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-   -   [OpenFOAM.org] OpenFoam 3 on centOS (https://www.cfd-online.com/Forums/openfoam-installation/172057-openfoam-3-centos.html)

Karakal May 23, 2016 11:35
OpenFoam 3 on centOS
 
Dear all,

I'm on the step #16 of the wiki with the buil of OpenFoam and I have some errors with libPstream.so

Quote:
g++ -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=64 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3 -DNoRepository -ftemplate-depth-100 -I/opt/OpenFOAM/OpenFOAM-3.0.x/sr
c/dynamicMesh/lnInclude -I/opt/OpenFOAM/OpenFOAM-3.0.x/src/meshTools/lnInclude -I/opt/OpenFOAM/OpenFOAM-3.0.x/src/finiteVolume/lnInclude -IlnInclude -I. -I/opt/OpenFOAM/OpenFOAM-3.0.x/src/OpenFOAM/lnInclude -I/opt/OpenFOAM/OpenFOAM-3.
0.x/src/OSspecific/POSIX/lnInclude -fPIC -c collapseEdges.C -o /opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/applications/utilities/mesh/advanced/collapseEdges/collapseEdges.o
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Abort'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_count'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_create'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_incl'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Init'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Probe'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_group'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Send'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Allreduce'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_detach'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Bsend'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Irecv'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Recv'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_free'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Wait'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Test'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Isend'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_size'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_free'
/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_rank'
collect2: erreur: ld a retourné 1 code d'état d'exécution
make[3]: *** [/opt/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64Opt/bin/autoRefineMesh] Erreur 1
make[2]: *** [autoRefineMesh] Erreur 2
make[2]: *** Attente des tâches non terminées....
Quote:
mpirun --version
mpirun (Open MPI) 1.8.1

which mpirun
/usr/lib64/openmpi/bin/mpirun

mpicc --version
gcc (OpenFOAM) 4.8.4

which mpicc
/usr/lib64/openmpi/bin/mpicc
Do you have any sugestions ?
Thanks for helping.

Karakal May 26, 2016 04:13
I just made a new install and now, I have this problem :

Quote:
g++ -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=64 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3 -DNoRepository -ftemplate-dep
th-100 -I/include -I/home/OF/OpenFOAM/ThirdParty-3.0.x/platforms/linux64Gcc48Int64/scotch_6.0.3/include/openmpi-system -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I.
-I/home/OF/OpenFOAM/OpenFOAM-3.0.x/src/OpenFOAM/lnInclude -I/home/OF/OpenFOAM/OpenFOAM-3.0.x/src/OSspecific/POSIX/lnInclude -fPIC -c ptscotchDecomp.C -o /home/OF/OpenFOAM/OpenFOAM-3.0.x/platf
orms/linux64Gcc48DPInt64OptSYSTEMOPENMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o
In file included from /usr/local/include/mpi.h:2194:0,
from ptscotchDecomp.C:125:
/usr/local/include/mpicxx.h:2737:34: erreur: declaration of C function ‘void MPI::Init(int&, char**&)’ conflicts with
extern void Init(int &, char **& );
^
/usr/local/include/mpicxx.h:2736:13: erreur: previous declaration ‘void MPI::Init()’ here
extern void Init(void);
^
/usr/local/include/mpicxx.h:2739:45: erreur: declaration of C function ‘int MPI::Init_thread(int&, char**&, int)’ conflicts with
extern int Init_thread(int &, char **&, int );
^
/usr/local/include/mpicxx.h:2738:12: erreur: previous declaration ‘int MPI::Init_thread(int)’ here
extern int Init_thread(int);
^
make: *** [/home/OF/OpenFOAM/OpenFOAM-3.0.x/platforms/linux64Gcc48DPInt64OptSYSTEMOPENMPI/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.o] Erreur 1
I try to modify the file ptscotchDecomp.C as I can see in this thread :
http://www.cfd-online.com/Forums/ope...ng-mpich2.html
But, it does not work.

Farid July 12, 2016 21:33
Did you solve this? I have the same problem.

Best regards,

Karakal July 25, 2016 03:16
I have try to reinstall openfoam on a new fresh install of centos 6.4 and the same problem persist.

jmdf July 27, 2016 09:15
Greetings,

With centOS mpirun should work just fine.
The line you should look on the error is this one:

Code:
collect2: erreur: ld a retourné 1 code d'état d'exécution
Do you have binutils installed?

Code:
sudo yum search binutils


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