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-   -   OpenFoam12 on a linux cluster (http://www.cfd-online.com/Forums/openfoam-installation/57717-openfoam12-linux-cluster.html)

tsjb00 September 10, 2005 14:28

Hi. I installed OpenFoam1.2 on
 
Hi. I installed OpenFoam1.2 on a linux cluster following the same procedure for PC installation. The linux package is also installed. When I run the program, it complains about not finding some library. The information displayed:

blockMesh: /lib/i686/libc.so.6: version `GLIBC_2.3' not found (required by /d/vnfe4/home/jinbei/OpenFOAM/linux/gcc-4.0.1/lib/libstdc++.so.6)
blockMesh: /lib/i686/libc.so.6: version `GLIBC_2.3.2' not found (required by /d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/lam-7.1.1/platforms/linuxGcc4Opt/ lib/libmpi.so.0)
blockMesh: /lib/i686/libc.so.6: version `GLIBC_2.3' not found (required by /d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/lam-7.1.1/platforms/linuxGcc4Opt/ lib/liblam.so.0)
blockMesh: /lib/i686/libpthread.so.0: version `GLIBC_2.3.2' not found (required by /d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/lam-7.1.1/platforms/linuxGcc4Opt/ lib/liblam.so.0)

I check the cluster and find the libc.so.6 file. The problem is (1)the path on cluster is not lib/i686; (2) the version seems to be 2.2.5. And as a user I can only change configurations under my own account.

How can I solve this problem? Many thanks!

JB

hjasak September 10, 2005 14:33

I assume you installed the bin
 
I assume you installed the binary pack - why don't you try to rebuild the thing yourself. This will avoid all compatibility problems.

Do:

foam
wcleanAll
src
rm -rf */platforms
foam
Allwmake

Enjoy,

Hrv

tsjb00 September 10, 2005 14:41

Hello, Dr. Jasak! So lucky for
 
Hello, Dr. Jasak! So lucky for me to meet you on-line! I hope you wouldn't mind if I ask you some other questions.

1.I have been studying the code for reacting flow. For the diesel engine case, when updating the properties, it seems to be done based on janafThermo model. It seems to me that the coef. of mixuture= (coef. of speicies* mass fraction) is used, and the new janafThermo coef.s are used to evaluate T, etc. Is that right?

2. I am trying to implement a fully compressible configuration. When I used PV=RT instead of transport equation for pressure, everything was wrong. Would you please five me some advice on that?

Thanks a lot! Have a nice weekend!

JB

hjasak September 10, 2005 15:47

Hi, (This is not one of my
 
Hi,

(This is not one of my solvers so I may be slightly off with some answers, but I'm sure the experts will correct me - thanks) :-)

1. Thermo type is run-time selectable. Have a look at constant/thermophysicalProperties and you will find entries like:

thermoType hhuMixtureThermo<inhomogeneousmixture<sutherlandtr ansport<speciethermo<janafther mo<perfectgas>>>>>;

(that one is JANAF, among other bits)

or

thermoType hMixtureThermo<reactingmixture>;


2. This is already fully compressible. However, the equation of state (that's what p = \rho R T is) is not sufficient. You also need to use the mass conservation (= continuity) equation and from those derived the pressure equation. If you throw away the pressure equation, you do not conserve mass and the thing goes boom!

Enjoy,

Hrv

tsjb00 September 10, 2005 19:34

Many thanks for the reply! I t
 
Many thanks for the reply! I try to rebuild OpenFoam as instructed. The compiler still complains about the library. I just copy a few lines of the error information below. Please tell me how to solve the problem. Thanks again and best regards!

JB




error information:


ln: `./zfstream.h': File exists
Making dependency list for source file adler32.c
Making dependency list for source file compress.c
Making dependency list for source file crc32.c
Making dependency list for source file deflate.c
Making dependency list for source file gzio.c
Making dependency list for source file infback.c
Making dependency list for source file inffast.c
Making dependency list for source file inflate.c
Making dependency list for source file inftrees.c
Making dependency list for source file trees.c
Making dependency list for source file uncompr.c
Making dependency list for source file zutil.c
libso
SOURCE_DIR=.
SOURCE=adler32.c ; gcc -m32 -Dlinux -Wall -O3 -I/d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/OpenFOAM/lnInclude -IlnInclude -I. -fPIC -c $SOURCE -o Make/linuxGcc4Opt/adler32.o
gcc: /lib/i686/libc.so.6: version `GLIBC_2.3' not found (required by gcc)
make: *** [Make/linuxGcc4Opt/adler32.o] Error 1
/d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/wmake/wmakeLnInclude: linking include files to /d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/foamUser/lnInclude

Making dependency list for source file libfoamUser.C
libso
SOURCE_DIR=.
SOURCE=libfoamUser.C ; g++ -m32 -Dlinux -Wall -W -Wno-unused-parameter -Wold-style-cast -O3 -ffast-math -DNoRepository -ftemplate-depth-30 -I/d/vnfe4/home/jinbei/OpenFOAM/OpenFOAM-1.2/src/OpenFOAM/lnInclude -IlnInclude -I. -fPIC -pthread -c $SOURCE -o Make/linuxGcc4Opt/libfoamUser.o
g++: /lib/i686/libc.so.6: version `GLIBC_2.3' not found (required by g++)
make: *** [Make/linuxGcc4Opt/libfoamUser.o] Error 1
gmake: *** No rule to make target `distclean'. Stop.

hjasak September 10, 2005 19:44

Looks like the compiler is bro
 
Looks like the compiler is broken as well. Try:

which gcc

For me it says:

/home/coyote/hjasak/OpenFOAM/linux/gcc-4.0.1/bin/gcc

Then try making a little HelloWorld program in C++ and try to compile that (probably won't work). Mine looks like this:

coyote*108-> cat ~/c++/test/helloWorld.C
#include <iostream>

using namespace std;

int main()
{
cout << "Hello, world!" << endl;

return 0;
}


If so, you will need to download gcc and built it from sources. Download is easy, make an object directory, configure and build:

tar xzf gcc-4.0.1.tgz
mkdir gcc-4.0.1-obj
cd gcc-4.0.1-obj

../gcc-4.0.1/configure --prefix=/usr/tmp/gcc-4.0.1 --exec-prefix=/usr/tmp/gcc-4.0.1 --enable-languages=c,c++ --enable-shared

gmake bootstrap
gmake install

Then pack up the /usr/tmp/gcc-4.0.1

cd /usr/tmp/

tar cvzf gcc-4.0.1.bin.tgz gcc-4.0.1

and install it in ~/OpenFOAM/linux

mv gcc-4.0.1.bin.tgz ~/OpenFOAM/linux

cd ~/OpenFOAM/linux
tar xzf gcc-4.0.1.bin.tgz

Update your environment and try hello world again. When you get that to work, foam will compile out of box.

There may be some other stuff you need to rebuild along the same lines, but I'm sure you can deal with that.

Have fun,

Hrv


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