[OpenFOAM.org] Inconsistency detected by ld.so - OF 2.3.0 in Ubuntu 14.04

seav · May 29, 2014, 08:26

Hello I have strange problem. After succesfull OF230 install on Ubuntu 14.04 (installation from openfoamwiki) I could normally use OF. I have been calculated simpleFoam/pitzDaily tutorial case.

Today I wanted to work with OF and using blockMesh and everything connected to OF i got an error :

Code:

Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed!

Any one knows whats happend ?

seav

seav · May 29, 2014, 14:41

Solved this.

If anyone have the same problem remove :

Code:

WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI

from your ~/.bashrc file.

Corrected one:

Code:

alias of230='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc' #WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI'

As far as I found out this is problem in system, and its on bugtracker.

Cheers
seav

wyldckat · May 31, 2014, 15:34

Greetings seav,

Thanks for the feedback on how you solved the problem in your case.

The result of not using "WM_MPLIB=SYSTEMOPENMPI" leads to OpenFOAM using its own Open-MPI build. As for not using "WM_NCOMPPROCS=4", means that the build will only be done with a single core, not with 4.

But I'm still wondering about what happened in the first place. My guess is that you might have installed another MPI toolbox in your Ubuntu installation, which disrupted the OpenFOAM installation. But I've tried to reproduce the same error and I wasn't able to do so.

Nonetheless, I've updated the wiki instructions to have a new step #5, which indicates how to ensure which MPI toolbox is used by the OpenFOAM installation, when following those instructions.

Best regards,
Bruno

seav · May 31, 2014, 17:43

Hi Bruno,

Installation went through without any problems. Even first tutorial case which I calculated worked fine. Than I rebooted my laptop and got problem described above.

If I follow #5 step after my installation will it work now ?

EDIT: I will check my packages tomorrow and post the result for detailed info.

Cheers,
seav

seav · June 1, 2014, 06:04

Hello.

Bruno u had right. I have default install of multi-passing-library.

Code:

dpkg --get-selections | grep mpi

Code:

libexempi3:amd64				install
libhdf5-openmpi-7:amd64				install
libopenmpi-dev					install
libopenmpi1.6					install
mpi-default-bin					install
openmpi-bin					install
openmpi-common					install
sa-compile					install

Making links after all dont work.

Cheers
seav

wyldckat · June 1, 2014, 10:19

Hi seav,

To see which MPI toolboxes are available on your system, run:

Code:

update-alternatives --display mpi | grep priority

For example, in the virtual machine where I'm doing these tests, it shows this:

Code:

/usr/include/mpich - priority 40
/usr/lib/openmpi/include - priority 50

As for using the symbolic links, it depends if you're using the original alias command line that was created when following the instructions and ran Allwmake again in the updated shell environment.

As for it stopping to work after rebooting, in theory, there are at least a couple of possibilities:

You might have installed something, after OpenFOAM was installed and working in one or more terminals, which was simply not available on the working shell environments (one shell per terminal/console window). If you had started a new terminal/console before rebooting, it should have given you the same problem you witnessed after rebooting.
There might have been a disk writing issue and the Open-MPI installed with apt-get might have gotten damaged in the process.

If you use the original environment that is defined when calling the original of230, we can diagnose what is going on, by running:

Code:

ldd $(which blockMesh)

This will show us to which libraries it's trying to link to.

Best regards,
Bruno

seav · June 2, 2014, 03:27

Hi Bruno.

I have followed those commands and here are results.

Code:

/usr/lib/openmpi/include - priority 50

I switched alias in ~/.bashrc to original one and the error is the same.

Code:

ldd $(which blockMesh)

Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed!

Cheers,
seav

samurai_01 · July 4, 2014, 08:00

Hi

Changing the bashrc worked for me. Thanks

seav · July 4, 2014, 08:22

I am glad to hear that

Cheers,
seav

gohome · August 13, 2014, 00:00

Changing the bashrc in #2 does NOT work for me...
Reinstalling it from here does NOT work either...
Any other solution? Thanks a lot

wyldckat · August 17, 2014, 12:33

Greetings to all!

@gohome:

Quote:

Originally Posted by gohome

Changing the bashrc in #2 does NOT work for me...
Reinstalling it from here does NOT work either...
Any other solution? Thanks a lot

I have not yet managed to figure out how to correctly solve this problem, because I don't know how to reproduce the same error

So far some people who had similar issues to the ones above simply reinstalled Ubuntu and tried following the installation instructions from here: http://openfoamwiki.net/index.php/In...M-2.3.0/Ubuntu - and at the second try it worked fine for them.

Therefore, if you can detail every single step you've taken, so that I can try and reproduce the same error, then I should be able to figure out how to solve this problem. Otherwise, I don't know where else to look at for fixing this

Best regards,
Bruno

fobonacci · August 23, 2014, 00:00

Hey,
I had the same error too. I reran "./Allwmake > make.log 2>&1" and it works for me now.

hk318i · August 29, 2014, 18:27

I have the same error.
I noticed something very strange, the error is case dependent. For example I tried blockMesh on two different cases and I get the error from one case and worked fine in the other one.

Update:
I recompiled OpenFOAM-2.3.x again from scratch. It is my second time this week for different reason.

wyldckat · August 30, 2014, 09:23

Greetings Hassan,

Quote:

Originally Posted by hk318i

I noticed something very strange, the error is case dependent. For example I tried blockMesh on two different cases and I get the error from one case and worked fine in the other one.

It's possible that you used 2 different consoles, where one had a working OpenFOAM environment and the other did not, therefore it worked fine on the first console, but not on the second one.

If you haven't already, I suggest that you study a bit this page: http://openfoamwiki.net/index.php/In...with_the_Shell - feedback is welcome!

Best regards,
Bruno

hk318i · August 30, 2014, 09:45

Quote:

Originally Posted by wyldckat

Greetings Hassan,

It's possible that you used 2 different consoles, where one had a working OpenFOAM environment and the other did not, therefore it worked fine on the first console, but not on the second one.

If you haven't already, I suggest that you study a bit this page: http://openfoamwiki.net/index.php/In...with_the_Shell - feedback is welcome!

Best regards,
Bruno

Acutely I used the same terminal. I just moved from case one directory to case two directory and returned back. I tried manytimes and tried different OpenFOAM commands (checkMesh, mapFields, rhoCentralDyMFoam, pimpleDyMFoam, rhoCentralFoam,..)?! I still don't know what was the problem.

wyldckat · August 30, 2014, 10:56

Quote:

Originally Posted by hk318i

Acutely I used the same terminal. I just moved from case one directory to case two directory and returned back. I tried manytimes and tried different OpenFOAM commands (checkMesh, mapFields, rhoCentralDyMFoam, pimpleDyMFoam, rhoCentralFoam,..)?! I still don't know what was the problem.

Without more specific details on what were the cases exactly, I cannot even try to diagnose the problem

At the very least, I can imagine that it's possible that the case that did not work had the "libs" keyword in the file "system/controlDict", which would make blockMesh to load a library that was not compatible with the build you had of OpenFOAM. Or perhaps the path to the case have a space or invalid character, which lead to the crash for some reason...

hk318i · August 30, 2014, 11:11

Quote:

Originally Posted by wyldckat

Without more specific details on what were the cases exactly, I cannot even try to diagnose the problem

At the very least, I can imagine that it's possible that the case that did not work had the "libs" keyword in the file "system/controlDict", which would make blockMesh to load a library that was not compatible with the build you had of OpenFOAM. Or perhaps the path to the case have a space or invalid character, which lead to the crash for some reason...

Don't worry, I couldn't reproduce the same error on two different machines, however I used the same cases with the same folders hierarchy.

cuzco · September 14, 2014, 13:08

As non of the above mentioned worked for me, I did a little research and found a solution. According to https://bugs.launchpad.net/ubuntu/+s...9/+bug/1248642, the cause for the error

Code:

Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed!

is a bug in the libGL library. Although I don't use the nVidia drivers, I was able to figure out a little workaround. For x64 systems, you can type

Code:

export LD_PRELOAD= /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1

into the terminal and compile the ThirdParty source again. When I was trying to execute mpirun afterwards, I got another error:

Code:

--> FOAM FATAL ERROR: 
Trying to use the dummy Pstream library.
This dummy library cannot be used in parallel mode

    From function UPstream::init(int& argc, char**& argv)
    in file UPstream.C at line 37.

I was able to fix it by following this instructions: http://www.cfd-online.com/Forums/ope...e-openmpi.html

Summary:

Code:

cd $FOAM_LIBBIN
mv dummy dummy.backup

cd $FOAM_SRC
cd Pstream
./Allwmake

cd $FOAM_SRC
cd dummyThirdParty
./Allwmake

I hope, my workaround is working for others, too.

Bye Marco

vitor.geraldes@ist.utl.pt · May 3, 2015, 20:58

I solve the problem including the following command in the file ~/.bashrc :
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1

May 29, 2014, 08:26	Inconsistency detected by ld.so - OF 2.3.0 in Ubuntu 14.04	#1
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	Hello I have strange problem. After succesfull OF230 install on Ubuntu 14.04 (installation from openfoamwiki) I could normally use OF. I have been calculated simpleFoam/pitzDaily tutorial case. Today I wanted to work with OF and using blockMesh and everything connected to OF i got an error : Code: Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed! Any one knows whats happend ? seav

May 31, 2014, 15:34		#3
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,982 Blog Entries: 45 Rep Power: 128	Greetings seav, Thanks for the feedback on how you solved the problem in your case. The result of not using "WM_MPLIB=SYSTEMOPENMPI" leads to OpenFOAM using its own Open-MPI build. As for not using "WM_NCOMPPROCS=4", means that the build will only be done with a single core, not with 4. But I'm still wondering about what happened in the first place. My guess is that you might have installed another MPI toolbox in your Ubuntu installation, which disrupted the OpenFOAM installation. But I've tried to reproduce the same error and I wasn't able to do so. Nonetheless, I've updated the wiki instructions to have a new step #5, which indicates how to ensure which MPI toolbox is used by the OpenFOAM installation, when following those instructions. Best regards, Bruno __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

June 1, 2014, 10:19		#6
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,982 Blog Entries: 45 Rep Power: 128	Hi seav, To see which MPI toolboxes are available on your system, run: Code: update-alternatives --display mpi \| grep priority For example, in the virtual machine where I'm doing these tests, it shows this: Code: /usr/include/mpich - priority 40 /usr/lib/openmpi/include - priority 50 As for using the symbolic links, it depends if you're using the original alias command line that was created when following the instructions and ran Allwmake again in the updated shell environment. As for it stopping to work after rebooting, in theory, there are at least a couple of possibilities: You might have installed something, after OpenFOAM was installed and working in one or more terminals, which was simply not available on the working shell environments (one shell per terminal/console window). If you had started a new terminal/console before rebooting, it should have given you the same problem you witnessed after rebooting. There might have been a disk writing issue and the Open-MPI installed with apt-get might have gotten damaged in the process. If you use the original environment that is defined when calling the original of230, we can diagnose what is going on, by running: Code: ldd $(which blockMesh) This will show us to which libraries it's trying to link to. Best regards, Bruno __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

June 2, 2014, 03:27		#7
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	Hi Bruno. I have followed those commands and here are results. Code: /usr/lib/openmpi/include - priority 50 I switched alias in ~/.bashrc to original one and the error is the same. Code: ldd $(which blockMesh) Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void *)0)' failed! Cheers, seav

August 23, 2014, 00:00		#12
fobonacci New Member Anup Join Date: Aug 2014 Posts: 1 Rep Power: 0	Hey, I had the same error too. I reran "./Allwmake > make.log 2>&1" and it works for me now. wyldckat and lordvon like this.

May 29, 2014, 14:41		#2
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	Solved this. If anyone have the same problem remove : Code: WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI from your ~/.bashrc file. Corrected one: Code: alias of230='source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc' #WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI' As far as I found out this is problem in system, and its on bugtracker. Cheers seav

May 31, 2014, 17:43		#4
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	Hi Bruno, Installation went through without any problems. Even first tutorial case which I calculated worked fine. Than I rebooted my laptop and got problem described above. If I follow #5 step after my installation will it work now ? EDIT: I will check my packages tomorrow and post the result for detailed info. Cheers, seav

June 1, 2014, 06:04		#5
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	Hello. Bruno u had right. I have default install of multi-passing-library. Code: dpkg --get-selections \| grep mpi Code: libexempi3:amd64 install libhdf5-openmpi-7:amd64 install libopenmpi-dev install libopenmpi1.6 install mpi-default-bin install openmpi-bin install openmpi-common install sa-compile install Making links after all dont work. Cheers seav

July 4, 2014, 08:00		#8
samurai_01 Member Join Date: Oct 2012 Posts: 46 Rep Power: 14	Hi Changing the bashrc worked for me. Thanks

July 4, 2014, 08:22		#9
seav Member Join Date: May 2013 Posts: 51 Rep Power: 13	I am glad to hear that Cheers, seav

August 13, 2014, 00:00		#10
gohome New Member Carl Liu Join Date: Apr 2014 Posts: 3 Rep Power: 12	Changing the bashrc in #2 does NOT work for me... Reinstalling it from here does NOT work either... Any other solution? Thanks a lot

August 29, 2014, 18:27		#13
hk318i Senior Member Hassan Kassem Join Date: May 2010 Location: Germany Posts: 242 Rep Power: 18	I have the same error. I noticed something very strange, the error is case dependent. For example I tried blockMesh on two different cases and I get the error from one case and worked fine in the other one. Update: I recompiled OpenFOAM-2.3.x again from scratch. It is my second time this week for different reason. Last edited by hk318i; August 30, 2014 at 06:18.

September 14, 2014, 13:08		#18
cuzco New Member Marco Trott Join Date: Mar 2014 Location: Magdeburg, Germany Posts: 2 Rep Power: 0	As non of the above mentioned worked for me, I did a little research and found a solution. According to https://bugs.launchpad.net/ubuntu/+s...9/+bug/1248642, the cause for the error Code: Inconsistency detected by ld.so: dl-version.c: 224: _dl_check_map_versions: Assertion `needed != ((void )0)' failed! is a bug in the libGL library. Although I don't use the nVidia drivers, I was able to figure out a little workaround. For x64 systems, you can type Code: export LD_PRELOAD= /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 into the terminal and compile the ThirdParty source again. When I was trying to execute mpirun afterwards, I got another error: Code: --> FOAM FATAL ERROR: Trying to use the dummy Pstream library. This dummy library cannot be used in parallel mode From function UPstream::init(int& argc, char& argv) in file UPstream.C at line 37. I was able to fix it by following this instructions: http://www.cfd-online.com/Forums/ope...e-openmpi.html Summary: Code: cd $FOAM_LIBBIN mv dummy dummy.backup cd $FOAM_SRC cd Pstream ./Allwmake cd $FOAM_SRC cd dummyThirdParty ./Allwmake I hope, my workaround is working for others, too. Bye Marco wyldckat and Hamzeh_Mirab like this. Last edited by cuzco; September 14, 2014 at 18:02.*

May 3, 2015, 20:58		#19
vitor.geraldes@ist.utl.pt New Member Vitor Geraldes Join Date: Dec 2009 Location: Lisbon, Portugal Posts: 26 Rep Power: 16	I solve the problem including the following command in the file ~/.bashrc : export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 benqing likes this.

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