session, suitable for build
 
−
environment):
 
−
 
 
 
<pre>
 
<pre>
−
#Change the mention of RHEL4_x64 and Linux_x64-x64 for other platforms.
+
Met with Maurik and Sarah.
−
 
+
Should see if GEMC crashes on the farm.  Login to login.jlab.org, then ssh to ifarml1, remembering to
−
export PLATFORM=RHEL4_x64
+
forward X. But where is it?  Where can I run it from?  It is not in /apps. Ask Maurizio.
−
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"
 
 
</pre>
 
</pre>
  
−
'''Friday,22'''
+
'''Thursday 22'''
 
<pre>
 
<pre>
−
09:00-10:00
+
Wrapped-up first draft of new user guide.
−
11:00-12:30
+
Put-up copy of Mauruzio's First SVT Results page, started filling with our tests.  With source code!
 +
</pre>
  
−
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.
 
−
</pre>
 
  
−
'''Monday,25'''
+
'''Monday 28'''
 +
14:00-17:00
 
<pre>
 
<pre>
−
16:00-17:45
+
 
−
Recompiled RHEL4_x32 with debugging symbols, now get the following when run:
+
Touching-up ROOT programs and uploading them to UNH SVT Results page.
 +
My p vs phi does not look like Maurizio's, but seems to make sense.  Why does his "curve" at low momentums?
 +
Asked him.  My theta vs z also looks different, will investigate next time.
 +
Tried accessing elog on Sarah's workstation with her instructions, but couldn't get it to work.
 
</pre>
 
</pre>
  
 +
'''Tuesday 29'''
 +
11:30-14:30
 
<pre>
 
<pre>
−
[dan@benfranklin GEMC-RHEL4_x32]$ gemc
+
Maurizio said that he used a magnetic field on the p vs phi graphs, explaining the discrepancy.  Did he
−
 
+
on others? I will generate a new data set and re-run our ROOT programs, and see what happens.
−
 
+
Reading through the GEMC code, trying to trace variables through.
−
  >>> 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]$
 
  
 
</pre>
 
</pre>
−
 
−
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-
 
−
<pre>
 
−
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...
 

Latest revision as of 16:21, 27 August 2008

Progress and Task Log for Daniel

Tasks

  • Play with the user-modifiable database and get ADC output all the way through to ROOT.
  • Add capability to add electronic noise to the SVT's raw data
  • -> Create noise, and figure-out how to filter it out
  • Ability to list/change variables
  • 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

Dan's Old Logs

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.
Also, I don't think Maurizio cut the data for phi=0 from his phi_z graph, as "0" appears as the lower bound.
If he had set it higher, 0 would not have appeared, based on my experience.  But hopefully he will say.
Oh, some database info:  http://clasweb.jlab.org/wiki/index.php/12/10/2007_hands_on



Edep vs strip

Tuesday 15
13:00-14:45, 15:45-17:00



Met with Maurik and Sarah.
Should see if GEMC crashes on the farm.  Login to login.jlab.org, then ssh to ifarml1, remembering to
forward X.  But where is it?  Where can I run it from?  It is not in /apps.  Ask Maurizio.




Thursday 22



Wrapped-up first draft of new user guide.
Put-up copy of Mauruzio's First SVT Results page, started filling with our tests.  With source code!





Monday 28
14:00-17:00




Touching-up ROOT programs and uploading them to UNH SVT Results page.
My p vs phi does not look like Maurizio's, but seems to make sense.  Why does his "curve" at low momentums?
Asked him.  My theta vs z also looks different, will investigate next time.
Tried accessing elog on Sarah's workstation with her instructions, but couldn't get it to work.



Tuesday 29
11:30-14:30



Maurizio said that he used a magnetic field on the p vs phi graphs, explaining the discrepancy.  Did he
on others?  I will generate a new data set and re-run our ROOT programs, and see what happens.
Reading through the GEMC code, trying to trace variables through.










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