OpenFoam-1.6-ext Allwmake compilation error - one last barrier
 

Hello,

I have compiled the ThirdParty packages under openLinux 12.1. With this patches it was completely successful:

http://openfoam-extend.git.sourcefor...8d5a40e5581224

I did edit the prefs.sh with:

compilerInstall=System
export WM_COMPILER_DIR=/usr

export WM_MPLIB=SYSTEMOPENMPI
export OPENMPI_DIR=/usr/lib64/mpi/gcc/openmpi
export OPENMPI_BIN_DIR=$OPENMPI_DIR/bin

export QT_DIR=/usr
export QT_BIN_DIR=$QT_DIR/bin


How I've said, the ThirdParty compilation was without errors.

My problem now is, that the compilation of the Allwmake in the OpenFOAM-1.6-ext directory leads to some errors.









And so on..
I think it is the same failure, that leads to all that errors.
Is someone able to help me? I'm trying to install OpenFoam-ext since 3 days without success :(
System gcc is Ver. 4.6

> My problem now is, that the compilation of the Allwmake in the OpenFOAM-1.6-ext directory leads to some errors.

Double check your logs, you certainly have additional errors occurring earlier in the compilation process.

For my compilation recipe for OpenSUSE 12.1, you can check here:

http://openfoam-extend.git.sourcefor...3472fd1ef579fa

I have started to publish my compilation recipes for various operating systems under the directory docs/buildInstructions.

Hope this helps.

Martin

Thank you very much.
I have tried to make a new compilation by follow your instructions, and the whole third party compilation was successful. But now I have big trouble compiling the Allwmake.

All of my Allwmake files are attached.

[ MB: I am editing this post because the answer I posted earlier is for another thread. Sorry for the noise]

Indeed, there is something missing for gcc 4.6.x under the head branch.

You could fix it yourself like this, until a proper fix is uploaded:

cp -r /home/patrick/OpenFOAM/OpenFOAM-1.6-ext/wmake/rules/linux64Gcc /home/patrick/OpenFOAM/OpenFOAM-1.6-ext/wmake/rules/linux64Gcc46

Martin

Just making sure the Email version of my post will get updated as well. Again, sorry for the noise.
Martin

This fix seems to be a compromise, isn't it? It is compiling, but do I have to recompile it when the proper fix is uploaded?

Thank you for the support!

> This fix seems to be a compromise, isn't it? It is compiling, but do I have to recompile it when the proper fix is uploaded?

Nope, this IS the solution. You won't have to recompile anything.

You will only have to destroy the directory OpenFOAM-1.6-ext/wmake/rules/linux64Gcc46 before doing "git update" in order to get rid of the version conflict. The update will recreate the 'linux64Gcc46' directory for you.

Martin

That sounds very good. Thank you very much!

But I have a question again:
In your buildinstructions -> openSuse 12.1 in the line

37 sed -i s/"compilerInstall=System"/"compilerInstall=System\nWM_COMPILER=Gcc46"/g ~/OpenFOAM/OpenFOAM-1.6-ext/etc/prefs.sh

there is only a WM_COMPILER=Gcc46. Is it enough, or did you forget the "export" in front of it?

I also exported the WM_COMPILER_DIR=/usr , but I don't know if it's necessary.

---------------------------- update ----------------------------

I have checked my log.Allwmake and there are errors like in my first post, starting with

I was not able to solve the problem.. It is so frustrating!

That "ld" links to /usr/bin/ld while that ld is a link to the ld.bdf in the same directory. Is that correct?

I have attached the log.AllMake.stage1 - 4 files. There is no errors (fehler in german), but there are lots of warnings. Maybe this is the reason for the errors in the Allwmake compilation.

> /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lmesquite

You are missing the Mesquite library, which is compiled and installed by ThirdParty/AllMake.stage3

Martin

From your log files, it looks like the Mesquite package was compiled correctly.

Now, just make sure you did update your environment variables before compiling OpenFOAM

line 94: . ~/OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc

This is important because a lot of ThirdParty environment variables are not yet exported at that stage, and the compilation of OpenFOAM relies on the existence of those variables, for example, $MESQUITE_DIR which seems to be missing in your case.

Martin

Thank you Martin,

I have updated my variables after the Allmake.stage1 - 4 with:

source ~/OpenFOAM/OpenFOAM-1.6-ext/etc/bashrc

like described in your buildinstructions.

Echo $MESQUITE_DIR provides follow directory:

I also source the OpenFOAM bashrc in the ~/.bashrc

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

I got it!
The problem is, that the environment variable MESQUITE_LIB_DIR includes the directory:
$MESQUITE_DIR/lib
while the proper directory is:
$MESQUITE_DIR/lib64

This is set by the mesquite-2.1.2.spec, which creates the mesquite-2.1.2.sh file in the
~/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linux64Gcc46DPOpt/etc/
directory

Editing the "export MESQUITE_LIB_DIR=$MESQUITE_DIR/lib" line to "export MESQUITE_LIB_DIR=$MESQUITE_DIR/lib64" solves the problem.

I think that editing the spec file before compilation will also solve the problem.

Also the critical error:
disappears after adding "export WM_COMPILER_DIR= /usr" to the prefs.sh

Thank you!

Arrrrghghh! I am very sorry about this. I spend most of my time working under the mixingPlane_RC1 git branch, where that problem was solved already. I forgot to push this correction for the Mesquite package under the master branch as well.

It is done now. The spec file for the Mesquite package will force the installation of the package libraries under $MESQUITE_DIR/lib, and not under $MESQUITE_DIR/lib64 which was chosen by default by configure under openSuse 12.1.

This correction should be more portable under various OSes.

You will have to recompile the Mesquite package because of this change.

Before doing so, you will need to remove the file

ThirdParty/rpmBuild/RPMS/x86_64/mesquite-2.1.2-linux64Gcc46DPOpt.x86_64.rpm

You might as well remove the directory ThirdParty/packages/mesquite-2.1.2 in order to start from a clean slate.

Regards,

Martin

Hi Martin,

I have deleted the
/home/patrick/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/
folder, the RPM you described and the mesquite-2.1.2.tar.gz in the SOURCES directory, but after compiling the Allmake.stage3 there is again only a lib64 folder under
/home/patrick/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/mesquite-2.1.2/platforms/linux64Gcc46DPOpt/

Patrick

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

Ok, after updating the spec file the lib64 directory has now been replaced by lib. Has the linux64Gcc46 directory under /home/patrick/OpenFOAM/OpenFOAM-1.6-ext/wmake/rules been updated too?
Sorry, but how does the updating with git works? I have no idea.

Great!

Yup, this should have been updated too, but only if you first deleted your "manual modification" I suggested you did yesterday as a temporary fix. Otherwise, the command "git pull" probably complained about a conflict with your local repo.

As for a brief explanation about git and git updating, there are many good documents out there that will explain this. Google is your friend here.

Basically, the main git repository for 1.6-ext is located on the openfoam-extend project on SourceForge.net. What you got on your machine is a local clone or copy of that repository, containing the full source code of OF-1.6-ext.

Every time someone is publishing changes on the main repository located on openfoam-extend (adding/removing/modifying files, creating new branches for bug fixes or new features), your local repository will be out of sync.

When you invoke the command "git pull", you are basically forcing your local repo to get in sync with the remote repo on openfoam-extend; all the changes that did occur on the remote repo since your last update will be applied to your local copy too. Then you update your binaries by invoking the main OpenFOAM compilation scripts, and you will be a happy camper.

So it is a good idea to watch this space on a regular basis:
http://openfoam-extend.git.sourcefor...-ext;a=summary

and to pull in the latest changes in order for your local repo to be in sync with the latest bug fixes or with the latest additions to the source code for 1.6-ext.

Hope this helps,

Martin

Many thanks for your help Martin!
I have already done a successful git pull with your instructions :)

Have I to compile everything new, or only a certain Allmake stage?
Ok, in my case the git pull was only to be in sync with the main.

Now I have to install the edcSimpleFoam solver from Domenik Christ.. I hope this will be easier ;)

scotch not building
 

build started throwing errors at me; going through the logs it seems scotch is not building correctly. Relevant log quote attached. libscotch seems OK (immediately preceding). It tries to install from rpm, but fails for some reason. I am tempted to just install the current version using Synaptic, but I have a feeling that will introduce new problems. I have thrown the entire 1.6-ext folder away and reinstalled from scratch using what I think are Martin's latest instructions, but this error persists. Any thoughts appreciated,

Karl
Ubuntu 12.04 64bit

make[1]: Entering directory `/home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/scotch_5.1.10b/src/scotch'
rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst
make CC="gcc" SCOTCHLIB=scotch \
acpl \
amk_ccc \
amk_fft2 \
amk_grf \
amk_hy \
amk_m2 \
amk_p2 \
atst \
gbase \
gcv \
gmap \
gmk_hy \
gmk_m2 \
gmk_m3 \
gmk_msh \
gmk_ub2 \
gmtst \
gord \
gotst \
gout \
gpart \
gscat \
gtst \
mcv \
mmk_m2 \
mmk_m3 \
mord \
mtst
make[2]: Entering directory `/home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/scotch_5.1.10b/src/scotch'
gcc -O3 -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -DSCOTCH_PTHREAD -Drestrict=__restrict -I../../include -I../libscotch acpl.c -o acpl -L../../lib -lscotch -lscotcherrexit -lz -lm -lrt
gcc -O3 -fPIC -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -DSCOTCH_PTHREAD -Drestrict=__restrict -I../../include -I../libscotch amk_ccc.c -o amk_ccc -L../../lib -lscotch -lscotcherrexit -lz -lm -lrt
../../lib/libscotch.so: error: undefined reference to 'pthread_create'
../../lib/libscotch.so: error: undefined reference to 'pthread_detach'
collect2: ld returned 1 exit status
make[2]: *** [acpl] Error 1
make[2]: *** Waiting for unfinished jobs....
../../lib/libscotch.so: error: undefined reference to 'pthread_create'
../../lib/libscotch.so: error: undefined reference to 'pthread_detach'
collect2: ld returned 1 exit status
make[2]: *** [amk_ccc] Error 1
make[2]: Leaving directory `/home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/scotch_5.1.10b/src/scotch'
make[1]: *** [scotch] Error 2
make[1]: Leaving directory `/home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/BUILD/scotch_5.1.10b/src/scotch'
make: *** [scotch] Error 2
error: Bad exit status from /home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.tYjd4V (%build)


RPM build errors:
Bad exit status from /home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/tmp/rpm-tmp.tYjd4V (%build)
Installing package: scotch-5.1.10b
Uninstalling scotch-5.1.10b using RPM: scotch-5.1.10b-linux64Gcc46DPOpt.x86_64
Installing scotch-5.1.10b using RPM file: /home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/scotch-5.1.10b-linux64Gcc46DPOpt.x86_64.rpm
error: open of /home/karl/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/RPMS/x86_64/scotch-5.1.10b-linux64Gcc46DPOpt.x86_64.rpm failed: No such file or directory
Done installing package