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Re: New external packages (jan12) [message #12975 is a reply to message #12974] Mon, 23 January 2012 22:45 Go to previous messageGo to next message
Maria Patsyuk is currently offline  Maria Patsyuk
Messages: 58
Registered: April 2010
continuous participant
 From: *pools.arcor-ip.net
Dear Mohammad,

thank you,

I updated the cmake directory (at revision 14216), then hit 'cmake', '. ./config.sh', 'make' and tried the simulation again.

Unfortunately I have the same error again.

root -l sim_dirc.C
root [0]
Processing sim_dirc.C...
Warning in <TClassTable::Add>: class PndSdsMCPoint already in TClassTable
Warning in <TClassTable::Add>: class PndSdsStrip already in TClassTable
Warning in <TClassTable::Add>: class PndSdsDigi already in TClassTable
Warning in <TClassTable::Add>: class PndSdsDetector already in TClassTable
Info in <TGeoManager::TGeoManager>: Geometry FAIRGeom, FAIR geometry created
-I- FairGeoMedia Read media
Loading Geant4 global libraries ...Our Macro
sh: /home/masha/PANDA/External_Jan2012/bin/geant4-config: not found
Error in <TUnixSystem::GetFromPipe>: command "$SIMPATH/bin/geant4-config --libs" returned 32512
Loading VGM libraries ...
Loading g4root library ...
dlopen error: /home/masha/PANDA/External_Jan2012/transport/geant4_vmc/lib/tgt_linux/li bg4root.so: undefined symbol: _ZTI27G4VUserDetectorConstruction
Load Error: Failed to load Dynamic link library /home/masha/PANDA/External_Jan2012/transport/geant4_vmc/lib/tgt_linux/li bg4root.so
Warning: Return value of void g4libs_global() ignored /home/masha/PANDA/External_Jan2012/transport/macro/g4libs.C:135:
Error: Symbol TG4RunConfiguration is not defined in current scope /home/masha/PANDA/trunk/gconfig/g4Config.C:29:
Error: Symbol TG4RunConfiguration is not defined in current scope /home/masha/PANDA/trunk/gconfig/g4Config.C:29:
Error: type TG4RunConfiguration not defined FILE:/home/masha/PANDA/trunk/gconfig/g4Config.C LINE:29
Error: Invalid type 'TG4RunConfiguration*' in declaration of 'runConfiguration' /home/masha/PANDA/trunk/gconfig/g4Config.C:29:
*** Interpreter error recovered ***
SetCuts Macro: Setting Processes..
Error: illegal pointer to class object gMC 0x0 839 /home/masha/PANDA/trunk/gconfig/SetCuts.C:23:
*** Interpreter error recovered ***

*** Break *** segmentation violation



===========================================================
There was a crash (kSigSegmentationViolation).
This is the entire stack trace of all threads:
===========================================================
#0 0xb78b9424 in __kernel_vsyscall ()
#1 0xb67acc53 in waitpid () from /lib/libc.so.6
#2 0xb674d343 in ?? () from /lib/libc.so.6
#3 0xb687f9dd in system () from /lib/libpthread.so.0
#4 0xb72d19c3 in TUnixSystem::Exec (this=0x8377730, shellcmd=0x8c27b38 "/home/masha/PANDA/External_Jan2012/tools/root/etc/gdb-backtrace.sh 11466 1>&2") at /home/masha/PANDA/External_Jan2012/tools/root/core/unix/src/TUnixSystem. cxx:2058
#5 0xb72d227b in TUnixSystem::StackTrace (this=0x8377730) at /home/masha/PANDA/External_Jan2012/tools/root/core/unix/src/TUnixSystem. cxx:2306
#6 0xb72cfc09 in TUnixSystem::DispatchSignals (this=0x8377730, sig=kSigSegmentationViolation) at /home/masha/PANDA/External_Jan2012/tools/root/core/unix/src/TUnixSystem. cxx:1184
#7 0xb72cdba1 in SigHandler (sig=kSigSegmentationViolation) at /home/masha/PANDA/External_Jan2012/tools/root/core/unix/src/TUnixSystem. cxx:367
#8 0xb72d5871 in sighandler (sig=11) at /home/masha/PANDA/External_Jan2012/tools/root/core/unix/src/TUnixSystem. cxx:3588
#9 0xb7305f4c in textinput::TerminalConfigUnix::HandleSignal (this=0xb7877ba0, signum=11) at /home/masha/PANDA/External_Jan2012/tools/root/core/textinput/src/textinp ut/TerminalConfigUnix.cpp:96
#10 0xb7305a7e in (anonymous namespace)::TerminalConfigUnix__handleSignal (signum=11) at /home/masha/PANDA/External_Jan2012/tools/root/core/textinput/src/textinp ut/TerminalConfigUnix.cpp:36
#11 <signal handler called>
#12 0xb30c5115 in FairMCApplication::InitMC (this=0x8e44f08, setup=0x8e4e1a8 "/home/masha/PANDA/trunk/gconfig/g4Config.C", cuts=0x8e4e160 "/home/masha/PANDA/trunk/gconfig/SetCuts.C") at /home/masha/PANDA/trunk/base/FairMCApplication.cxx:200
#13 0xb30f9959 in FairRunSim::SetMCConfig (this=0x882e290) at /home/masha/PANDA/trunk/base/FairRunSim.cxx:345
#14 0xb30f7f79 in FairRunSim::Init (this=0x882e290) at /home/masha/PANDA/trunk/base/FairRunSim.cxx:196
#15 0xb31669f8 in G__FairDict_982_0_4 (result7=0xbfb1a9b8, funcname=0x8c54298 "", libp=0xbfb10374, hash=0) at /home/masha/PANDA/build_Jan2012/base/FairDict.cxx:15281
#16 0xb6a7ab2f in Cint::G__ExceptionWrapper (funcp=0xb31669d2 <G__FairDict_982_0_4(G__value*, char const*, G__param*, int)>, result7=0xbfb1a9b8, funcname=0x8c54298 "", libp=0xbfb10374, hash=0) at cint/cint/src/Api.cxx:393
#17 0xb6b462e3 in G__execute_call (result7=0xbfb1a9b8, libp=0xbfb10374, ifunc=0x8c54298, ifn=0) at cint/cint/src/newlink.cxx:2406
#18 0xb6b46b22 in G__call_cppfunc (result7=0xbfb1a9b8, libp=0xbfb10374, ifunc=0x8c54298, ifn=0) at cint/cint/src/newlink.cxx:2610
#19 0xb6b21c79 in G__interpret_func (result7=0xbfb1a9b8, funcname=0x8386b20 "Init", libp=0xbfb10374, hash=404, p_ifunc=0x8c54298, funcmatch=1, memfunc_flag=1) at cint/cint/src/ifunc.cxx:5795
#20 0xb6afdb87 in G__getfunction (item=0x8383a06 "Init()", known3=0xbfb1dea8, memfunc_flag=1) at cint/cint/src/func.cxx:2665
#21 0xb6c23b56 in G__getstructmem (store_var_type=112, varname=..., membername=0x8383a06 "Init()", memnamesize=2147483647, tagname=0x8384210 "fRun", known2=0xbfb1dea8, varglobal=0xb6cdd220, objptr=2) at cint/cint/src/var.cxx:6818
#22 0xb6c1446d in G__getvariable (item=0x8383a00 "fRun->Init()", known=0xbfb1dea8, varglobal=0xb6cdd220, varlocal=0x0) at cint/cint/src/var.cxx:5404
#23 0xb6aedce1 in G__getitem (item=0x8383a00 "fRun->Init()") at cint/cint/src/expr.cxx:1906
#24 0xb6aeb805 in G__getexpr (expression=0x83a1c60 "fRun->Init()") at cint/cint/src/expr.cxx:1488
#25 0xb6b767b0 in G__exec_function (statement=..., pc=0xbfb1fdf8, piout=0xbfb1fdf0, plargestep=0xbfb1fde0, presult=0xbfb1fce4) at cint/cint/src/parse.cxx:645
#26 0xb6b8680d in G__exec_statement (mparen=0xbfb1feb4) at cint/cint/src/parse.cxx:7372
#27 0xb6ac1386 in G__exec_tempfile_core (file=0x83a1458 "/home/masha/PANDA/trunk/macro/drc/./sim_dirc.C", fp=0x0) at cint/cint/src/debug.cxx:265
#28 0xb6ac2d53 in G__exec_tempfile (file=0x83a1458 "/home/masha/PANDA/trunk/macro/drc/./sim_dirc.C") at cint/cint/src/debug.cxx:813
#29 0xb6b94d2f in G__process_cmd (line=0x8701078 ".x /home/masha/PANDA/trunk/macro/drc/./sim_dirc.C", prompt=0x837b394 "", more=0x837b38c, err=0xbfb20fb4, rslt=0xbfb20f70) at cint/cint/src/pause.cxx:3182
#30 0xb72803e1 in TCint::ProcessLine (this=0x837b360, line=0x8701078 ".x /home/masha/PANDA/trunk/macro/drc/./sim_dirc.C", error=0xbfb21ba0) at /home/masha/PANDA/External_Jan2012/tools/root/core/meta/src/TCint.cxx:53 8
#31 0xb728093c in TCint::ProcessLineSynch (this=0x837b360, line=0x8701078 ".x /home/masha/PANDA/trunk/macro/drc/./sim_dirc.C", error=0xbfb21ba0) at /home/masha/PANDA/External_Jan2012/tools/root/core/meta/src/TCint.cxx:61 7
#32 0xb71b61c0 in TApplication::ExecuteFile (file=0xbfb21bad "sim_dirc.C", error=0xbfb21ba0, keep=false) at /home/masha/PANDA/External_Jan2012/tools/root/core/base/src/TApplication .cxx:1023
#33 0xb71b5978 in TApplication::ProcessFile (this=0x843d9c0, file=0xbfb21bad "sim_dirc.C", error=0xbfb21ba0, keep=false) at /home/masha/PANDA/External_Jan2012/tools/root/core/base/src/TApplication .cxx:899
#34 0xb71b588d in TApplication::ProcessLine (this=0x843d9c0, line=0xbfb21baa ".x sim_dirc.C", sync=false, err=0xbfb21ba0) at /home/masha/PANDA/External_Jan2012/tools/root/core/base/src/TApplication .cxx:872
#35 0xb69dff36 in TRint::Run (this=0x843d9c0, retrn=false) at /home/masha/PANDA/External_Jan2012/tools/root/core/rint/src/TRint.cxx:41 8
#36 0x08048ed3 in main (argc=1, argv=0xbfb23d04) at /home/masha/PANDA/External_Jan2012/tools/root/main/src/rmain.cxx:29
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#12 0xb30c5115 in FairMCApplication::InitMC (this=0x8e44f08, setup=0x8e4e1a8 "/home/masha/PANDA/trunk/gconfig/g4Config.C", cuts=0x8e4e160 "/home/masha/PANDA/trunk/gconfig/SetCuts.C") at /home/masha/PANDA/trunk/base/FairMCApplication.cxx:200
#13 0xb30f9959 in FairRunSim::SetMCConfig (this=0x882e290) at /home/masha/PANDA/trunk/base/FairRunSim.cxx:345
#14 0xb30f7f79 in FairRunSim::Init (this=0x882e290) at /home/masha/PANDA/trunk/base/FairRunSim.cxx:196
===========================================================

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Re: New external packages (jan12) [message #12976 is a reply to message #12975] Mon, 23 January 2012 22:48 Go to previous messageGo to next message
Mohammad Al-Turany is currently offline  Mohammad Al-Turany
Messages: 518
Registered: April 2004
Location: GSI, Germany
first-grade participant
 From: *dip.t-dialin.net
Hi Maria,

Please delete the config.sh and the CMakeCache.txt in your build directory and run the cmake again, this worked for me on Ubuntu!

Mohammad

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Re: New external packages (jan12) [message #12977 is a reply to message #12976] Mon, 23 January 2012 23:03 Go to previous messageGo to next message
Mohammad Al-Turany is currently offline  Mohammad Al-Turany
Messages: 518
Registered: April 2004
Location: GSI, Germany
first-grade participant
 From: *dip.t-dialin.net
Hallo Maria,

Finally I found it, you need to call svn update in:
$SIMPATH/transport/macro

to update the g4libs.C macro.

Sorry for that.

Mohammad

[Updated on: Mon, 23 January 2012 23:04]

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Re: New external packages (jan12) [message #12980 is a reply to message #12888] Tue, 24 January 2012 15:26 Go to previous messageGo to next message
Ralf Kliemt is currently offline  Ralf Kliemt
Messages: 507
Registered: May 2007
Location: GSI, Darmstadt
first-grade participant
From: *pool.mediaWays.net
Hello everyone,

After downloading the jan12 release (updated) this morning it compiles until VGM (log below in the spoiler). I used a separate build path.

Regards.
Ralf

Toggle Spoiler

[Updated on: Tue, 24 January 2012 15:27]

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Re: New external packages (jan12) [message #12981 is a reply to message #12888] Tue, 24 January 2012 17:41 Go to previous messageGo to next message
Ralf Kliemt is currently offline  Ralf Kliemt
Messages: 507
Registered: May 2007
Location: GSI, Darmstadt
first-grade participant
From: *pool.mediaWays.net
Hello again,

The problem could be cornered! I have still the same issue that the G4 compilation fails due to libExpat. I have a 32bit version installed, while G4 wants to install in 64bit. The check for the library presence seems to not check the 64bit compatibility and hence doesn't use the built in version of it.

Thanks to Mohammad. Now we just need a fix for that...

Cheers
Ralf

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Re: New external packages (jan12) [message #12982 is a reply to message #12977] Tue, 24 January 2012 19:50 Go to previous messageGo to next message
Maria Patsyuk is currently offline  Maria Patsyuk
Messages: 58
Registered: April 2010
continuous participant
 From: *pools.arcor-ip.net
Mohammad,

thank you very much,
now the DIRC simulation is working with the Jan12 external packages!

Best regards,
Maria

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Re: New external packages (jan12) [message #12983 is a reply to message #12981] Tue, 24 January 2012 20:46 Go to previous messageGo to next message
Mohammad Al-Turany is currently offline  Mohammad Al-Turany
Messages: 518
Registered: April 2004
Location: GSI, Germany
first-grade participant
 From: *dip.t-dialin.net
Hi Ralf,

Unfortunately, I did not find anyway to switch of the usage of the system expat library without hacking the G4 code! So may be you can try to install the proper Expat library for your system, i.e:

> sudo port install expat

This should fetch and install "expat-2.0.1_1.darwin_11.x86_64.tgz"

In case this does not work you have to edit the file: geant4.9.5/cmake/Modules/Geant4OptionalComponents.cmake and comment out the line 72. i.e:

find_package(EXPAT)

but this I would do as last solution!

Cheers,

Mohammad

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Re: New external packages (jan12) [message #12986 is a reply to message #12983] Wed, 25 January 2012 11:16 Go to previous messageGo to next message
Ralf Kliemt is currently offline  Ralf Kliemt
Messages: 507
Registered: May 2007
Location: GSI, Darmstadt
first-grade participant
From: *cb.uni-bonn.de
Mohammad Al-Turany wrote on Tue, 24 January 2012 20:46



> sudo port install expat

This should fetch and install "expat-2.0.1_1.darwin_11.x86_64.tgz"



I only get:
expat @2.0.1_1+universal

This is ppc and i386, but no 64bit. I found a ticket for that, 18 months old, but deleted after 1 year of inactivity. So it seems there is no 64bit expat in macports.

Ralf

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Re: New external packages (jan12) [message #12987 is a reply to message #12986] Wed, 25 January 2012 11:28 Go to previous messageGo to next message
Mohammad Al-Turany is currently offline  Mohammad Al-Turany
Messages: 518
Registered: April 2004
Location: GSI, Germany
first-grade participant
 From: *gsi.de
HI,

Is your MAC 64 or 32? because for me I get exactly this:

expat-2.0.1_1.darwin_11.x86_64.tgz

DO you have a MaCbook or MacBook Pro?

Mohammad

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Re: New external packages (jan12) [message #12989 is a reply to message #12888] Wed, 25 January 2012 11:33 Go to previous messageGo to next message
Ralf Kliemt is currently offline  Ralf Kliemt
Messages: 507
Registered: May 2007
Location: GSI, Darmstadt
first-grade participant
From: *cb.uni-bonn.de
Well, the label reads MacBook, but it is one of the early aluminim shell models (now "Pro"). So, yes! 64bit System.

Ralf

EDIT: Commenting the find_package(EXPAT) did the job. At least I've it compiled, finally.
Tahnks Mohammad.

Ralf

[Updated on: Wed, 25 January 2012 12:38]

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Re: New external packages (jan12) [message #13065 is a reply to message #12888] Thu, 16 February 2012 17:55 Go to previous messageGo to next message
Christian Hammann is currently offline  Christian Hammann
Messages: 24
Registered: July 2009
Location: Bonn
continuous participant
From: *cb.uni-bonn.de
Hi everybody,

unfortunately there are still problems with the new external packages here in Bonn. We had the problem compiling Geant4 which was reported by Simone. He solved it by compiling Geant4 as a static library instead of a dynamic one.
At first this seemed to work, but it turned out Simone only tested it with Geant3. If one tries to use Geant4 root is not able to load (some of) the required Geant4 libs and gives the following error:

dlopen error: /disk/user/bianco/ext_jan12_32/build/lib/libG4Tree.a: invalid ELF header
Load Error: Failed to load Dynamic link library /disk/user/bianco/ext_jan12_32/build/lib/libG4Tree.a


So we are back to the original compilation error of Geant:

-- [download 70% complete]
[ 83%] Building CXX object source/processes/CMakeFiles/G4processes.dir/transportation/src/G4StepLimiter.cc.o
[ 83%] Building CXX object source/processes/CMakeFiles/G4processes.dir/transportation/src/G4Transportation.cc.o
[ 83%] Building CXX object source/processes/CMakeFiles/G4processes.dir/transportation/src/G4UserSpecialCuts.cc.o
[ 83%] Building CXX object source/processes/CMakeFiles/G4processes.dir/transportation/src/G4VTrackTerminator.cc.o
Linking CXX shared library ../../outputs/library/Linux-g++/libG4processes.so
Error running link command: Argument list too long
make[2]: *** [outputs/library/Linux-g++/libG4processes.so] Error 2
make[1]: *** [source/processes/CMakeFiles/G4processes.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....


Any ideas on that?

Cheers,
Christian

Christian Hammann
Universität Bonn
Helmholz-Institut für Strahlen und Kernphysik
Nußallee 14-16
53115 Bonn
Tel: +49 228 733895
Fax: +49 228 732505

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Re: New external packages (jan12) [message #13066 is a reply to message #13065] Thu, 16 February 2012 20:14 Go to previous messageGo to next message
Mohammad Al-Turany is currently offline  Mohammad Al-Turany
Messages: 518
Registered: April 2004
Location: GSI, Germany
first-grade participant
 From: *dip.t-dialin.net
Hallo Christian,

Unfortunately it is a problem of Geant4 itself with the max argument length in the kernel of your linux. As far as I can see you use Debian Etch, so it is 5 years old and the support was stopped in Feb. 2010 (http://www.debian.org/releases/etch/) . in the new linux releases they remove this limit completely.

This problem was also reported on the G4 site with out any solution! except a hint on how to increase the maximum length of the argument list by recompiling the kernel (see: http://www.gnu.org/software/coreutils/faq/#Argument-list-too-long) so I am not sure if this is really an option for you.


best regards,

Mohammad

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Re: New external packages (jan12) [message #13072 is a reply to message #13066] Fri, 17 February 2012 10:13 Go to previous messageGo to next message
Florian Uhlig is currently offline  Florian Uhlig
Messages: 424
Registered: May 2007
first-grade participant
 From: *gsi.de
Hi Christian,

please have a look which kernel version you use at Bonn.
According to http://www.in-ulm.de/~mascheck/various/argmax/ there was a change in the handling the maximum number of arguments with kernel version 2.6.23.

Before this version the value was hardcoded in the kernel source code, with this version the size is set to 1/4 of the stack size which can be changed ( at least if I am correct).

This size you can check with "ulimit -s" inside a terminal. At the GSI Etch system it is set to 8192 kB.
With "ulimit -s <newsize in kB>" you can change the size. Maybe increasing the size
on your system solves the problem for you, but I am not sure about that. But I think it is worth a try. The changes are only in the actual shell and newly created sub shells.

Ciao

Florian

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Re: New external packages (jan12) [message #13074 is a reply to message #13072] Tue, 21 February 2012 15:17 Go to previous messageGo to next message
Christian Hammann is currently offline  Christian Hammann
Messages: 24
Registered: July 2009
Location: Bonn
continuous participant
From: *cb.uni-bonn.de
Hi,

thanks for the tips. On most machines we are running a 2.6.18 kernel. This kernel seems to have a fixed size of 128kB for the argument list.

We also have a test machine with a 2.6.32 kernel. For this machine the argument list can be 2MB (1/4 of the stacksize). On this machine I can compile the external packages without problem. Unfortunately I can then run geant4 only on that machine.

I'll live with that for now, and look into a more permanent solution after the panda meeting.

Cheers
Christian

P.S.: one can check the maximum size for the argument list with 'getconf ARG_MAX'.

Christian Hammann
Universität Bonn
Helmholz-Institut für Strahlen und Kernphysik
Nußallee 14-16
53115 Bonn
Tel: +49 228 733895
Fax: +49 228 732505

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Re: New external packages (jan12) [message #13075 is a reply to message #13074] Tue, 21 February 2012 16:45 Go to previous messageGo to next message
Florian Uhlig is currently offline  Florian Uhlig
Messages: 424
Registered: May 2007
first-grade participant
 From: *gsi.de
Hi Christian,

is the test machine also a machine with Debian Etch? By the way there are no security updates for Etch since some time, so maybe you should move to a newer version of the operating system.

Ciao

Florian

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Re: New external packages (jan12) [message #13076 is a reply to message #13075] Tue, 21 February 2012 17:41 Go to previous message
Christian Hammann is currently offline  Christian Hammann
Messages: 24
Registered: July 2009
Location: Bonn
continuous participant
From: *cb.uni-bonn.de
Hi Florian,

no the test machine is not a etch but squeeze. I'm aware that etch doesn't get any more updates. I agree that an update of our systems is inevitable at some point. But this will require quite some work, as we are also running some old (analysis) software on our machines.

Cheers
Christian

Christian Hammann
Universität Bonn
Helmholz-Institut für Strahlen und Kernphysik
Nußallee 14-16
53115 Bonn
Tel: +49 228 733895
Fax: +49 228 732505

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