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dosxyznrc n_split segfault
DOSXYZnrc seems to segfault if n_split > 1 and the phase space plane is outside of the phantom.
some_title #!GUI1.0
1
H2O521ICRU
0.521, 0.01, 0, 0
-1, -1, -1, 0
-1
1, 2
-1
1, 2
-1
1, 2
0, 0, 0, 0, 0, 0, 0, 0
0, 0, 0, 0, 0, 0, 0, 0
0, 0, 0, 0, 0, 0, 0, 0
0, 2, 0, 0, 0, 180, 0, 1.1, 180, 0, 0, 0, 0, 0
2, 0, 0, 1000, 0, , ,
$EGS_HOME/dosxyznrc/tiny.egsphsp
100000, 0, 999, 0, 1, 100, 0, 0, 0, 0, , 0, 1, 0, 10, 1, 0
#########################
:start MC Transport Parameter:
Global ECUT = 0.521
Global PCUT = 0.01
Global SMAX = 5
ESTEPE = 0.25
XIMAX = 0.5
Boundary crossing algorithm = PRESTA-I
Skin depth for BCA = 0
Electron-step algorithm = PRESTA-II
Spin effects = On
Brems angular sampling = Simple
Brems cross sections = BH
Bound Compton scattering = Off
Compton cross sections = default
Pair angular sampling = Simple
Pair cross sections = BH
Photoelectron angular sampling = Off
Rayleigh scattering = Off
Atomic relaxations = Off
Electron impact ionization = Off
Photon cross sections = xcom
Photon cross-sections output = Off
:stop MC Transport Parameter:
#########################
$ dosxyznrc -i segfault -p 521icru
================================================================================
EGSnrc version 4 for x86_64-unknown-linux-gnu Thu Jan 2 07:08:36 2020
================================================================================
configuration...............................................ansible
user code...................................................dosxyznrc
pegs file...................................................521icru on HEN_HOUSE
using host..................................................ptwlinuxvm
input file..................................................segfault
output file(s)..............................................segfault
================================================================================
Begin execution with large arrays being zeroed
Thisis only needed for Linux g77 compiler - comment
this code near the top of dosxyznrc.mortran if you are
not using a linux g77 compiler
*******************************************************************************
NRCC/UW EGSnrc user-code DOSXYZnrc
ON linux (ansible) 07:08:36 Jan 2 2020
*******************************************************************************
** **
** DOSXYZnrc **
** Z pronounced zed **
** **
** Code developed at the National Research Council of Canada and **
** University ofWisconsin as part of the OMEGA project **
** **
** **
** **
*******************************************************************************
The following parameters may be adjusted in dosxyz_user_macros.mortran
$MXMED: Max number of media: 7
$MXSTACK: Max stack size: 10000
$IMAX,etc: Max dose scoring regions in x,y,z directions: 360 360 360
$MAXDOSE: Max dose scoring regions consistent with above:*******
$DOSEZERO(=1) 1=> all doses with uncert > 50% are zeroed in .3ddose file
The following parameters may be adjusted in srcxyz.macros
$INVDIM: number of elements in inverse CPD for input energy spectra = 1000
$NENSRC: number of bins in input energy spectrum = 200
===============================================================================
-------------------------------------------------------------------------------
Title: some_title
-------------------------------------------------------------------------------
===============================================================================
Number of media (min = 1, max = 7, 0 => CT data): 1
Medium 1: H2O521ICRU
ECUTIN,PCUTIN,(ESTEPE,SMAX--DUMMY INPUTS):
0.521 0.010 0.000 0.000
# regions in x (max= 360),y (max= 360),z (max= 360) directions
(if<0,implies # groups of reg), IPHANT (1 to output a .egsphant
file for dosxyz_show, 0[default] to not output this file)
: -1 -1 -1 0
Input boundaries in the x-direction
-----------------------------------
Initial boundary: -1.000
Width in this group, number of regions in group: 1.000 2
Boundaries
-1.000 0.000 1.000
Input boundaries in the y-direction
-----------------------------------
Initial boundary: -1.000
Width in this group, number of regions in group: 1.000 2
Boundaries
-1.000 0.000 1.000
Input boundaries in the z-direction
-----------------------------------
Initial boundary: -1.000
Width in this group, number of regions in group: 1.000 2
Boundaries
-1.000 0.000 1.000
Total # regions including exterior = 9
Input groups of regions for which density and medium are not defaults
Lower,upper i, j, k, MEDIUM, DENSITY
Found blank line => end of this input
Input groups of regions for which ECUT and PCUT are not defaults
NB This option is disabled, just input 8 zeros.
Dummy values of lower,upper i, j, k, ECUT, PCUT
Found blank line => end of this input
Enter 8 numbers on one line
3 pairs defininglower,upper x,y,z indicies of dose regions
for which results are to be output
IZSCAN: non-zero for z-scan/page
MAX20: if any one = 1, output summary of max 20 doses.
end signaled by first pair both zero
forno dose printed, MAX20 is still read from first line
Found blank line => end of this input
No doses will be output to egslst file
Source configuration
(0) Parallel, rectangular beam incident from the front
Requires 9 inputs:
charge (-1,0,1),
0 (mandatory, to identify source type),
lower x-coordinate of the beam (cm),
upper x-coordinate of the beam (cm),
lower y-coordinate of the beam (cm),
upper y-coordinate of the beam (cm),
angle of beam with respect to the positive x-axis (degrees),
angle of beam with respect to the positive y-axis (degrees),
angle of beam with respect to the negative z-axis (degrees)
(angles default to 90,90,0--incident on front of phantom)
or (1) Parallel, rectangular beam incident from any direction
Requires 10 inputs:
charge (-1,0,1),
1 (mandatory, to identify source type),
x-coordinate of the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
angle between +z direction and the line joining the
center of the beam (collimator) to the isocenter
--called the polar angle(degrees),
angle between +x direction and the projection of the
line joining the center of the beam (collimator)
to the isocenter on the xy plane--called the azimuthal
angle (degrees),
total x-widthof the beam in the plane perpendicular
to the beam direction (cm),
total y-width of the beam in the plane perpendicular
to the beam direction (cm),
angle by which the collimator is rotated in the
collimator plane perpendicular to the beam
direction (degrees),
(+ve rotation is counterclockwise looking along
the beam direction
or (2) Full phase-space of each particle
Requires 9 inputs plus data stored in units 43 and 44:
charge (-1 electron,0 photon,1 positron, 2 all),
2 (mandatory, to identify source type),
x-coordinateof the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
angle between +z direction and the line joining the
origin in the phase space plane to the isocenter
--called the polar angle(degrees),
angle between +x direction and the projection of the
line joining the origin in the phase space plane
tothe isocenter on the xy plane--called the azimuthal
angle (degrees),
absolute distance from the isocenter to the origin
in the phase space plane
angle by which the source is rotated in the
phase space plane perpendicular to the beam
direction (degrees),
(+ve rotation is counterclockwise looking down
from the origin in the phase space plane),
i_dbs--set to 1 if DBS was used in BEAM simulation used
to generate the phsp source and you want to reject fat
photons, 0 otherwise,
DBS splitting radius (cm),
SSD at which splitting radius defined (cm),
Z at which phsp source collected (cm),
No. of times to split charged particles.
or (3) Point, rectangular beam incident from the front
Requires 7 inputs:
charge (-1,0,1),
3 (mandatory, to identify source type),
lower x-coordinate of the beam (cm),
upper x-coordinate of the beam (cm),
lower y-coordinate of the beam (cm),
upper y-coordinate of the beam (cm),
distance to the plane (cm),
or (6) Uniform isotropically radiating parallelepiped within
the phantom
Requires 8 inputs:
charge (-1,0,1),
6 (mandatory, to identify source type),
lower x-coordinate of active volume (cm)
upper x-coordinate of active volume (cm),
lower y-coordinate of active volume (cm)
upper y-coordinate of active volume (cm),
lower z-coordinate of active volume (cm)
upper z-coordinate of active volume (cm)
or (7) Parallel beam incident from multiple, user-selected angles
Requires 9 inputs on this line:
charge (-1,0,1),
7 (mandatory, to identify source type),
x-coordinate of the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
number of incident theta-phi pairs or -ve number of
groups of incident theta-phi pairs where, within a group
only theta or phi can vary, the varying angles are
evenly distributed and have equal probability,
total x-width of the beam in the plane perpendicular
to the beamdirection (cm),
total y-width of the beam in the plane perpendicular
to the beam direction (cm),
angle by which the collimator is rotated in the
collimator plane perpendicular to the beam
direction (degrees),
(+ve rotation is counterclockwise looking along
thebeam direction
or (8) Full phase-space incident from multiple angles
Requires 8 inputs on this line and data stored in units 43,44:
charge (-1 electron,0 photon,1 positron, 2all),
2 (mandatory, to identify source type),
x-coordinate of the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
number of incident theta-phi pairs or -ve number of
groups of incident theta-phi pairs where, within a group
only theta or phi can vary, the varying angles are
evenly distributed and have equal probability,
absolute distance from the isocenter to the origin
in the phase space plane
angle by which the source is rotated in the
phase space plane perpendicular to the beam
direction (degrees),
(+ve rotation is counterclockwise looking down
from the origin in the phase space plane),
i_dbs--set to 1 if DBS was used in BEAM simulation used
to generate the phsp source and you want to reject fat
photons, 0 otherwise,
DBS splitting radius (cm),
SSD at which splitting radius defined(cm),
Z at which phsp source collected (cm)
No. of times to split charged particles.
or (9) BEAM simulation of treatment head
Requires 11 inputs plus name of accelerator simulation,
input file used in accelerator simulation, and pegs4
data used in accelerator simulation:
charge (-1 electron,0 photon,1 positron, 2 all),
9 (mandatory, to identify source type),
x-coordinate of the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
angle between beam central axis and +z axis in DOSXYZ
geometry--called the polar angle(degrees),
angle between +x direction in DOSXYZ geometry and
beam central axis projected on the DOSXYZ xy plane
--called the azimuthal angle (degrees),
absolute distance from the isocenter to centre of
scoring plane in BEAM simulation,
angle to rotate BEAM simulation about its central
axis (degrees) (+ve rotation is counterclockwise
looking down the axis),
i_dbs--set to 1 if DBS is being used in BEAM simulation
and you want to reject fat photons, 0 otherwise,
No. of times to split charged particles.
or (10) BEAM simulation source incident from multiple angles
Requires 10 inputs plus name of accelerator simulation,
input file used in accelerator simulation,and pegs4
data used in accelerator simulation:
charge (-1 electron,0 photon,1 positron, 2 all),
9 (mandatory, to identify source type),
x-coordinate of the isocenter (cm),
y-coordinate of the isocenter (cm),
z-coordinate of the isocenter (cm),
number of incident theta-phi pairs or -ve number of
groups of incident theta-phi pairs where, within a group
only theta or phi can vary, the varying angles are
evenly distributed and have equal probability,
absolute distance from the isocenter to centre of
scoring plane in BEAM simulation,
angle to rotate BEAM simulation about its central
axis (degrees) (+ve rotation is counterclockwise
looking down the axis),
i_dbs--set to 1 if DBS is being used in BEAM simulation
and you want to reject fat photons, 0 otherwise,
No. of times to splitcharged particles.
or (20) Phase Space Incident from multiple settings
optionally through an MLC or through a BEAM accel.
Requires 6 inputs plus name of the input file used
forBEAM/vcu SIM. and the BEAM/VCU code if used
data used in simulation:
charge (-1 electron,0 photon,1 positron, 2 all),
20 (mandatory, to identify source type),
number of control points,
i_dbs: set to 1 if DBS is being used in simulation
and you want to reject fat photons, 0 otherwise,
r_dbs: radius of DBS splitting field in original
BEAM simulation,
ssd_dbs: SSD of DBS splitting field,
z_dbs: Z position where phase space was scored
in original BEAM simulation,
No. of times to splitcharged particles,
i_muidx_out: Set to 1 to include fractional MU index
in output phase space (i_phsp_out=1 or 2)
calflag: Set to 1 to skip the calibrationrun performed
to refine the estimate of NRCYCL.
or (21) BEAM simulation of treatment head will multiple settings
optionally through a MLC
Requires name of accelerator simulation,
input file used in accelerator simulation, and pegs4
data used in accelerator simulation, name of input file
for vcu SIM. and the VCU code (particleDmlc) if using MLC
charge (-1 electron,0 photon,1 positron, 2 all),
21 (mandatory, to identify source type),
number of control points
i_dbs: set to 1 if DBS is being used in BEAM simulation
and you want to reject fat photons, 0 otherwise,
No. of times to split charged particles.
i_muidx_out: Set to 1 to include fractional MU index
in output phase space (i_phsp_out=1 or 2)
All inputs on one line:
Full phase space from an arbitrary direction
x-coordinate of the isocenter: 0.0000
y-coordinate of the isocenter: 0.0000
z-coordinate of the isocenter: 0.0000
Polar angle of origin in source plane: 180.0000
Azimuthal angle of origin in source plane: 0.0000
Distance from isocenter to origin in source plane: 1.1000
Source rotation angle: 180.0000
No. of times to split e+/e-: 0
Charge of incident particles to use: 0
Enflag(0=mono-E,1=spectr,2=phsp or full BEAM sim.,3=dosecomp,4=beam model),
Mode(0,2), medsur(0 = vacuum), dsurround(1), dflag(0=1 dsurround,
1=4 dsurrounds), dsurround(2), dsurround(3), dsurround(4)
: 2 0 01000.000 0
The material in the region outside the phantom is vacuum.
The thickness of this region (in x, y & z direction) is:1000.000 cm
Input name of phase space file (A256)
:
Particles will be read from file:
$EGS_HOME/dosxyznrc/tiny.egsphsp
Retrieving file: /home/ptwlinuxvm/EGSnrc/egs_home//dosxyznrc/tiny.egsphsp
******WARNING*****
PHASE SPACE SOURCE WAS GENERATED USING AN OLDER
VERSION OF BEAM IN WHICH # OFPARTICLES INCIDENT FROM
ORIGINAL SOURCE WAS NOT STORED. THISNUMBER WILL
BE SET EQUAL TO THE NUMBER OF PARTICLES IN THE PHASE
SPACE SOURCE, AND DOSE WILL BE NORMALIZED
WITH RESPECTTO THE # OF HISTORIES RUN...NOT
THE # OF INCIDENT PARTICLES FROM THE ORIGINAL SOURCE
Total number of particles in file : 1
Total number of photons : 1
The rest are electrons/positrons.
Maximum kinetic energyof the particles: 1.000 MeV
Minimum kinetic energy ofthe electrons: Infinity MeV
# of particles incident fromoriginal source: 1.0
NCASE,IWATCH,TIMMAX,INSEED1,INSEED2,BEAM_SIZE,ISMOOTH,IRESTART,IDAT,
IREJECT,ESAVE_GLOBAL,NRCYCL,IPARALLEL,PARNUM,n_split,ihowfarless,i_phsp_out
: First RN seed outside allowed range and default value set
100000 0 999.00 1802 1 100.00 0 0 0 0 0.00**** 1 0 10 1 0
***************** Warning:
File /home/ptwlinuxvm/EGSnrc/egs_home/dosxyznrc/egsrun_15748_segfault_ptwlinuxvm/segfault.errors
is already opened and connected to unit 15
Will not try to re-open this file, assuming it has been opened
by specifying it in the .io file.
Bound Compton start region
Setting all to 0
Rayleigh start region
Setting all to 0
Relaxations start region
Setting all to 0
PE sampling start region
Setting all to 0
Call hatch
----------
===> Photonuclear flag: 0
Rayleigh data available for medium 1 in PEGS4 data set.
(Re)-initializing photon cross sections with files from the series: xcom
Compton cross sections: default
Using Compton cross sections from /home/ptwlinuxvm/EGSnrc/HEN_HOUSE/data/compton_sigma.data
Working on medium 1 ... OK
old PRESTA calculates default min. step-size for BCA:
minimum ECUT found: 0.52100000000000002
default BLCMIN is: 3.2034336048218699
this corresponds to 24.616909991620847 elastic MFPs
Reading screened Rutherford MS data ............... done
Reading spin data base from /home/ptwlinuxvm/EGSnrc/HEN_HOUSE/data/spinms.data
EGSnrc spin data, version 2.0
Data generated on a machine with 1234 endianess
The endianess of this CPU is 1234
Ranges: 1.00 100.00 0.30054 1.00000
medium 1 ..................... done
Medium 1 sige = 6.3784170227787529 6.1807995067678911 monotone = F F
Initializing tmxs for estepe = 0.25000000000000000 and ximax = 0.50000000000000000
Output from subroutine EDGSET:
==============================
Atomic relaxations not requested!
Bound Compton scattering not requested!
EGSnrc SUCCESSFULLY 'HATCHED' FOR ONE MEDIUM.
================================================================================
Electron/Photon transport parameter
================================================================================
Photon cross sections xcom
Compton cross sections default
Photon transport cutoff(MeV) 0.1000E-01
Pair angular sampling SIM
Pair cross sections BH
Triplet production Off
Bound Compton scattering OFF
Radiative Compton corrections Off
Rayleigh scattering OFF
Atomic relaxations OFF
Photoelectron angular sampling OFF
Electron transport cutoff(MeV) 0.5210
Bremsstrahlung cross sections BH
Bremsstrahlung angular sampling SIM
Spin effects On
Electron Impact Ionization Off
Maxium electron step in cm (SMAX) 5.000
Maximum fractional energy loss/step (ESTEPE) 0.2500
Maximum 1st elastic moment/step (XIMAX) 0.5000
Boundary crossing algorithm PRESTA-I
Skin-depth for boundary crossing (MFP) 24.62
Electron-step algorithm PRESTA-II
================================================================================
****WARNING****
ECUTIN > ECUT input in EGSnrc parameters ( 0.5210 MeV).
ECUT defaults to ECUTIN.
Will recyle each phase space particle **** times before going on
to next particle.
Restarted phase space files and recycled particles are not
redistributed
Starting a new calculation
Store intermediate files for each batch
*******************************************************************************
Summary of source parameters (srcxyznrc)
*******************************************************************************
Full phase space input for each incident particle
x-coordinate of the isocenter, 0.0000 cm
y-coordinate of the isocenter, 0.0000 cm
z-coordinate of the isocenter, 0.0000 cm
Polar angle of source plane: 180.0000 degrees
Azimuthal angle of origin in source plane: 0.0000 degrees
Distance from isocenter to origin in source plane: -1.1000 cm
Source plane rotation angle, 180.0000 degrees
Total number of particles in phase space file: 1
Particles to be simulated: photon only
Medium AE AP
H2O521ICRU 0.521 0.010
No range rejection.
Photons will be split 10 times
***************************************************************
Histories to be simulated for this run 100000
Histories to be analyzed after this run 100000
***************************************************************
Elapsed wall clock time to this point= 0.400 s
CPU time so far for this run = 0.400 s
BATCH # TIME-ELAPSED TOTAL CPUTIME RATIO TIME OF DAY RNG pointers
1 0.0 0.0 0.00 07:08:36 ixx jxx = 97 33
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f323b1b231a
#1 0x7f323b1b1503
#2 0x7f323a82ef1f
#3 0x55a5e6d1222d
#4 0x55a5e6d12f3c
#5 0x55a5e6d79d86
#6 0x55a5e6cd980e
#7 0x7f323a811b96
#8 0x55a5e6cd9839
#9 0xffffffffffffffff
Segmentation fault (core dumped)
You seem to have a warning of using an old phsp file format and I'm not sure is this a problem or not: "Minimum kinetic energy ofthe electrons: Infinity MeV".
Could you try with any "normal" phsp file?
@ojalaj good point. I tested and it also segafaults with a "normal" phsp file.
@jw3126 OK...does simulation run otherwise normally with nsplit=1? I see that you have increased IMAX,JMAX,KMAX from default values to 360. Your dsurround is quite large as well - 1000cm. Could these have some effect. Could you run your simulation starting with some of the example files and one by one changing the values towards your input file above.
Yeah it also segfaults if I don't touch IMAX etc. Starting with an example file is a good idea.