[mborgraeve]

Hello !
This is my first post on this forum, so do not hesitate to correct me if i do something wrong ;-)
Here is my problem :
When compiling OpenFoam (Allwmake) on Kubuntu 12.04 64bit, on 6 cores, i get the following error (this is only the first one, as there is a lot of them after which seem linked with this one) :

Note: ignore spurious warnings about missing mpicxx.h headers

wmake libso mpi
/usr/bin/ld: error: --add-needed is not supported but is required for libdl.so.2 in /home/matthieu/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib/libmpi.so
collect2: ld a retourné 1 code d'état d'exécution

The problem is that after this, a lot of similar errors occurs, and

/usr/bin/ld: error: cannot find -lfiniteVolume

and other "cannot find -lsomething" error, and the compiler starts to missing a lot of things.
I am following the tutorial from http://www.openfoam.org/download/git.php, and installed it in my $home/OpenFOAM/OpenFOAM-2.1.x.
I compiled ThirdParty-2.1.x without problems ($HOME/OpenFOAM/ThirdParty-2.1.x)

Is there somebody who had the same kind of errors, or who have any idea of how resolving these ?

Thank you
Best regards,
Matthieu Borgraeve

[wyldckat]

Greetings Matthieu and welcome to the forum!

Mmm... interesting error message. OK, let's try diagnosing this without having me reproduce the same installation in a virtual machine.

1. Run Allwmake like this:

   ./Allwmake > make.log 2>&1

2. When it's done, open the log file "make.log" and search for the first occurrence of "Error ". That should be the first problem and the one that needs to be dealt with.
3. If you're unable to figure it out, search-and-replace any sensitive data (user name, paths and so on) in that log file, packed it an attach it.
   You can pack it by running:

   tar -czf make.log.tar.gz make.log

Now, a few more questions:

• Did you install any specific GCC version or any other building utilities? Intel compilers, LLVM or something like that?
• How are you taking advantage of the 6 cores for building OpenFOAM? Did you run, before Allwmake, this command :

  export WM_NCOMPPROCS=6

• Do you have any other OpenFOAM installations in your machine? If so, what steps have you taken for keeping them separate?

Best regards,
Bruno

[mborgraeve]

Hi,
Thank you for this short reply !!
Here is more informaiton :

1. done
2. The first error is the one i gave in my first message, here is a copy of the make.log file part where it appears :

   Note: ignore spurious  warnings about missing mpicxx.h headers
   wmake libso mpi
   /usr/bin/ld: error: --add-needed is not supported but is required for  libdl.so.2 in  /home/matthieu/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/lib/libmpi.so
   collect2: ld a retourné 1 code d'état d'exécution
   make: ***

3. The beggining and end of the make.log file is attached (full targzipped is 490KB...)

Concerning the others questions :

• the gcc version is 4.6.3 (given by gcc --version), but 4.4 .7is also installed as i am willing to test SpeedIT and ofgpu with openFoam (version given by gcc-4.4 --version
• I ran

  export WM_NCOMPPROCS=6

  (not echo, but i assume you mean export)
• No, Idon't have other installation now, but i already tried a first time before, i then delete the OpenFoam folder, remove the source path/to/old/openfoam/etc/bashrc, redownload OpenFOAM from git and add the new source (/$HOME/OpenFOAM/OpenFOAM-2.1.x/etc/bashrc)

Thank you very much !


Best regards,
Matthieu Borgraeve

[wyldckat]

Yep, it's "export" not "echo"

Mmm, Kubuntu in French... On second thought, I'm going to give it a try in a virtual machine, because it's the second time today I see problems with Kubuntu and OpenFOAM. The other one was here: http://www.cfd-online.com/Forums/ope...tml#post375597

And from the "make.log" file you got, it's not clear as to what the specific issue is, although Open-MPI is not built using the same ld commands as OpenFOAM...

Like I wrote, I'm going to test this in a virtual machine.
In the mean time, do you have any special environment flags for building software? Such as "CFLAGS", "CXXFLAGS" and "LDFLAGS"?

[mborgraeve]

Yes, i'm franch, so if you nedd me to translate some parts of the make.log, do not hesistate ;-)

I will have a look on this post, thank you !

I dont know what you mean by flags. I did not do anything approaching thant on purpose (i installed kubuntu yesterday on a new drive for testing OpenFoam and gpu computing without making a mess of the company drive disk with drivers, cuda installation and OpenFoam modifications), so unless it has been done automatically by installing NVIDIA drivers, Cuda drivers and developpment kit or installing OpenFoam and relatives, i would say no.
I may not be able to test furtermore this afternoon (the computer is needed by somebody else, with the real drive), but i will tomorrow morning at least.
Thank you for your help !
Regards,
Matthieu

[wyldckat]

Hi Matthieu,

Well, I guess NVidia is the one to be blamed... I finished testing in Kubuntu 12.04 x86_64, fully up-to-date - in both English and French - and had no problems building OpenFOAM 2.1.x.

Attached is the environment I got from my virtual machine, without the OpenFOAM environment activated; you can see yours by running:

export

From there you can for example use:

export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

You should also clean up "LD_LIBRARY_PATH":

unset LD_LIBRARY_PATH

Then activate OpenFOAM's environment:

                 source $HOME/OpenFOAM/OpenFOAM-2.1.x/etc/bashrc

But compare your shell environment with the one attached and look for any suspicious looking stuff...

Best regards,
Bruno

[mborgraeve]

Hello,
Here is some news :
whern compiling cuda applications from the Nvidia sdk examples, i get an error with mpicxx or something like that, but actually i do not manage to reproduce it (yet...), so it can confirm that Cuda & Nvidia stuff may interfer with OpenFOAM.


I compared our 'export' data, without Openfoam bashrc sourcing, and almost differences differences concern Cuda, installed on my computer, not on yours. The only other is the PWD variable, with points to my Download folder in my $HOME, as yours go to /home/myusername/OpenFOAM/OpenFOAM-2.1.x.
my log is attached if you want to see it.

I am trying to uninstall cuda and see if it changes something in compiling OpenFoam after cleaning.

After that, i will try to resintall Cuda and recompile to see if it changes something.

Another question concerning .bash_profile and .bashrc : i know rc is called while starting a bash window, and profile when starting the computer, but the openfoam's bashrc file is in the .bashrc, as the modifications for sourcing Cuda libs are in the .bash_profile. Can it change something ? (i reboot after each change of bash_profile).

Regards,
Matthieu

[mborgraeve]

sorry for doubleposting, i forget the attached file...

[wyldckat]

Hi Matthieu,

If you can see the changes, then you can isolate them using aliases! Here's an long explanation I wrote sometime ago: Advanced tips for working with the OpenFOAM shell environment

Best regards,
Bruno

[mborgraeve]

Hi,
Currently compiling, the problem stays the same : I have two errors :

/usr/bin/ld: error: --add-needed is not supported but is  required for libpthread.so.0 in  /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/librt.so
 collect2: ld a retourné 1 code d'état d'exécution
make: *** [/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libscotchDecomp.so] Erreur 1
+ [ -d /home/matthieu/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/openmpi-1.5.3 ]

and

SOURCE=fvFieldDecomposer.C ;  g++ -m64 -Dlinux64 -DWM_DP  -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor  -O3  -DNoRepository -ftemplate-depth-100  -I/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/src/finiteVolume/lnInclude  -I/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/src/meshTools/lnInclude  -I/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/src/lagrangian/basic/lnInclude  -IlnInclude -I.  -I/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/src/OpenFOAM/lnInclude  -I/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/src/OSspecific/POSIX/lnInclude    -fPIC -c $SOURCE -o Make/linux64GccDPOpt/fvFieldDecomposer.o
/usr/bin/ld: error: cannot find -lfiniteVolume
/usr/bin/ld: error: cannot find -lmeshTools
/usr/bin/ld: error: cannot find -llagrangian
collect2: ld a retourné 1 code d'état d'exécution

Tryning to run autogen.sh in ThirdParty/openmpi, it says that

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/ThirdParty-2.1.x/openmpi-1.5.3$ ./autogen.sh 
[Checking] command line parameters
[Checking] prerequisites
Configuring projects: opal orte ompi
I could not find a recent enough copy of autom4te.
Need at least 2.59 but found  in autom4te.
I am gonna abort.  :-(

Please make sure you are using at least the following versions of the
GNU tools:

GNU Autoconf 2.59
GNU Automake 1.9.6
    NOTE: You may need Automake 1.8.5 (or higher) in order to run
    "make dist" successfully
GNU Libtool  1.5.22

Should i install it with apt-get install ?

[wyldckat]

Didn't you follow these instructions: http://www.openfoam.org/download/git.php ?

Check if the necessary packages are installed:

sudo apt-get install build-essential flex bison cmake zlib1g-dev qt4-dev-tools libqt4-dev gnuplot libreadline-dev libncurses-dev libxt-dev

[mborgraeve]

Yes i did, i just checked, and they are installed :

matthieu@INOPRO-HPPORT-KUBUNTU:~$ sudo apt-get install build-essential flex bison cmake zlib1g-dev qt4-dev-tools libqt4-dev gnuplot libreadline-dev libncurses-dev libxt-dev
[sudo] password for matthieu: 
Lecture des listes de paquets... Fait
Construction de l'arbre des dépendances       
Lecture des informations d'état... Fait
Note : sélection de « libncurses5-dev » au lieu de « libncurses-dev »
bison est déjà la plus récente version disponible.
build-essential est déjà la plus récente version disponible.
cmake est déjà la plus récente version disponible.
flex est déjà la plus récente version disponible.
libncurses5-dev est déjà la plus récente version disponible.
libreadline-dev est déjà la plus récente version disponible.
libxt-dev est déjà la plus récente version disponible.
zlib1g-dev est déjà la plus récente version disponible.
gnuplot est déjà la plus récente version disponible.
libqt4-dev est déjà la plus récente version disponible.
qt4-dev-tools est déjà la plus récente version disponible.
0 mis à jour, 0 nouvellement installés, 0 à enlever et 0 non mis à jour.

[wyldckat]

Mmm... OK, I guess it's best to go hardcore and install Ubuntu's own build of Open-MPI:

1. Edit OpenFOAM's "etc/bashrc", and change "WM_MPLIB=OPENMPI" to "WM_MPLIB=SYSTEMOPENMPI".

2. sudo apt-get install mpi-default-bin mpi-default-dev

3. Reboot the machine, just in case... although you can try simply starting a new terminal window/tab.
4. Check if mpirun is operational:
   

   sudo update-alternatives --config mpirun

5. Check if the proper MPI option is chosen by OpenFOAM's "bashrc":
   

   mpirun --version
   echo $FOAM_MPI
   echo $PINC
   echo $PLIBS
   echo $MPI_ARCH_PATH

[mborgraeve]

Hi,
Here are the results :

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ sudo update-alternatives --config mpirun
[sudo] password for matthieu: 
Sorry, try again.
[sudo] password for matthieu: 
Il n'existe qu'une « alternative » dans le groupe de liens mpirun : /usr/bin/mpirun.openmpi.
Rien à configurer.
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ mpirun --version
mpirun (Open MPI) 1.4.3

Report bugs to http://www.open-mpi.org/community/help/
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ echo $FOAM_MPI
openmpi-system
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ echo $PINC
-I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ echo $PLIBS
-pthread -L/usr/lib/openmpi/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ echo $MPI_ARCH_PATH
/usr/lib/openmpi

I restart Allwmake without cleaning, and it did some things more in ThirdParty, but i still get the same errors after :

+ wmake libso meshTools
/usr/bin/ld: error: --add-needed is not supported but is required for libfileFormats.so in /home/matthieu/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libtriSurface.so
collect2: ld a retourné 1 code d'état d'exécution
make: *** [/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libmeshTools.so] Erreur 1

and then it doen't find -lmeshtool :

+ wmake libso edgeMesh
/usr/bin/ld: error: cannot find -lmeshTools
collect2: ld a retourné 1 code d'état d'exécution
make: *** [/home/matthieu/OpenFOAM/OpenFOAM-2.1.x/platforms/linux64GccDPOpt/lib/libedgeMesh.so] Erreur 1

EDIT : after cleaning, ThirdParty compile without any error, I am compiling OpenFoam.

[wyldckat]

Hi Matthieu,

I hate to have to say this, but either you need to try and rebuild OpenFOAM from scratch, or you might even have to reinstall Kubuntu And then build OpenFOAM before installing anything else CUDA related...

I don't know what it is, but something messed up your Kubuntu installation, at least when compared to a clean installation. It might have been ld or something else, I don't know and unfortunately I'm unable to diagnose it fast enough...

One last attempt - what do these commands output:

gcc --version
g++ --version
ld --version
automake --version
flex --version
make --version
cpp --version

For me, on the clean installation I did with success:

$ gcc --version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

$ g++ --version
g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

$ ld --version
GNU ld (GNU Binutils for Ubuntu) 2.22
Copyright 2011 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.
bmss@bmss-virtual-machine:~$ automake --version
Le programme 'automake' peut être trouvé dans les paquets suivants :
 * automake
 * automake1.10
 * automake1.4
 * automake1.9
 * automake1.7
Essayez : sudo apt-get install <paquet sélectionné>

$ flex --version
flex 2.5.35

$ make --version
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
Ceci est un logiciel libre ; voir le source pour les conditions de copie.
Il n'y a PAS de garantie ; tant pour une utilisation COMMERCIALE que pour
RÉPONDRE À UN BESOIN PARTICULIER.

Ce logiciel est construit pour x86_64-pc-linux-gnu

$ cpp --version
cpp (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

I didn't even had automake installed...

I haven't looked at the environment log you posted before... I'm going to look at it now... maybe something comes to mind...

Best regards,
Bruno

[mborgraeve]

Hi,
I think i have all the same than you, except from the probleming ld :

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ ld --version
GNU gold (GNU Binutils for Ubuntu 2.22) 1.11
Copyright 2011 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.

It might be that one, but i installed it copy-pasting the line on the tutorial..

Here are the others versions :

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ gcc --version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ g++ --version
g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ ld --version
GNU gold (GNU Binutils for Ubuntu 2.22) 1.11
Copyright 2011 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ automake --version
automake (GNU automake) 1.11.3
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv2+: GNU GPL version 2 or later <http://gnu.org/licenses/gpl-2.0.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Tom Tromey <tromey@redhat.com>
       and Alexandre Duret-Lutz <adl@gnu.org>.
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ flex --version
flex 2.5.35
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ make --version
GNU Make 3.81
Copyright (C) 2006  Free Software Foundation, Inc.
Ceci est un logiciel libre ; voir le source pour les conditions de copie.
Il n'y a PAS de garantie ; tant pour une utilisation COMMERCIALE que pour
RÉPONDRE À UN BESOIN PARTICULIER.

Ce logiciel est construit pour x86_64-pc-linux-gnu
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ cpp --version
cpp (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright © 2011 Free Software Foundation, Inc.
Ce logiciel est libre; voir les sources pour les conditions de copie.  Il n'y a PAS
GARANTIE; ni implicite pour le MARCHANDAGE ou pour un BUT PARTICULIER.

matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$ 
matthieu@INOPRO-HPPORT-KUBUNTU:~/OpenFOAM/OpenFOAM-2.1.x$

EDIT : Could you give what answer ld --help (at least the --add-needed line) ? It igave me Not Supported, and OpenFoam compiling complains about that.

EDIT2 : it is still compiling, without errors (yet...). I will tell you the state tomorrow morning ;-), and if it still crashes, i will try to reinstall Kubuntu. I am currently doing it on another computer (with a fresh kubuntu installed) also, and it does the same (but i also installed CUDA & drivers before..) I'll keep you informed !
Thank you very much for your help

EDIT : just starting to do the same problem missing -lmeshTools or others -lsomething...

[wyldckat]

Hi Matthieu,

I didn't manage to answer you sooner... attached is the full help given by "ld --help".

As for more on the ld version:

$ dpkg-query -W binutils
binutils        2.22-6ubuntu1

Best regards,
Bruno

[mborgraeve]

Hi,
in mine, there is a line missing in yours comparing to me, as we have (nearly) the same version :

matthieu@INOPRO-HPPORT-KUBUNTU:~/Téléchargements$ dpkg-query -W binutils
binutils        2.22-6ubuntu1

I really do not understand...

I will try to reinstall kubuntu, from a fresh downloaded ISO, with a new installation on my usbkey.

[mborgraeve]

Hi,
After a clean reinstallation, the problem seems to disapear (without installing nvidia-current-updates, nor CUDA stuff).

matthieu@INOPRO-HPPort:~/OpenFOAM/ThirdParty-2.1.x$  dpkg-query -W binutils
binutils        2.22-6ubuntu1

matthieu@INOPRO-HPPort:~/OpenFOAM/ThirdParty-2.1.x$ ld --version
GNU ld (GNU Binutils for Ubuntu) 2.22
Copyright 2011 Free Software Foundation, Inc.
This program is free software; you may redistribute it under the terms of
the GNU General Public License version 3 or (at your option) a later version.
This program has absolutely no warranty.

Attached is the ld--version log, i think it is the same as you, where my --add-needed problem line is absent.

I am compiling ThirdParty, and i will compile OpenFoam during lunch time, and keep you informed. I will then try to install first nvidia-current-updates, retest it, and then try cuda.

[wyldckat]

Hi Matthieu,

Originally Posted by mborgraeve

I am compiling ThirdParty, and i will compile OpenFoam during lunch time, and keep you informed. I will then try to install first nvidia-current-updates, retest it, and then try cuda.

I'm looking forward to it

My guess is that the CUDA instructions need the older variant of ld, which does a more relaxed linking strategy, while the recent versions use a very strict linking method.
Here's a little reading material about this when it was discovered in OpenFOAM:

• http://www.openfoam.org/mantisbt/view.php?id=15
• http://www.openfoam.org/mantisbt/view.php?id=316

Wait... now that I think of it... aaaarrg... it should have been as easy as removing the string "-Xlinker --add-needed -Xlinker --no-as-needed" from the rule files
You'll find this string in the following files:

• wmake/rules/linux64Gcc/c
• wmake/rules/linux64Gcc/c++

But still, I don't know if this would have fixed the problem... it might simply bring up some other problems ...


Best regards,
Bruno