CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM

Debuggingoptimizing a code

Register Blogs Members List Search Today's Posts Mark Forums Read

Reply
 
LinkBack Thread Tools Display Modes
Old   August 12, 2005, 16:41
Default Hi, I've been trying to opti
  #1
Member
 
Fabian Peng Karrholm
Join Date: Mar 2009
Posts: 61
Rep Power: 8
fabianpk is on a distinguished road
Hi,
I've been trying to optimize my code, by running kcachegrind/valgrind on a version of my code compiled with the debug flags (changed it in that cshrc file). After running 'Allwmake' and then also recompiling lam-7.1.1 to create the libPstream file, I'm at loss what to do.

Down here is what I get when I try to run wmake on my code.

/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/wmake/tcshScripts/mkObjectDir /users/tfd/f98faka/OpenFOAM/f98faka-1.1/applications/bin/linuxDebug/cavDebugFoam
g++ -m32 -Dlinux -Wall -W -Wno-unused-parameter -O0 -fdefault-inline -ggdb3 -DFULLDEBUG -DNoRepository -ftemplate-depth-30 -I/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/src/OpenFOAM/lnInclude -IlnInclude -I. -I/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/src/cfdTools/incompressible -I/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/src/cfdTools/lnInclude -I/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/src/transportModels -DFACE_DECOMP -fPIC -pthread Make/linuxDebug/cavDebugFoam.o -L/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug \
-L/users/tfd/f98faka/OpenFOAM/f98faka-1.1/lib/linuxDebug -ldynamicMesh -lfaceDecompFiniteElement -lincompressibleTransportModels -lcfdTools -lOpenFOAM -ggdb3 -DFULLDEBUG -lm -o /users/tfd/f98faka/OpenFOAM/f98faka-1.1/applications/bin/linuxDebug/cavDebugFoam
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `dlerror'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `MPI::Is_initialized()'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `PMPI::Comm::mpi_comm_map'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `dlclose'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `MPI:p::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `MPI:p::Free()'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `dlopen'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `dlsym'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `op_intercept'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `PMPI::Intracomm::current_op'
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `PMPI::Comm::mpi_err_map'
collect2: ld returned 1 exit status
make: *** [/users/tfd/f98faka/OpenFOAM/f98faka-1.1/applications/bin/linuxDebug/cavDebugFoa m] Error 1

What else should I recompile?

/Fabian
fabianpk is offline   Reply With Quote

Old   August 13, 2005, 16:34
Default Hey Fabian OK the help
  #2
New Member
 
Michael McWilliam
Join Date: Mar 2009
Location: Waterloo, Ontario, Canada
Posts: 5
Rep Power: 8
pilot is on a distinguished road
Hey Fabian

OK the help disclaimer: I am not an expert but I have had troubles/experience compiling and installing OpenFoam so I know a couple things. So let me give you a couple of my thoughts:

**** Compiling libPstream.so ****

Go into:
OpenFOAM/OpenFOAM-1.1/src/Pstream/mpi

you should see a Pstream.C file there. That is the source for this missing .so file. That is what you compile to get the library. So to have it compiled you type in its directory:

wmake libso ./

That will compile just the Pstream library. The library should be placed in

OpenFOAM/OpenFOAM-1.1/lib/linuxOpt/lam-7.1.1

You may not need to compile Pstream it you might just need to link it properly.

**** Linking libPstream.so ****

So from your output it seems that your compiler is looking for Pstream in:

OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1

Once you are sure that you have libPstream.so compiled you can place a symbolic link in the "linuxDebug/lam-7.1.1" folder. Or you can go into the Make folder of what you are compiling/optimising and add the following to the EXE.LIB section of options file.

-l/<openfoam>/OpenFOAM-1.1/lib/linuxOpt/lam-7.1.1

**** Debug version of libPstream.so ****

There is another option you can re-compile the PStream lib with debugging options as you are trying to do by going into:

OpenFOAM/OpenFOAM-1.1/src/Pstream/mpi/Make

Add the -ggdb3 -DFULLDEBUG flags (Along with any other flags you want) mannually to the options file. Then the libPstream.so will have all your debugging symbols. Then you can place the compiled libPstream.so directly in the "linuxDebug/lam-7.1.1" folder. Then you can recompile libPstream.so without the debug flags and place it in linuxOpt folder. That way you will have a debug version and a optimised version.

There are my thoughts hopefully that will help you out.

Take Care
Mike McW
pilot is offline   Reply With Quote

Old   August 15, 2005, 08:44
Default I'm afraid nothing changes whe
  #3
Member
 
Fabian Peng Karrholm
Join Date: Mar 2009
Posts: 61
Rep Power: 8
fabianpk is on a distinguished road
I'm afraid nothing changes when I compile the Pstream library, it just says that they compile fine (I did a wclean first), but my code still won't compile using the debug binary libraries. The error message is the same.

/Fabian
fabianpk is offline   Reply With Quote

Old   August 15, 2005, 13:18
Default Seems your linking of cavDebug
  #4
Super Moderator
 
Mattijs Janssens
Join Date: Mar 2009
Posts: 1,416
Rep Power: 16
mattijs is on a distinguished road
Seems your linking of cavDebugFoam does not pick up all libraries. It misses:

libdl.so (dlopen etc.)
liblam.so (mpi_init)

Could it be that you do not have the correct settings to use lam for your architecture 'linuxDebug' and it picks up the default system mpi?

Check your $WM_DIR/rules for linuxDebug.
mattijs is offline   Reply With Quote

Old   August 16, 2005, 11:57
Default I managed to get it working by
  #5
Member
 
Fabian Peng Karrholm
Join Date: Mar 2009
Posts: 61
Rep Power: 8
fabianpk is on a distinguished road
I managed to get it working by changing WM_MPLIB to MPICH instead of LAM. Now I can't run mpirun and lamboot, so this means I can't run in parallel?


/Fabian
fabianpk is offline   Reply With Quote

Old   August 16, 2005, 12:05
Default MPICH does not use a deamon so
  #6
Senior Member
 
Hrvoje Jasak
Join Date: Mar 2009
Location: London, England
Posts: 1,758
Rep Power: 21
hjasak will become famous soon enough
MPICH does not use a deamon so if you've done everything right it should just run with mpirun.

Hrv
__________________
Hrvoje Jasak
Providing commercial FOAM/OpenFOAM and CFD Consulting: http://wikki.co.uk
hjasak is offline   Reply With Quote

Old   March 30, 2006, 13:32
Default Dear All, 1.3 there are thr
  #7
Super Moderator
 
Mattijs Janssens
Join Date: Mar 2009
Posts: 1,416
Rep Power: 16
mattijs is on a distinguished road
Dear All,

1.3 there are three useful environment variable when developing:

FOAM_ABORT : make OF abort and produce a core dump if there is an error in an input. This is useful e.g. when there is an error in a dictionary and you're trying to find out which dictionary.

FOAM_SIGFPE : make OF abort if there is a floating point exception (e.g. division by 0)

FOAM_SETNAN (new): initialize all blocks of dynamically allocated memory to a special floating point value (NaN). It will catch usage of unitialized memory.
- only if the numbers are floating point numbers
- only works on Linux (see sigFpe.C)
- only tested for double precision
mattijs is offline   Reply With Quote

Old   May 11, 2006, 13:09
Default For the problem due to dlerror
  #8
liu
Senior Member
 
Xiaofeng Liu
Join Date: Mar 2009
Location: State College, PA, USA
Posts: 118
Rep Power: 8
liu is on a distinguished road
For the problem due to dlerror, dlopen etc like:
/users/tfd/f98faka/OpenFOAM/OpenFOAM-1.1/lib/linuxDebug/lam-7.1.1/libPstream.so: undefined reference to `dlerror'

Solution: in the corresponding Make/options file
LIB_LIBS = ...\
...\
-dl

The linking flag '-dl' is not generated in my RHEL either. So I added it explicitly and solve the problem.
__________________
Xiaofeng Liu, Ph.D., P.E.,
Assistant Professor
Department of Civil and Environmental Engineering
Penn State University
223B Sackett Building
University Park, PA 16802


Web: http://water.engr.psu.edu/liu/
liu is offline   Reply With Quote

Old   May 11, 2006, 13:10
Default sorry, it should be '-ldl'.
  #9
liu
Senior Member
 
Xiaofeng Liu
Join Date: Mar 2009
Location: State College, PA, USA
Posts: 118
Rep Power: 8
liu is on a distinguished road
sorry, it should be '-ldl'.
__________________
Xiaofeng Liu, Ph.D., P.E.,
Assistant Professor
Department of Civil and Environmental Engineering
Penn State University
223B Sackett Building
University Park, PA 16802


Web: http://water.engr.psu.edu/liu/
liu is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
From 2D compressible code to 3D code David Liu Main CFD Forum 22 June 26, 2012 17:59
DLR TAU Code Tobias Hoell Main CFD Forum 2 June 11, 2011 13:32
A new CFD code! Apu@minimart.springfield Main CFD Forum 16 June 19, 2006 10:03
UDF-code Timo FLUENT 1 January 25, 2003 12:14
own Code vs. commercial code Bernhard Mueck Main CFD Forum 10 February 16, 2000 11:07


All times are GMT -4. The time now is 23:39.