PS if I run with -start_in_debugger and do a backtrace I get the following:
Thread 1 "waiwera" received signal SIGSEGV, Segmentation fault.
0x00007fe12231b761 in PetscObjectComm (obj=0xfffffffffffffffe)
at /home/acro018/software/PETSc/code/src/sys/objects/gcomm.c:33
33 return obj->comm;
(gdb) bt
#0 0x00007fe12231b761 in PetscObjectComm (obj=0xfffffffffffffffe)
at /home/acro018/software/PETSc/code/src/sys/objects/gcomm.c:33
#1 0x00007fe12231488c in PetscLogEventBeginDefault (event=133, t=0,
o1=0xfffffffffffffffe, o2=0x0, o3=0x0, o4=0x0)
at
/home/acro018/software/PETSc/code/src/sys/logging/utils/eventlog.c:647
#2 0x00007fe1231bcbbd in DMPlexDistributeFieldIS (dm=0xfffffffffffffffe,
pointSF=0x55857b89eb40, originalSection=0x55857b7bdaf0,
originalIS=0x55857b793270, newSection=0x55857b8a26d0,
newIS=0x7ffc52486d58)
at
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexdistribute.c:832
#3 0x00007fe1233e5c9a in dmplexdistributefieldis_ (
dm=0x55857a4cdea8 <simulation+232>,
pointSF=0x55857a4cdf20 <simulation+352>,
originalSection=0x7ffc52486d88,
originalIS=0x55857a4cdf10 <simulation+336>, newSection=0x7ffc52486d50,
newIS=0x7ffc52486d58, __ierr=0x7ffc52486d4c)
at
/home/acro018/software/PETSc/code/src/dm/impls/plex/ftn-auto/plexdistributef.c:135
#4 0x000055857a202cc8 in mesh_module::mesh_distribute_index_set (self=...,
sf=..., section=..., index_set=...) at ../src/mesh.F90:3393
#5 0x000055857a22b60c in mesh_module::mesh_distribute (self=...)
at ../src/mesh.F90:152
#6 0x000055857a224626 in mesh_module::mesh_configure (self=...,
gravity=...,
json=0x55857b574180, logfile=..., err=0) at ../src/mesh.F90:826
#7 0x000055857a1baf14 in flow_simulation_module::flow_simulation_init (
---Type <return> to continue, or q <return> to quit---Quit
On 13/09/19 2:31 PM, Adrian Croucher wrote:
hi
My code is using DMPlexDistributeFieldIS() to distribute an index set,
and it seems to work ok, except if I run with -log_view.
In that case I get the error below.
The code (Fortran) looks like this:
call PetscSectionCreate(PETSC_COMM_WORLD, dist_section, ierr)
CHKERRQ(ierr)
call ISCreate(PETSC_COMM_WORLD, dist_index_set, ierr)
CHKERRQ(ierr)
call DMPlexDistributeFieldIS(self%dm, sf, section, &
index_set, dist_section, &
dist_index_set, ierr); CHKERRQ(ierr)
call PetscSectionDestroy(dist_section, ierr); CHKERRQ(ierr)
call ISDestroy(index_set, ierr); CHKERRQ(ierr)
index_set = dist_index_set
I'm running the master branch.
Any clues?
- Adrian
--
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[0]PETSC ERROR: or see
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[1]PETSC ERROR: or see
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
OS X to find memory corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: --------------------- Stack Frames
------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[1]PETSC ERROR: INSTEAD the line number of the start of the
function
[1]PETSC ERROR: is given.
[1]PETSC ERROR: [1] PetscLogEventBeginDefault line 642
/home/acro018/software/PETSc/code/src/sys/logging/utils/eventlog.c
[1]PETSC ERROR: [1] DMPlexDistributeFieldIS line 831
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[0]PETSC ERROR: INSTEAD the line number of the start of the
function
[0]PETSC ERROR: is given.
[0]PETSC ERROR: [0] PetscLogEventBeginDefault line 642
/home/acro018/software/PETSc/code/src/sys/logging/utils/eventlog.c
[0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[1]PETSC ERROR: Signal received
[1]PETSC ERROR: See
https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.
[1]PETSC ERROR: Petsc Development GIT revision:
v3.11.3-1582-gcb66735359 GIT Date: 2019-08-04 16:01:27 -0500
[1]PETSC ERROR: waiwera on a linux-gnu-c-debug named en-354401 by
acro018 Fri Sep 13 14:20:41 2019
[1]PETSC ERROR: Configure options --with-x --download-hdf5
--download-zlib --download-netcdf --download-pnetcdf
--download-exodusii --download-triangle --download-ptscotch
--download-chaco --download-hypre
[1]PETSC ERROR: #1 User provided function() line 0 in unknown file
[0] DMPlexDistributeFieldIS line 831
/home/acro018/software/PETSc/code/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See
https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
shooting.
[0]PETSC ERROR: Petsc Development GIT revision:
v3.11.3-1582-gcb66735359 GIT Date: 2019-08-04 16:01:27 -0500
[0]PETSC ERROR: waiwera on a linux-gnu-c-debug named en-354401 by
acro018 Fri Sep 13 14:20:41 2019
[0]PETSC ERROR: Configure options --with-x --download-hdf5
--download-zlib --download-netcdf --download-pnetcdf
--download-exodusii --download-triangle --download-ptscotch
--download-chaco --download-hypre
[0]PETSC ERROR: #1 User provided function() line 0 in unknown file
--
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
University of Auckland, New Zealand
email: [email protected]
tel: +64 (0)9 923 4611
