# OpenFoam12 on a linux cluster

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 September 10, 2005, 14:28 Hi. I installed OpenFoam1.2 on #1 New Member   Bei Join Date: Mar 2009 Posts: 21 Rep Power: 9 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

 September 10, 2005, 14:33 I assume you installed the bin #2 Senior Member   Hrvoje Jasak Join Date: Mar 2009 Location: London, England Posts: 1,779 Rep Power: 22 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 __________________ Hrvoje Jasak Providing commercial FOAM/OpenFOAM and CFD Consulting: http://wikki.co.uk

 September 10, 2005, 14:41 Hello, Dr. Jasak! So lucky for #3 New Member   Bei Join Date: Mar 2009 Posts: 21 Rep Power: 9 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

 September 10, 2005, 15:47 Hi, (This is not one of my #4 Senior Member   Hrvoje Jasak Join Date: Mar 2009 Location: London, England Posts: 1,779 Rep Power: 22 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>>>>; (that one is JANAF, among other bits) or thermoType hMixtureThermo; 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 __________________ Hrvoje Jasak Providing commercial FOAM/OpenFOAM and CFD Consulting: http://wikki.co.uk

 September 10, 2005, 19:34 Many thanks for the reply! I t #5 New Member   Bei Join Date: Mar 2009 Posts: 21 Rep Power: 9 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.

 September 10, 2005, 19:44 Looks like the compiler is bro #6 Senior Member   Hrvoje Jasak Join Date: Mar 2009 Location: London, England Posts: 1,779 Rep Power: 22 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 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 __________________ Hrvoje Jasak Providing commercial FOAM/OpenFOAM and CFD Consulting: http://wikki.co.uk

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