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-   -   Segmentation fault when starting paraFoam (http://www.cfd-online.com/Forums/openfoam-installation/57286-segmentation-fault-when-starting-parafoam.html)

gaffu March 9, 2006 08:51

Hi! I have installed OpenFO
 
Hi!

I have installed OpenFOAM on a Suse linux 10.0 machine and it works fine, but paraFoam fails to start due to a segmentation fault:

/home/gaffu/OpenFOAM/OpenFOAM-1.2/bin/paraFoam: line 57: 1638 Segmentation fault paraview paraFoam.pvs

The installation test script gives no error:
Executing ./foamInstallationTest:

************************************************** ******
Checking basic setup...
-------------------------------------------------------------------------------
Shell: bash
Host: linux
OS: Linux version 2.6.13-15-default
User: gaffu
User_config: /home/gaffu/.bashrc
Foam_config: /home/gaffu/.OpenFOAM-1.2/bashrc sourced correctly.
-------------------------------------------------------------------------------


Checking main FOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /home/gaffu/OpenFOAM yes yes
$WM_PROJECT_USER_DIR /home/gaffu/OpenFOAM/gaffu-1.2 yes no
$FOAM_JOB_DIR /home/gaffu/OpenFOAM/jobControl no yes
-------------------------------------------------------------------------------


Checking the FOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR /home/gaffu/OpenFOAM/OpenFOAM-1.2 yes yes yes

$FOAM_USER_APPBIN ...fu-1.2/applications/bin/linuxGcc4Opt yes yes no
$FOAM_APPBIN ...AM-1.2/applications/bin/linuxGcc4Opt yes yes yes
$WM_DIR /home/gaffu/OpenFOAM/OpenFOAM-1.2/wmake yes yes yes
$FOAMX_PATH ...ations/utilities/preProcessing/FoamX yes no yes
$CEI_HOME /usr/local/ensight/CEI no no

$JAVA_PATH /home/gaffu/OpenFOAM/linux/j2sdk1.4.2_05 yes yes no
$MICO_ARCH_PATH ...c/mico-2.3.11/platforms/linuxGcc4Opt yes yes yes
$LAM_ARCH_PATH ...src/lam-7.1.1/platforms/linuxGcc4Opt yes yes yes
$MPICH_ARCH_PATH --------- env variable not set --------- no
-------------------------------------------------------------------------------


Checking the FOAM env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN ...enFOAM/OpenFOAM-1.2/lib/linuxGcc4Opt yes yes yes
$FOAM_USER_LIBBIN .../OpenFOAM/gaffu-1.2/lib/linuxGcc4Opt yes yes no
$LAM_ARCH_PATH ...src/lam-7.1.1/platforms/linuxGcc4Opt yes yes yes
-------------------------------------------------------------------------------


Software versions
-------------------------------------------------------------------------------
Software Version Location
-------------------------------------------------------------------------------
gcc 4.0.1 /home/gaffu/OpenFOAM/linux/gcc-4.0.1/bin/gcc
java 1.4.2_05 /home/gaffu/OpenFOAM/linux/j2sdk1.4.2_05/bin/java
gzip 1.3.5 /usr/bin/gzip
tar 1.3.5 /bin/tar
icoFoam ...OAM/OpenFOAM-1.2/applications/bin/linuxGcc4Opt/icoFoam
-------------------------------------------------------------------------------


Checking file/directory permissions...
-------------------------------------------------------------------------------
File/directory Set Reqd Crit
-------------------------------------------------------------------------------


Checking networking...
-------------------------------------------------------------------------------
Action Result Crit
-------------------------------------------------------------------------------
Pinging_linux Successful yes
Pinging_localHost Successful yes
Test_rsh: Unsuccessful_connection_refused* yes
Test_ssh: Successful yes
(*) Only one of rsh or ssh is required by the Foam enviroment.

-------------------------------------------------------------------------------

Base configuration ok.

Critical systems ok.

************************************************** *******




I have paraview 2.4.2 installed in /usr/local/, can this create a conflict with paraview 2.2.0 installed in $HOME/Openfoam/linux/ ?

Any suggestions are welcomed!

theof March 9, 2006 09:14

You should check the LD_LIBRAR
 
You should check the LD_LIBRARY_PATH and make sure it is not conflicting with you paraview-2.4.2 version. Look into $WM_PROJECT_DIR/.OpenFOAM-1.2/apps/paraview/cshrc (bashrc).

For your information it is possible to compile OpenFOAM-1.2 with your own paraview-2.4.2, by making adequat modifications in the previous cshrc (bashrc) files and in $WM_PROJECT_DIR/applications/utilities/postProcessing/graphics/PVFoamReader/
You have to recompile the libvtkFoam and libPVFoamReader specifying a CMake-2.2.* installation.
I have successfully done it with paraview-2.4.2 and the current CVS paraview-2.5, on a Suse 10 box (both paraview and openfoam compiled with gcc-2.0.4).
HTH
Theophane

gschaider March 9, 2006 09:25

Propably. If the parafoam-exec
 
Propably. If the parafoam-executable of 2.4.2 is found before the OpenFOAM-paraview (check with 'which paraview') you have this problem. Reorganize the PATH-variable in this case (the same is true for the LD_LIBRARY_PATH-variable for the dynamically-linked libraries)

gaffu March 9, 2006 10:03

I modified the path in $WM_PRO
 
I modified the path in $WM_PROJECT_DIR/.OpenFOAM-1.2/apps/paraview/bashrc

Now it works fine

Thank you!

zzli November 11, 2008 09:44

Help please! I ahve the same p
 
Help please! I ahve the same problems. How did you modify the path?

yannH March 31, 2010 08:38

Hi everybody !

I got a segmentation fault when running paraview. When I installed it last week, everything works, but since I use groovyBC, it doesn't work any more, even for (tutorial cases).

I recompile but no changes, and I try to debug it, (but I'm not a debugger at all !) :

--------------
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0xb18f26f0 (LWP 14008)]
0x00018810 in ?? ()
(gdb) bt
#0 0x00018810 in ?? ()
#1 0xafc7498c in ?? () from /home/yhh/OpenFOAM/OpenFOAM-1.6/lib/linuxGccDPOpt/libdecompositionMethods.so
#2 0xb7f1e9d0 in ?? () from /lib/ld-linux.so.2
#3 0xb7f1eb03 in ?? () from /lib/ld-linux.so.2
#4 0xb7f227b4 in ?? () from /lib/ld-linux.so.2
#5 0xb7f1e606 in ?? () from /lib/ld-linux.so.2
#6 0xb7f21f8e in ?? () from /lib/ld-linux.so.2
#7 0xb6b61c19 in ?? () from /lib/tls/i686/cmov/libdl.so.2
#8 0xb7f1e606 in ?? () from /lib/ld-linux.so.2
#9 0xb6b622bc in ?? () from /lib/tls/i686/cmov/libdl.so.2
#10 0xb6b61b51 in dlopen () from /lib/tls/i686/cmov/libdl.so.2
#11 0xb2f45765 in vtksys::DynamicLoader::OpenLibrary () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtksys.so.pv3.6
#12 0xb30f607d in vtkDynamicLoader::OpenLibrary () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtkCommon.so.pv3.6
#13 0xb62524a8 in vtkPVPluginLoader::SetFileName () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtkPVServerCommon.so
#14 0xb7a132a8 in pqPluginManager::loadServerExtension () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#15 0xb7a14e6b in pqPluginManager::loadExtension () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#16 0xb7a15361 in pqPluginManager::loadExtensions () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#17 0xb7a15bc9 in pqPluginManager::loadExtensions () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#18 0xb7a16a0e in pqProcessModuleGUIHelper::preAppExec () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#19 0xb6222b04 in vtkProcessModule::StartClient () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtkPVServerCommon.so
#20 0xb6224625 in vtkProcessModule::Start () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtkPVServerCommon.so
#21 0xb622b054 in vtkProcessModuleGUIHelper::Run () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libvtkPVServerCommon.so
#22 0xb79e6329 in pqMain::Run () from /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/libpqCore.so
#23 0x0804ad5e in main ()
(gdb) at
A program is being debugged already. Kill it? (y or n) y
Argument required (process-id to attach).
(gdb) run
Starting program: /home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/paraview-real
/home/yhh/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linuxGcc/bin/paraview-real: error while loading shared libraries: libpqComponents.so: cannot open shared object file: No such file or directory

Program exited with code 0177.
(gdb)
----------------------

The curious thing is that it says libpqComponents.so cannot open, but I check and it's present in /platforms/linuxGcc/bin and /platforms/linuxGcc/lib !

Is it a problem of path ?

robingilbert November 4, 2011 21:55

Quote:

Originally Posted by yannH (Post 252491)
The curious thing is that it says libpqComponents.so cannot open, but I check and it's present in /platforms/linuxGcc/bin and /platforms/linuxGcc/lib !

did you solve this issue?? i have the exact same error.. :confused:

wyldckat November 5, 2011 04:15

Greeting Robin...

:eek: this is a really old thread...

Robin, can you please describe the following details:
  • What Linux distribution and version you are using.
  • What Gcc version or Icc version you are using.
  • What version of OpenFOAM you are using.
  • What version of ParaView and Qt you are using and whether they are custom builds or installed with the distro package manager (apt-get, yast, yum, zypper, ...).
  • When did it stop working, if it ever worked.
Otherwise, it'll be a long guessing game :(

Best regards,
Bruno

robingilbert November 10, 2011 19:35

Greetings wyldckat,

Thank you for your reply.

Quote:

Originally Posted by wyldckat (Post 330805)
What Linux distribution and version you are using.

I am using ubuntu 10.04
Quote:

Originally Posted by wyldckat (Post 330805)
What Gcc version or Icc version you are using.

gcc version 4.3.3 (OpenFOAM)

Quote:

Originally Posted by wyldckat (Post 330805)
What version of OpenFOAM you are using.

OpenFOAM 1.6.x

Quote:

Originally Posted by wyldckat (Post 330805)
What version of ParaView and Qt you are using and whether they are custom builds or installed with the distro package manager (apt-get, yast, yum, zypper, ...).

Paraview version 3.6.1 and i installed it along with OpenFOAM

Quote:

Originally Posted by wyldckat (Post 330805)
When did it stop working, if it ever worked.

It used to work properly but stopped working after i installed swak4Foam

But recently i found a work around. I go to this location in my computer :

/home/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linux64Gcc/bin and open paraview directly. only thing is i have to convert all files to VTK before postprocessing. Any ideas on how i can rectify the problem??

Sorry for the late reply

wyldckat November 12, 2011 04:51

Hi Robin,

OK, a quick and dirty way to fix this is to edit the file "OpenFOAM-1.6.x/bin/paraFoam" and add the following line (the one in bold) right after the first block of comments:
Code:

# Description
#    start paraview with the OpenFOAM libraries
#
#------------------------------------------------------------------------------
export LD_LIBRARY_PATH=$ParaView_DIR:$LD_LIBRARY_PATH
usage() {
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done

And this should do the trick!

The odd thing is that it stopped working after swak4foam was built... maybe this is one of those bugs that has already been fixed in more recent versions of swak4foam and OpenFOAM ;)

Best regards,
Bruno

robingilbert November 14, 2011 14:33

Hi Bruno,

What you said did not work. What is LD_LIBRARY_PATH ? which directory does it point to? i cd-ed it and it said this:
Code:

bash: cd: /home/bluesim/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/openmpi-1.3.3:/home/bluesim/OpenFOAM/ThirdParty-1.6.x/openmpi-1.3.3/platforms/linux64GccDPOpt/lib:/home/bluesim/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/lib64:/home/bluesim/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux64/lib:/home/bluesim/OpenFOAM/ThirdParty-1.6.x/gmp-4.2.4/platforms/linux64/lib:/home/bluesim/OpenFOAM/ThirdParty-1.6.x/mpfr-2.4.1/platforms/linux64/lib:/home/bluesim/OpenFOAM/bluesim-1.6.x/lib/linux64GccDPOpt:/home/bluesim/OpenFOAM/site/1.6.x/lib/linux64GccDPOpt:/home/bluesim/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt:/home/bluesim/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/dummy: No such file or directory
Thank you.

wyldckat November 14, 2011 16:09

Hi Robin,

Quote:

Originally Posted by robingilbert (Post 332068)
What is LD_LIBRARY_PATH ? which directory does it point to?

Quoting from wikipedia:
Quote:

Originally Posted by http://en.wikipedia.org/wiki/Environment_variable#Examples_of_Unix_environment_ variables
$LD_LIBRARY_PATH

On many Unix systems with a dynamic linker, contains a colon-separated list of directories that the dynamic linker should search for shared objects when building a process image after exec, before searching in any other directories.

As briefly explained in the above quote, LD_LIBRARY_PATH has a list of folders/directories to search for libraries; such library is the missing library "libpqComponents.so".

If the modification I wrote about in the previous post didn't work, then could you please check if:
  1. The variable "ParaView_DIR" has anything assigned to it? To see what it has, run:
    Code:

    echo $ParaView_DIR
  2. If anything was outputted from the previous command, then run the following two commands:
    Code:

    ls -l $ParaView_DIR
    ls -l $ParaView_DIR/libpqComponents*

    The first command will show you the contents of the ParaView folder and the second one will try to show you the missing library.
Best regards,
Bruno

robingilbert November 16, 2011 16:05

Greetings Bruno,

Quote:

Originally Posted by wyldckat (Post 332079)
  1. The variable "ParaView_DIR" has anything assigned to it? To see what it has, run:
    Code:

    echo $ParaView_DIR

That gives this:
Code:

/home/bluesim/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/platforms/linux64Gcc
Quote:

Originally Posted by wyldckat (Post 332079)
ls -l $ParaView_DIR/libpqComponents*

This gives me:
Code:

ls: cannot access /home/bluesim/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/platforms/linux64Gcc/libpqComponents*: No such file or directory
Thank you so much,
Robin

wyldckat November 16, 2011 17:30

Hi Robin,

You didn't post what the following command displays:
Code:

ls -l $ParaView_DIR
My guess is that I guessed wrong the folder where the library really is. Try this instead:
Code:

ls -l $ParaView_DIR/bin/libpqComponents*
If this shows the missing library, then edit once more the paraFoam file and edit it to look like this instead:
Code:

# Description
#    start paraview with the OpenFOAM libraries
#
#------------------------------------------------------------------------------
export LD_LIBRARY_PATH=$ParaView_DIR/bin:$LD_LIBRARY_PATH
usage() {
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done

Best regards,
Bruno

robingilbert November 17, 2011 18:50

Hi Bruno,

Code:

ls -l $ParaView_DIR
That displays the following:

Code:

total 432
-rw-r-----  1 bluesim bluesim  1087 2011-11-04 17:51 about.html
drwxr-xr-x  4 bluesim bluesim  4096 2011-11-04 18:17 Applications
drwxr-xr-x  2 bluesim bluesim  12288 2011-11-04 19:13 bin
drwxr-xr-x  3 bluesim bluesim  4096 2011-11-04 17:51 CMake
-rw-r--r--  1 bluesim bluesim 127257 2011-11-04 18:17 CMakeCache.txt
drwxr-xr-x 34 bluesim bluesim  4096 2011-11-04 18:17 CMakeFiles
-rw-r--r--  1 bluesim bluesim  6021 2011-11-04 18:17 cmake_install.cmake
-rw-r--r--  1 bluesim bluesim  1547 2011-11-04 18:17 CMakeOutput.log
drwxr-xr-x  2 bluesim bluesim  4096 2011-11-04 17:51 CMakeTmp
drwxr-xr-x  4 bluesim bluesim  4096 2011-11-04 18:17 Common
-rw-r-----  1 bluesim bluesim  4350 2011-11-04 18:17 CPackConfig.cmake
-rw-r-----  1 bluesim bluesim  4622 2011-11-04 18:17 CPackSourceConfig.cmake
-rw-r-----  1 bluesim bluesim  3940 2011-11-04 17:51 CTestCustom.ctest
-rw-r--r--  1 bluesim bluesim    570 2011-11-04 18:17 CTestTestfile.cmake
-rw-r-----  1 bluesim bluesim  1798 2011-11-04 17:51 DartConfiguration.tcl
drwxr-xr-x  3 bluesim bluesim  20480 2011-11-04 18:17 Documentation
drwxr-xr-x  2 bluesim bluesim  4096 2011-11-04 18:17 lib
-rw-r--r--  1 bluesim bluesim  88984 2011-11-04 17:51 Makefile
-rw-r--r--  1 bluesim bluesim  9840 2011-11-04 18:17 ParaView3CompileToolsConfig.cmake
-rw-r-----  1 bluesim bluesim  1000 2011-11-04 18:17 ParaView3CPackOptions.cmake
-rw-r-----  1 bluesim bluesim  3370 2011-11-04 18:17 ParaViewConfig.cmake
-rw-r--r--  1 bluesim bluesim  28445 2011-11-04 17:51 ParaViewLibraryDepends.cmake
-rw-r--r--  1 bluesim bluesim    550 2011-11-04 17:51 PluginList.txt
drwxr-xr-x  6 bluesim bluesim  4096 2011-11-04 18:17 Plugins
-rw-r--r--  1 bluesim bluesim  31814 2011-11-04 18:17 pqClient.adp
drwxr-xr-x  8 bluesim bluesim  4096 2011-11-04 18:17 Qt
drwxr-xr-x  8 bluesim bluesim  4096 2011-11-04 18:17 Servers
drwxr-xr-x  3 bluesim bluesim  4096 2011-11-04 17:51 Testing
drwxr-xr-x  5 bluesim bluesim  4096 2011-11-04 17:51 Utilities
drwxr-xr-x 24 bluesim bluesim  4096 2011-11-04 18:17 VTK
-rw-r-----  1 bluesim bluesim  1763 2011-11-04 17:51 vtkPQConfig.h
-rw-r-----  1 bluesim bluesim  1645 2011-11-04 17:51 vtkPVConfig.h

Code:

ls -l $ParaView_DIR/bin/libpqComponents*
That gives:
Code:

-rwxr-xr-x 1 bluesim bluesim 4834428 2011-11-04 18:16 /home/bluesim/OpenFOAM/ThirdParty-1.6.x/paraview-3.6.1/platforms/linux64Gcc/bin/libpqComponents.so
With the edit that you suggested, it still shows segmentation fault. Thanks a lot for taking time to help me out.

Robin.

wyldckat November 18, 2011 17:42

Hi Robin,

OK, I guess that we'll have to try and to isolate the problem on the other side. You wrote before that things stopped working when you compiled/installed swak4foam, correct?
Then try renaming the folder "/home/bluesim/OpenFOAM/bluesim-1.6.x/" to something else. For example, run:
Code:

cd /home/bluesim/OpenFOAM
mv bluesim-1.6.x bluesim-1.6.x_tmp

Then try running paraFoam or paraview once again, to see if it still complains about the same problem.

If it still complains about the same problem, then it should be because you changed something else as well, when you built swak4foam.

Best regards and good luck!
Bruno

gschaider November 18, 2011 20:05

Quote:

Originally Posted by wyldckat (Post 332727)
Hi Robin,

OK, I guess that we'll have to try and to isolate the problem on the other side. You wrote before that things stopped working when you compiled/installed swak4foam, correct?

Don't think these two aspects have been discussed here. To my knowledge there are two ways for swak4Foam to 'break' paraview (it only plays libraries into $FOAM_USER_LIBBIN).

- Does paraview fail for all cases or only those where groovyBC is used? Try adding "libOpenFOAM.so" to the libs-list in the controlDict BEFORE libgroovyBC.so. Funnily enough this is only needed on Linux (not on the other OS with X in the end)
- Is it possible that some libraries ended up in $PV_PLUGIN_PATH (possibly because $FOAM_USER_LIBBIN is there)? Because then paraview will try to load them as plugins and fail miserably

Bernhard


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