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June 7, 2013, 09:12 |
OF 2.2 installation on cluster HELP.
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#1 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
hello,
it is some time that i am trying to install OF 2.2 on a cluster ( i am not administrator) . And something always go wrong. one of the errors is similar to http://www.cfd-online.com/Forums/ope...xx-h-file.html but can not completely understand what to do. So i was looking for some extra help. I tried both OpenMPI or SYSTEMOPENMPI. Do you have any suggestion? thank you a lot francesco So if I use SYSTEMOPENMPI option the first error is : ================================================== ================================================== ============ wmake libso ptscotchDecomp /usr/lib/gcc/x86_64-redhat-linux6E/4.4.6/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' collect2: ld returned 1 exit status SOURCE=ptscotchDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/include -I/home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0/include/openmpi-system -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOptSYSTEMOPENMPI/ptscotchDecomp.o In file included from /opt/parastation/mpi2/include/mpi.h:1188:0, from ptscotchDecomp.C:125: /opt/parastation/mpi2/include/mpicxx.h:2698:34: error: declaration of C function ‘void MPI::Init(int&, char**&)’ conflicts with /opt/parastation/mpi2/include/mpicxx.h:2697:13: error: previous declaration ‘void MPI::Init()’ here /opt/parastation/mpi2/include/mpicxx.h:2700:45: error: declaration of C function ‘int MPI::Init_thread(int&, char**&, int)’ conflicts with /opt/parastation/mpi2/include/mpicxx.h:2699:12: error: previous declaration ‘int MPI::Init_thread(int)’ here ptscotchDecomp.C: In member function ‘Foam::label Foam:tscotchDecomp::decompose(const Foam::fileName&, int, const int*, int, const int*, const scalarField&, Foam::List<int>&) const’: ptscotchDecomp.C:551:39: warning: use of old-style cast [-Wold-style-cast] make: *** [Make/linux64GccDPOptSYSTEMOPENMPI/ptscotchDecomp.o] Error 1 ================================================== ================================================== =============== If instead i use the option OPENMPI, I have : ================================================== ================================================== =============== + wmake all utilities /home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3/libPstream.so: undefined reference to `pthread_getspecific' /home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3/libPstream.so: undefined reference to `pthread_key_create' /home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3/libPstream.so: undefined reference to `pthread_atfork' /home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.3/libPstream.so: undefined reference to `pthread_setspecific' collect2: ld returned 1 exit status make[3]: *** [/home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/autoRefineMesh] Error 1 make[2]: *** [autoRefineMesh] Error 2 ================================================== ================================================== ============== |
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June 7, 2013, 14:10 |
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#2 | |
Senior Member
Niels Nielsen
Join Date: Mar 2009
Location: NJ - Denmark
Posts: 556
Rep Power: 27 |
Hello there
I can see that you are running a RHEL cluster version 6.x Here is the official statement from openfoam.com http://www.openfoam.org/download/git.php Quote:
You can have a check and see if centFOAM works for you. http://sourceforge.net/projects/centfoam/?source=navbar
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Linnemann PS. I do not do personal support, so please post in the forums. |
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June 7, 2013, 17:14 |
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#3 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
Thank you,
yes I was aware of the gcc problem, so I had already loaded the gcc 4.6.4 module. The system passed also the SystemCheck(see below). Sorry for not stating that clearly from the beginning. But i noticed that in the error i had : /usr/lib/gcc/x86_64-redhat-linux6E/4.4.6/../../../../lib64/crt1.o: In function `_start': DOes it means that the 4.6.4 module has some wrong link? thank you a lot for your help... francesco [flucci@ipazia ~]$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/home/apps/gcc/4.6.4/libexec/gcc/x86_64-unknown-linux-gnu/4.6.4/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ../gcc-4.6.4/configure --prefix=/home/apps/gcc/4.6.4 Thread model: posix gcc version 4.6.4 (GCC) [flucci@ipazia ~]$ foamSystemCheck Checking basic system... ----------------------------------------------------------------------- Shell: /bin/bash Host: ipazia OS: Linux version 2.6.18-194.8.1.el5 User: flucci System check: PASS ================== Continue OpenFOAM installation. |
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June 9, 2013, 06:39 |
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#4 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,978
Blog Entries: 45
Rep Power: 128 |
Greetings to all!
@Luca: you should also check if g++ is also 4.6.4 or just 4.4.6: Code:
g++ --version Best regards, Bruno
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June 11, 2013, 03:22 |
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#5 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
Hi Bruno,
Thank you for the reply. Also g++ seems ok (is it?) ... [flucci@ipazia ~]$ g++ -v Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/home/apps/gcc/4.6.4/libexec/gcc/x86_64-unknown-linux-gnu/4.6.4/lto-wrapper Target: x86_64-unknown-linux-gnu Configured with: ../gcc-4.6.4/configure --prefix=/home/apps/gcc/4.6.4 Thread model: posix gcc version 4.6.4 (GCC) I have done the procedure again with SYSTEMOPENMPI, load the module for 4.6.4 ,run wcleanAll, wcleanLnIncludeAll, and Allwmake. The error is still there but before i may have overlooked a problem that I am surprised i haven't seen it since usually i do a grep 'error'. But I have some : gcc: error: unrecognized option ‘--showme:compile’ preatty early in the installation. below there is the beginning of the log file. Any idea? Should i try again with the procedure that Bruno suggested me for the case that i did not had g++ ? Thank you a lot for the help. francesco make: Nothing to be done for `all'. ======================================== Start ThirdParty Allwmake ======================================== ======================================== Build MPI libraries if required ======================================== Build Scotch decomposition library scotch_6.0.0 /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0 scotch header in /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0/include scotch libs in /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64GccDPOpt/lib ======================================== Build PTScotch decomposition library scotch_6.0.0 (uses MPI) /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0 ptscotch header in /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0/include/openmpi-system ptscotch libs in /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64GccDPOpt/lib/openmpi-system ======================================== Build Tecio optional component was not found ======================================== Done ThirdParty Allwmake ======================================== + wmakePrintBuild -check same version as previous build + wmakeLnInclude OpenFOAM wmakeLnInclude: linking include files to OpenFOAM/lnInclude + wmakeLnInclude OSspecific/POSIX wmakeLnInclude: linking include files to OSspecific/POSIX/lnInclude + Pstream/Allwmake + wmake libso dummy wmakeLnInclude: linking include files to ./lnInclude Making dependency list for source file UPstream.C Making dependency list for source file UIPread.C Making dependency list for source file UOPwrite.C SOURCE=UPstream.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/UPstream.o SOURCE=UIPread.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/UIPread.o SOURCE=UOPwrite.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/UOPwrite.o '/home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/dummy/libPstream.so' is up to date. + case "$WM_MPLIB" in + set +x Note: ignore spurious warnings about missing mpicxx.h headers wclean mpi wmake libso mpi wmakeLnInclude: linking include files to ./lnInclude gcc: error: unrecognized option ‘--showme:compile’ Making dependency list for source file UOPwrite.C could not open file mpi.h for source file UOPwrite.C gcc: error: unrecognized option ‘--showme:compile’ Making dependency list for source file UIPread.C could not open file mpi.h for source file UIPread.C gcc: error: unrecognized option ‘--showme:compile’ Making dependency list for source file UPstream.C could not open file mpi.h for source file UPstream.C gcc: error: unrecognized option ‘--showme:compile’ Making dependency list for source file PstreamGlobals.C could not open file mpi.h for source file PstreamGlobals.C gcc: error: unrecognized option ‘--showme:compile’ SOURCE=UOPwrite.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOptSYSTEMOPENMPI/UOPwrite.o In file included from /opt/parastation/mpi2/include/mpi.h:1188:0, from UOPwrite.C:29: /opt/parastation/mpi2/include/mpicxx.h: In constructor ‘MPI:atatype:atatype()’: /opt/parastation/mpi2/include/mpicxx.h:161:47: warning: use of old-style cast [-Wold-style-cast] /opt/parastation/mpi2/include/mpicxx.h: In member function ‘virtual void MPI:atatype::Commit()’: ================================================= If It is of help i add also the error that come later in the compilation .... : ================================================= wclean ptscotchDecomp wmake libso ptscotchDecomp wmakeLnInclude: linking include files to ./lnInclude gcc: error: unrecognized option ‘--showme:compile’ Making dependency list for source file ptscotchDecomp.C could not open file mpi.h for source file ptscotchDecomp.C gcc: error: unrecognized option ‘--showme:compile’ SOURCE=ptscotchDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/include -I/home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/scotch_6.0.0/include/openmpi-system -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/home/flucci/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOptSYSTEMOPENMPI/ptscotchDecomp.o In file included from /opt/parastation/mpi2/include/mpi.h:1188:0, from ptscotchDecomp.C:125: /opt/parastation/mpi2/include/mpicxx.h:2698:34: error: declaration of C function ‘void MPI::Init(int&, char**&)’ conflicts with /opt/parastation/mpi2/include/mpicxx.h:2697:13: error: previous declaration ‘void MPI::Init()’ here /opt/parastation/mpi2/include/mpicxx.h:2700:45: error: declaration of C function ‘int MPI::Init_thread(int&, char**&, int)’ conflicts with /opt/parastation/mpi2/include/mpicxx.h:2699:12: error: previous declaration ‘int MPI::Init_thread(int)’ here ptscotchDecomp.C: In member function ‘Foam::label Foam:tscotchDecomp::decompose(const Foam::fileName&, int, const int*, int, const int*, const scalarField&, Foam::List<int>&) const’: ptscotchDecomp.C:551:39: warning: use of old-style cast [-Wold-style-cast] make: *** [Make/linux64GccDPOptSYSTEMOPENMPI/ptscotchDecomp.o] Error 1 + wmake libso decompositionMethods wmakeLnInclude: linking include files to ./lnInclude |
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June 13, 2013, 03:54 |
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#6 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
Hi All,
i still have problems with this installation. Do you think i can proceed with this instructions : http://openfoamwiki.net/index.php/In...HEL#CentOS_6.4 even though i do not have administrator privileges? So i can not perform point 1: ================================================== =========== su - yum groupinstall 'Development Tools' yum install openmpi openmpi-devel qt-devel zlib-devel texinfo #This one is useful, but not crucial yum upgrade exit ================================================== ============ Does anybody knows a work around? thank you for the help Last edited by Luchini; June 13, 2013 at 07:09. |
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June 15, 2013, 11:16 |
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#7 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,978
Blog Entries: 45
Rep Power: 128 |
Hi Luca,
Sorry, long week at work and couldn't reply sooner. The error you got is because "mpicc" was unable to provide a good answer to these lines of code at "mplibSYSTEMOPENMPI": https://github.com/OpenFOAM/OpenFOAM...bSYSTEMOPENMPI Quote:
I took a look at your first post on this thread and it looks like you're using a specific MPI toolbox, possibly MPICH2? Code:
/opt/parastation/mpi2/
Bruno
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June 17, 2013, 08:11 |
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#8 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
Dear Bruno,
Thank you a lot for your help. I have followed your suggestions and it seems the installation went much better. I still have some errors ( see attachment) but i guess that with a clean installation they will go away. the /foamInstallationTest gives me : Summary ------------------------------------------------------------------------------- Base configuration ok. Critical systems ok. Done Tonight i will to a clean up and run a clean installation. Hope that this will the end of it. Thank you a lot |
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June 18, 2013, 04:17 |
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#9 |
New Member
Luca Franceschini
Join Date: Aug 2012
Posts: 29
Rep Power: 14 |
Hello everybody.
So i have finished the clean installation. I think the installation it was successful but i still have the same errors as before. In attachment there is a summary of the make.log. All major applications seem installed correctly. To me the errors seems kind of minor but i would be grateful if somebody can comment on them to give me an idea of their criticality and eventually an hint on how to solve them. Summarizing even further the attachment i have : A) could not open file zoltanRenumber.H for source file renumberMesh.C B) /usr/lib/../lib64/libreadline.so: undefined reference to `PC' /usr/lib/../lib64/libreadline.so: undefined reference to `tgetflag' collect2: ld returned 1 exit status make[3]: *** [/home/flucci/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/setSet] Error 1 make[3]: Leaving directory `/home/flucci/OpenFOAM/OpenFOAM-2.2.x/applications/utilities/mesh/manipulation/setSet' C) ERROR: ParaView not found in /home/flucci/OpenFOAM/ThirdParty-2.2.x/platforms/linux64Gcc/paraview-3.12.0 D)make[1]: Leaving directory `/home/flucci/OpenFOAM/OpenFOAM-2.2.x/applications/utilities/thermophysical' make: Target `application' not remade because of errors. Anything to be warried of? Thank you a lot for the HELP. francesco |
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June 20, 2013, 16:26 |
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#10 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,978
Blog Entries: 45
Rep Power: 128 |
Hi Luca,
Based on the summary of errors you've provided:
If you do want to have setSet up and running, it'll be necessary to figure out which header file it's using and if it's related to the same version as the library file itself. Best regards, Bruno
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