Why did my program crash

1
Why did my program crash? or How to debug your
OpenFOAM codes using GDB
2
Running your code

• Coding your own software good bad
• Programming your own codes without bugs is near
  impossible
• even for Weller Jasak

3
Debugging your code

• Debugging is a necessary evil to resolve bugs and
  examine crashes when developing all codes, and
  OpenFOAM is not an exception
• Built-in debug feature shows more details, but
  gives only passive information

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Debugging your code built-in

• Debugflags available in
• .OpenFOAM-1.4.1/controlDict
• lduMatrix 2
• Will give output for each matrix-iteration
• DICPCG Iteration 475 residual 0.542126
• No Recompilation of code needed.
• Flags set in code by
• defineTypeNameAndDebug(PCG, 0)

5
Debugging your code

• Alternative way
• Inserting
• Info ltlt "U is " ltlt Ucelli ltlt endl
• Requires Re-compilation (usually many times)

6
GDB - Introduction

• GDB is the GNU project debugger
• It can be used for
• - Programs written in C, C, Ada, Pascal etc
• - Run Stop at specific positions
• - Examine variables at run-time
• - Change your program at run-time

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Before we start Bad news
You need to recompile EVERYTHING! Debug version
of OpenFOAM requires 1 Gb of diskspace, vs 64 Mb
for Opt It is also slower Even slower when run
with GDB

• You need to recompile

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Compiling with Debug

• File
• .OpenFOAM-1.4.1/bashrc
• Comment
• setenv WM_COMPILE_OPTION Opt
• Uncomment
• setenv WM_COMPILE_OPTION Debug
• Then run the Allwmake script and go for a very
  long break.
• When you're back, some packages (e.g. the
  paraview reader) will have failed

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Compiling with Debug

• These packages can be compiled seperately with
  debug flags
• Quick Solution
• Use the Opt version, as we're most likely not
  interested in debugging such packages
• Done by simple copy of libPackageName.so

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Setup on Student Installation

• Pre-compiled version of Debug done by Håkan
• Used by copying
• .OpenFOAM-1.4.1 from local installation to
• /chalmers/users/userdir/
• And editing .cshrc/.bashrc like described before

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First Debug

• Objective To find out what a part of the code
  does
• Code icoFoam - for incompressible, laminar flow
• Simple code, suitable to start debugging, as
  there are not that many files included.

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Example icoFoam

• 73 U rUAUEqn.H()
• 74 phi (fvcinterpolate(U) mesh.Sf())
• fvcddtPhiCorr(rUA, U, phi)
• 77 adjustPhi(phi, U, p)
• 79 for (int nonOrth0 nonOrthltnNonOrthCorr
  nonOrth)
• fvScalarMatrix pEqn
• (
• fvmlaplacian(rUA, p) fvcdiv(phi)
• )

What does adjustPhi do?
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Example - icoFoam

• Start GDB in case directory
• gdb icoFoam
• GNU gdb 6.5 ...
• (gdb)

Start off by inserting a breakpoint where we want
to inspect the code
b icoFoam.C77
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Starting the Debug

• Program can be started in two ways
• start ltrootgt ltcasegt - Stops at main
• or
• run . . - Runs Program
• If all is well, program should now stop at line
  77 of icoFoam

Breakpoint 1, main (argc3, argv0x7fffc346b128)
at icoFoam.C77 77
adjustPhi(phi, U, p)
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Two Ways of Stepping

• Next n Step until next line in the current
  program, will not debug functions and included
  files
• Step s Step until next source line, will
  debug subfunctions
• Both commands can be followed by a number to step
  a certain amount of lines

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adjustPhi

• where shows which file we are debugging and
  which file called it
• list gives a listing of the source code around
  the current line, e.g. list 40,60 lists lines
  40-60
• Now in
• cfdTools/general/adjustPhi/adjustPhi.C42
• Stepping and listing the code will show how
  adjustPhi ensures continuity

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Useful Commands

• See GDBCommands.pdf for a quick guide to the
  commands available in GDB. This list is by no
  means complete and a full listing is available
  at
• http//sourceware.org/gdb/documentation/

18
Tutorial Example

• Why does Xoodles crash when starting the
  pitzDaily3D case?
• Known error from forums, output from Opt
• 6 main in "/c3se/users/f98faka/OpenFOAM/OpenFOAM
  -1.4.1/applications/bin/linux64GccDPOpt/Xoodles"
• 7 __libc_start_main in "/lib64/tls/libc.so.6"
• With Debug version of OF
• 7 main at /OpenFOAM/OpenFOAM-
• 1.4.1/applications/solvers/combustion/Xoodles/../X
  iFoam/bEqnn.H79
• 8 __libc_start_main in "/lib64/libc.so.6"

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Tutorial Example

• Start Xoodles with GDB and a breakpoint at this
  location
• Breakpoint 1, main (argc3, argv0x7fffb8830fc8)
  at ../XiFoam/bEqn.H79
• 79 volScalarField tauEta sqrt(thermo-gtmuu()/(rho
  uepsilon))
• Possible issue with division, inspection of some
  epsilon values shows low epsilon.

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Post-debugging

• Codes run without gdb that crash
• Set system to dump core-file
• Core-files can be used to inspect where errors
  occurred
• In cshrc
• limit coredumpsize unlimited
• In bashrc
• ulimit -c unlimited
• Then simply loaded in gdb by core-file
  ltcorefilenamegt

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Questions GDB can answer

• What does .flux do?
• What happens when .solve is issued?
• When does my variable go below x?
• How does scheme x work?
• Where did my code crash?

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End

• Thanks for listening!