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Re: halld analysis segfaults
Hi David,
I run reconstruction of single-photon hddm simulation (control.in attached),
using hd_example package (in ...src/programs/Analysis/hd_example).
The same problem occurs in my regular analysis tool (not in the repository)
which has the similar structure as the code in hd_example.
I believe that problem arises after
// Instantiate our event processor
MyProcessor myproc;
line in hd_example.cc, because it seems that
jerror_t MyProcessor::init()
has not been called. Thus program crashes after first event by trying
to fill undeclared histogram (or tree). So it might be JANA issue?
Thanks,
Mihajlo
Quoting David Lawrence <davidl@jlab.org>:
>
> Hi Mihajlo,
>
> I'm looking into this now. It would be useful if you could give me
> some more specifics so that I could reproduce the problem.
>
> Is this referring to a factory or an event processor?
>
> Is it code that's currently available in the repository? (if so where)
>
> What kind of data file are you using for input?
>
> Regards,
> -David
>
> Kornicer, Mihajlo wrote:
>>
>> Hi Mark and David,
>>
>> I compiled fresh checkout from halld repository and now I am getting
>> segmentation faults when trying to run analysis software. Running in
>> debug-mode shows that 'init' method, which is supposed to declare
>> root objects, has been skipped, regardless of the analysis tool.
>>
>> Other people from our group at IU encountered similar problems as well.
>> We are using Jana 0.4.9.
>>
>> Any suggestions?
>> Mihajlo
>>
>> Here is the output from hd_example, for example:
>> --------------------
>> Starting program: /home/s4/kornicer/halld/bin/Linux/hd_example_d
>> ~/halld_my/src/programs/Simulation/HDGeant/hdgeant.hddm
>> [Thread debugging using libthread_db enabled]
>> [New Thread -1208039744 (LWP 18288)]
>> [New Thread -1212986448 (LWP 18362)]
>> Opening source
>> "/s4/kornicer/halld_my/src/programs/Simulation/HDGeant/hdgeant.hddm"of type:
>> HDDM
>> Created JCalibration object of type: JCalibrationFile
>> Generated via: fallback creation of JCalibrationFile
>> Runs: requested=1 found=1 Validity range=1-10000
>> URL: file:///home/s4/kornicer/halld/src/calib
>> context: default
>> Reading Magnetic field map from Magnets/Solenoid/solenoid_1500 ...
>> 32481 entries found ( Nx=81 Ny=1 Nz=401 ) at 0xa5d65c8
>> Created Magnetic field map of type DMagneticFieldMapCalibDB.
>> Read 840 values from FDC/lorentz_deflections in calibDB
>> lorentz_deflections columns (alphabetical): bx bz nx nz x z
>> Info in <TGeoManager::TGeoManager>: Geometry Geometry, default geometry
>> created
>> Info in <TGeoManager::SetTopVolume>: Top volume is SITE. Master
>> volume is SITE
>> Info in <TGeoManager::CheckGeometry>: Fixing runtime shapes...
>> Info in <TGeoManager::CheckGeometry>: ...Nothing to fix
>> Info in <TGeoManager::CloseGeometry>: Counting nodes...
>> Info in <TGeoManager::Voxelize>: Voxelizing...
>> Info in <TGeoManager::CloseGeometry>: Building cache...
>> Info in <TGeoNavigator::BuildCache>: --- Maximum geometry depth set to 100
>> Info in <TGeoManager::CloseGeometry>: 42417 nodes/ 279 volume UID's
>> in default
>> geometry
>> Info in <TGeoManager::CloseGeometry>: ----------------modeler
>> ready----------------
>> Launching threads [New Thread -1256195152 (LWP 18363)]
>> .
>> Registering FDC factories
>> --- Configuration Parameters --
>> < all defaults >
>> -------------------------------
>> FCAL Geometry initialized with 2800 active blocks.
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> [Switching to Thread -1256195152 (LWP 18363)]
>> 0x0817caf6 in MyProcessor::evnt (this=0xbfede160, eventLoop=0xa5d6860,
>> eventnumber=1) at MyProcessor.cc:53
>> 53 fcal_y_vs_x->Fill(fcalhit->y,fcalhit->x);
>>
>> (gdb) bt
>> #0 0x0817caf6 in MyProcessor::evnt (this=0xbfede160, eventLoop=0xa5d6860,
>> eventnumber=1) at MyProcessor.cc:53
>> #1 0x081b4758 in jana::JEventLoop::OneEvent (this=0xa5d6860) at
>> JEventLoop.cc:451
>> #2 0x081b43c1 in jana::JEventLoop::Loop (this=0xa5d6860) at
>> JEventLoop.cc:356
>> #3 0x0818cbb2 in LaunchThread (arg=0xbfeddf80) at JApplication.cc:938
>> #4 0x033ac341 in start_thread () from /lib/tls/libpthread.so.0
>> #5 0x0210b6fe in clone () from /lib/tls/libc.so.6
>>
>>
>>
>>
>>
>>
>>
>
> --
>
> ------------------------------------------------------------------------
> David Lawrence Ph.D.
> Staff Scientist Office: (757)269-5567 [[[ [ [ [
> Jefferson Lab Pager: (757)584-5567 [ [ [ [
> [ [ http://www.jlab.org/~davidl davidl@jlab.org [[[ [[
> [[ [[[
> ------------------------------------------------------------------------
>
>
>
>
c This is the control file for the GEANT simulation. Parameters defined
c in this file control the kind and extent of simulation that is performed.
c The full list of options is given in section BASE-40 of the GEANT manual.
c
c In addition, some new cards have been defined to set up the input source
c for the simulation. Three kinds of simulation runs are available, selected
c by which of the following three "cards" are present below.
c 1. Input from Monte Carlo generator (card INFILE)
c 2. Built-in coherent bremsstrahlung source (card BEAM)
c 3. Built-in single-track event generator (card KINE)
c The order of the list is significant, that is if INFILE is present then the
c BEAM and KINE cards are ignored, otherwise if BEAM is present then KINE is
c ignored. For example, the 3-card sequence:
c INFILE 'phi-1680.hddm'
c SKIP 25
c TRIG 100
c instructs HDGeant to open ./phi-1680.hddm, skip the first 25 events and then
c process the following 100 input events and stop. If the end of the file is
c reached before the event count specified in card TRIG is exhausted then the
c processing will stop at the end of file.
cINFILE 'rhop.hddm'
TRIG 10
c The BEAM card configures the built-in coherent bremsstralung photon
c beam generator in HDGeant. If the INFILE card is not present and BEAM
c is specified, the internal coherent bremsstralung generator is the primary
c source of events for the simulation. If INFILE is specified, the primary
c event source is the external Monte Carlo generator that produced the file,
c but the BEAM card may still be present, and it is needed if beam-related
c backgrounds are being superimposed on top of the primary event signals,
c as requested with the BGRATE card (see below). The beam card accepts
c the following three parameters.
c Emax - end-point energy of the electron beam (GeV)
c Epeak - energy of the primary coherent peak edge (GeV)
c Emin - minimum energy of the coherent bremsstrahlung beam (GeV)
c Omitting the final parameter Emin results in the default value being used.
cBEAM 12. 9.
c Commenting out the following line will disable simulated hits output.
OUTFILE 'hdgeant.hddm'
c The following card enables single-track generation (for testing).
c For a single-particle gun, set the momentum (GeV/c), direction
c theta,phi (degrees) and vertex position (cm), and for the particle
c type insert the Geant particle type code plus 100 (eg. 101=gamma,
c 103=electron, 107=pi0, 108=pi+, 109=pi-, 114=proton). If you use
c the particle code but do not add 100 then theta,phi are ignored
c and the particle direction is generated randomly over 4pi sr.
c For a listing of the Geant particle types, see the following URL.
c http://wwwasdoc.web.cern.ch/wwwasdoc/geant_html3/node72.html
c The meaning of the arguments to KINE are as follows.
c - particle = GEANT particle type of primary track + 100
c - momentum = initial track momentum, central value (GeV/c)
c - theta = initial track polar angle, central value (degrees)
c - phi = initial track azimuthal angle, central value (degrees)
c - delta_momentum = spread in initial track momentum, full width (GeV/c)
c - delta_theta = spread in initial track polar angle, full width (degrees)
c - delta_phi = spread in initial track azimuthal angle, full width (degrees)
c
c If you do explicitly specify the momentum/angle (by adding 100 as
c described above, you may also choose to distibute tracks evenly in
c log(P) or log(theta) by setting the appropriate PLOG and TLOG flags
c to a non-zero value.
c PLOG 1
c TLOG 1
c
c particle momentum theta phi delta_momentum delta_theta delta_phi
KINE 101 0.5 5. 0. 0. 10. 360.
c The SCAP card determines the vertex position for the particle gun. It
c supports the following three arguments, all of which default to 0.
c
c vertex_x vertex_y vertex_z
SCAP 0. 0. 65.
c If you specify a non-zero value for vertex_x and/or vertex_y above then
c all tracks will emerge from the given point. If you leave them at zero,
c you have the option of specifying the HALO card which causes the simulation
c to generate events with a transverse profile modeled after the 12 GeV
c electron beam. The argument only argument to HALO is fhalo, the fraction
c of the beam that lies in the halo region surrounding the core gaussian.
c The nominal value taken from CASA technical note JLAB-TN-06-048 is 5e-5.
c This card is only effective for electron beam simulations with gxtwist.
c
c fhalo
HALO 5e-5
c The following lines control the rate (GHz) of background beam photons
c that are overlayed on each event in the simulation, in addition to the
c particles produced by the standard generation mechanism. A value of
c 1.10 corresponds to nominal GlueX running conditions at an intensity of
c 10^7 tagged photons on target per second. To disable the generation of
c random beam background, comment this line out or set the value of BGRATE
c to zero. Background beam photons are generated during the time interval
c given by the BGGATE card, whose two arguments specify the earliest and
c latest times (ns relative to the time of the original photon that caused
c the event) that a random beam photon could produce background hits
c somewhere in the detector. Note that for this to work, the BEAM card
c must be present (see above). This means that background generation is
c disabled when the simulation operates in particle gun mode.
c If Emin is set in the BEAM card (see above), the rate of background photons
c is automatically rescaled as follows:
c Rate(E_gamma > Thr) = Rate(E_gamma = 0.12 Gev) * K,
c where K is a scale factor calculated inside uginit.F:
c K = 1 for Thr = 0.12 GeV,
c K > 1 for Thr < 0.12 GeV.
c Note, K is calculated assuming the beam energies Emax = 12, Epeak = 9.
BGRATE 1.10
BGGATE -200. 200.
c The following card seeds the random number generator so it must be unique
c for each run. There are two ways to specify the random see for a run.
c 1. One argument, must be an integer in the range [1,215]
c 2. Two arguments, must be a pair of positive Integer*4 numbers
c In the first case, one of a limited set of prepared starting seeds is
c chosen from a list. These seeds have been certified to produce random
c sequences that do not repeat within the first 10^9 or so random numbers.
c For cases where more choices are needed, the two-argument form gives
c access to a total of 2^62 choices, with no guarantees about closed loops.
RNDM 121
c The following line controls the cutoffs for tracking of particles.
c CUTS cutgam cutele cutneu cuthad cutmuo bcute bcutm dcute dcutm ppcutm tofmax
c - cutgam = Cut for gammas (0.001 GeV)
c - cutele = Cut for electrons (0.001 GeV)
c - cutneu = Cut for neutral hadrons (0.01 GeV)
c - cuthad = Cut for charged hadrons (0.01 GeV)
c - cutmuo = Cut for muons (0.01 GeV)
c - bcute = Cut for electron brems. (CUTGAM)
c - bcutm = Cut for muon brems. (CUTGAM)
c - dcute = Cut for electron delta-rays. (10 TeV)
c - dcutm = Cut for muon delta-rays. (10 TeV)
c - ppcutm = Cut for e+e- pairs by muons. (0.01 GeV)
c - tofmax = Time of flight cut (1.E+10 sec)
c - gcuts = 5 user words (0.)
CUTS 1e-4 1e-4 1e-3 1e-3 1e-4
c The following line controls a set of generic flags that are used to
c control aspects of the simulation generally related to debugging.
c For normal debugging runs these should be left at zero (or omitted).
c At present the following functionality is defined (assumes debug on).
c SWIT(2) = 0 turns off trajectory tracing
c = 2 turns on step-by-step trace during tracking (verbose!)
c = 3 turns on trajectory plotting after tracking is done
c = 4 turns on step-by-step plotting during tracking
c SWIT(3) = 1 stores track trajectories for plotting after tracking is done
c SWIT(4) = 0 trace trajectories of all particle types
c = 3 trace only charged particle trajectories
SWIT 0 0 0 0 0 0 0 0 0 0
c The following card enables the GelHad package (from BaBar)
c on/off ecut scale mode thresh
GELH 1 0.2 1.0 4 0.160
c The following card selects the hadronic physics package
c HADR 0 no hadronic interactions
c HADR 1 GHEISHA only (default)
c HADR 2 GHEISHA only, with no generation of secondaries
c HADR 3 FLUKA (with GHEISHA for neutrons below 20MeV)
c HADR 4 FLUKA (with MICAP for neutrons below 20MeV)
HADR 1
c The following cards are needed if optical photons are being
c being generated and tracked in the simulation. The CKOV directive
c enables Cerenkov generation in materials for which the refractive
c index table has been specified. The LABS card enables absorption
c of optical photons. The ABAN directive controls a special feature
c of Geant which allows it to "abandon" tracking of charged particles
c once their remaining range drops below the distance to the next
c discrete interaction or geometric boundary. Particles abandoned
c during tracking are stopped immediately and dump all remaining energy
c where they lie. The remaining energy is dumped in the correct volume
c so this is OK in most cases, but it can cut into the yield of
c Cerenkov photons (eg. in a lead glass calorimeter) at the end of
c a particle track. If this might be important, set ABAN to 0.
CKOV 1
LABS 1
c The following card prevents GEANT tracking code from abandoning the
c tracking of particles near the end of their range, once it determines
c that their fate is just to stop (i.e. electrons and protons). This
c behaviour is normal in most cases, but in the case of Cerenkov light
c generation it leads to an underestimate for the yields.
c ABAN 1 abandon stopping tracks (default)
c ABAN 0 do not abandon stopping tracks
ABAN 0
c The following card sets up the simulation to perform debugging on
c a subset of the simulated events.
c DEBUG first last step
c - first (int) = event number of first event to debug
c - last (int) = event number of last event to debug
c - step (int) = only debug one event every step events
DEBUG 1 10 1000
c The following card can be used to turn off generation of secondary
c particles in the simulation, ordinarily it should be 0 (or omitted).
NOSECONDARIES 0
c The following card tells the simulation to store particle trajectories
c in the event output stream. This output can be verbose, use with caution.
c The value set here determines the amount of output recorded:
c
c TRAJECTORIES = 0 don't store trajectory info
c TRAJECTORIES = 1 store birth and death points of primary tracks
c TRAJECTORIES = 2 store birth and death points of all particles
c TRAJECTORIES = 3 store full trajectory of primary tracks
c TRAJECTORIES = 4 store full trajectory of primary tracks and birth/death points of secondaries
c TRAJECTORIES = 5 store full trajectory for all particles
c
TRAJECTORIES 0
c The following tracking parameters are defined for each tracking medium
c TMAXFD (REAL) maximum angular deviation due to the magnetic field
c permitted in one step (degrees)
c DEEMAX (REAL) maximum fractional energy loss in one step (0< DEEMAX <=0.1)
c STEMAX (REAL) maximum step permitted (cm)
c STMIN (REAL) minimum value for the maximum step imposed by energy loss,
c multiple scattering, Cerenkov or magnetic field effects (cm)
c Normally they are assigned appropriate values calculated automatically by
c Geant when the geometry is defined, overwriting the values declared by
c the user code in the GSTMED() call. Users who know what they are doing can
c force Geant to instead use the values passed in the arguments to GSTMED()
c by removing the comment in front of the following card. Any parameters with
c zero values are still assigned automatic values even when AUTO is turned off.
cAUTO 0
c The magnetic field map is accessed through the HDGEOMETRY library
c so that the same map can be used for both simulation and reconstruction.
c There are currently 2 alternatives to the type of map read in: 1.) A map
c of the inhomogeneous field and 2.) values representing a constant field. The map
c for 1.) is kept in the calibDB as Magnets/Solenoid/solenoid_1500. The
c 3 components for 2.) are also in the calibDB as Magnets/Solenoid/solenoid_const.
c To use 1.), either don't define the BFIELD card or set it to 'CalibDB'.
c To use 2.), set the BFIELD card to 'Const'.
c To maintain compatibility with the reconstruction, one must specify the
c same option on the command line to the reconstruction program like this:
c hd_root -PBFIELD_TYPE=Const file.hddm
c BFIELD 'Const'
c Use this card to enable/disable ( SAVEHITS 1/0 ) writing events with no
c hits in the detector to the hddm output file. Default value is 0.
SAVEHITS 0
c This card is used to enable/disable ( SHOWERS_IN_COL 1/0 ) simulation of
c showers in the primary and secondary collimators placed in the collimator cave.
c The default value is set to 0.
SHOWERSINCOL 0
c The following cards allow one to switch on/off some physics processes in GEANT:
c MULS 0 no multiple scattering
c 1 Moliere or Coulomb scattering (default)
c
c BREM 0 no bremsstrahlung
c 1 bremsstrahlung (default)
c
c COMP 0 no Compton
c 1 Compton scattering (default)
c
c PAIR 0 no pair production
c 1 pair production (default)
c
c LOSS 0 (controls energy losses) no energy loss
c 1 delta-rays are produced above the threshold. Reduced fluctuations from
c delta-rays below the threshold are added to the energy losses. The threshold
c energies for delta-ray production can be set using the CUTS card (see above).
c The fields 'dcute' and 'dcutm' in the CUTS card correspond to energy thresholds
c for electron and muon delta-rays, respectively. The default energy threshold
c value is 100 keV.
c 2 no delta-rays are produced. Complete fluctuations are calculated (default).
c
c DCAY 0 no decay in flight
c 1 decay in flight with generation of secondaries (default)
c 2 decay in flight without generation of secondaries
c
c DRAY 0 no delta ray production
c 1 delta ray production with generation of secondaries (default)
c 2 delta ray production without generation of secondaries
END