Dear Mahmoud, I think -DUSE_MPI=ON is required. Can you post the output of the dunecontrol run so that I can see what fails? Maybe I’ve seen the problem before. Just to be sure you can should opm-common/grid and re-download it using the installexternal.sh script in dumux.
Timo > On 30. Mar 2021, at 18:57, Mahmoud Atef Mahmoud Mohamed Aboelseoud S277151 > <[email protected]> wrote: > > > Dear Timo, > > Thanks a lot for your elaboration and advice. and also thanks for adim > suggesting to use mpirun when executing. I'm sorry for replying a bit late. > however, I'm afraid none of the suggestions solved my issue still. > > I installed OPM version: release/2020.04 and I made sure I had BLAS, LAPACK, > Boost, SuiteSparse and Zoltan all installed but whenever I try to run the > example, it gives me an error which is different from the first error and is > shown below: > Reading parameters from file params.input. > Found PORO... > Found PERMX... > PERMZ not found, set equal to PERMX... > [mahmoud-Inspiron-N5110:161801] *** Process received signal *** > [mahmoud-Inspiron-N5110:161801] Signal: Segmentation fault (11) > [mahmoud-Inspiron-N5110:161801] Signal code: Address not mapped (1) > [mahmoud-Inspiron-N5110:161801] Failing at address: 0x444e4500e8 > [mahmoud-Inspiron-N5110:161801] [ 0] > /lib/x86_64-linux-gnu/libpthread.so.0(+0x153c0)[0x7f02511c53c0] > [mahmoud-Inspiron-N5110:161801] [ 1] > /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Barrier+0x44)[0x7f02537bf6c4] > [mahmoud-Inspiron-N5110:161801] [ 2] > ./test_2p_cornerpoint(_ZN4Dune9VTKWriterINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE6pwriteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESE_SE_NS_3VTK10OutputTypeEii+0x1ef)[0x56534ede74cf] > [mahmoud-Inspiron-N5110:161801] [ 3] > ./test_2p_cornerpoint(_ZN4Dune21VTKSequenceWriterBaseINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE5writeEdNS_3VTK10OutputTypeE+0xc9)[0x56534ede8749] > [mahmoud-Inspiron-N5110:161801] [ 4] > ./test_2p_cornerpoint(_ZN5Dumux15VtkOutputModuleINS_15FVGridVariablesINS_20CCTpfaFVGridGeometryIN4Dune8GridViewINS3_25DefaultLeafGridViewTraitsINS3_6CpGridEEEEELb0ENS_31CCTpfaDefaultGridGeometryTraitsIS8_NS_19DefaultMapperTraitsIS8_NS3_35MultipleCodimMultipleGeomTypeMapperIS8_NS3_4Impl14MCMGFailLayoutEEESE_EEEEEENS_25CCTpfaGridVolumeVariablesINS_26TwoPCornerPointTestProblemINS_10Properties4TTag15TwoPCornerPointEEENS_19TwoPVolumeVariablesINS_25TwoPVolumeVariablesTraitsINS3_11FieldVectorIdLi2EEENS_12FluidSystems14TwoPImmiscibleIdNSS_10OnePLiquidIdNS_10Components9SimpleH2OIdEEEENSU_IdNSV_15TrichloroetheneIdEEEEEENS_20ImmiscibleFluidStateIdS12_EENS_12SolidSystems9OneCSolidIdNSV_8ConstantILi1EdEELb1EEENS_15InertSolidStateIdS19_EENS3_11FieldMatrixIdLi3ELi3EEENS_15TwoPModelTraitsILNS_15TwoPFormulationE0EEENS_31TwoPScvSaturationReconstructionILNS_20DiscretizationMethodE2ELb0EEEEEEELb0ENS_38CCTpfaDefaultGridVolumeVariablesTraitsISN_S1L_EEEENS_28CCTpfaGridFluxVariablesCacheISN_NS_44PorousMediu > mFluxVariablesCacheImplementationISM_LS1I_2EEENS_50PorousMediumFluxVariablesCacheFillerImplementationISM_LS1I_2EEELb0ENS_26CCTpfaDefaultGridFVCTraitsISN_S1R_S1T_EEEEEENS3_11BlockVectorISR_SaISR_EEEE16writeConforming_EdNS3_3VTK10OutputTypeE+0x1e85)[0x56534ee32d95] > [mahmoud-Inspiron-N5110:161801] [ 5] > ./test_2p_cornerpoint(+0x26e252)[0x56534ed4d252] > [mahmoud-Inspiron-N5110:161801] [ 6] > ./test_2p_cornerpoint(main+0xb87)[0x56534ed06f07] > [mahmoud-Inspiron-N5110:161801] [ 7] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f02501b00b3] > [mahmoud-Inspiron-N5110:161801] [ 8] > ./test_2p_cornerpoint(_start+0x2e)[0x56534ed4710e] > [mahmoud-Inspiron-N5110:161801] *** End of error message *** > Segmentation fault (core dumped) > ---------------------------------------------------------- > > I then turned -DUSE_MPI=ON and I tried to re-install opm-common but it won't > even install when that option is selected. So I commented -DUSE_MPI=ON and > re-installed both opm-common and opm-grid and I built the executable and > tried to run it using mpirun but it gave me the error below: > > Rank 1: No parameter file given. Defaulting to 'params.input' for input file. > Rank 1: Reading parameters from file params.input. > Rank 0: No parameter file given. Defaulting to 'params.input' for input file. > Rank 0: Reading parameters from file params.input. > CpGrid::scatterGrid() is non-trivial only with MPI support and if the target > Dune platform is sufficiently recent. > Found PORO... > Found PERMX... > PERMZ not found, set equal to PERMX... > CpGrid::scatterGrid() is non-trivial only with MPI support and if the target > Dune platform is sufficiently recent. > Found PORO... > Found PERMX... > PERMZ not found, set equal to PERMX... > [mahmoud-Inspiron-N5110:29320] *** Process received signal *** > [mahmoud-Inspiron-N5110:29320] Signal: Segmentation fault (11) > [mahmoud-Inspiron-N5110:29320] Signal code: Address not mapped (1) > [mahmoud-Inspiron-N5110:29320] Failing at address: 0x444e4500e8 > [mahmoud-Inspiron-N5110:29321] *** Process received signal *** > [mahmoud-Inspiron-N5110:29321] Signal: Segmentation fault (11) > [mahmoud-Inspiron-N5110:29321] Signal code: Address not mapped (1) > [mahmoud-Inspiron-N5110:29321] Failing at address: 0x444e4500e8 > [mahmoud-Inspiron-N5110:29320] [ 0] [mahmoud-Inspiron-N5110:29321] [ 0] > /lib/x86_64-linux-gnu/libpthread.so.0(+0x153c0)[0x7f615a62d3c0] > [mahmoud-Inspiron-N5110:29320] [ 1] > /lib/x86_64-linux-gnu/libpthread.so.0(+0x153c0)[0x7fa9c9ca23c0] > [mahmoud-Inspiron-N5110:29321] [ 1] > /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Barrier+0x44)[0x7fa9cc29c6c4] > /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Barrier+0x44)[0x7f615cc276c4] > [mahmoud-Inspiron-N5110:29320] [ 2] [mahmoud-Inspiron-N5110:29321] [ 2] > ./test_2p_cornerpoint(_ZN4Dune9VTKWriterINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE6pwriteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESE_SE_NS_3VTK10OutputTypeEii+0x1ef)[0x564e5a2589af] > [mahmoud-Inspiron-N5110:29320] [ 3] > ./test_2p_cornerpoint(_ZN4Dune9VTKWriterINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE6pwriteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESE_SE_NS_3VTK10OutputTypeEii+0x1ef)[0x564d533139af] > [mahmoud-Inspiron-N5110:29321] [ 3] > ./test_2p_cornerpoint(_ZN4Dune21VTKSequenceWriterBaseINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE5writeEdNS_3VTK10OutputTypeE+0xc9)[0x564e5a259c29] > [mahmoud-Inspiron-N5110:29320] [ 4] > ./test_2p_cornerpoint(_ZN4Dune21VTKSequenceWriterBaseINS_8GridViewINS_25DefaultLeafGridViewTraitsINS_6CpGridEEEEEE5writeEdNS_3VTK10OutputTypeE+0xc9)[0x564d53314c29] > [mahmoud-Inspiron-N5110:29321] [ 4] > ./test_2p_cornerpoint(_ZN5Dumux15VtkOutputModuleINS_15FVGridVariablesINS_20CCTpfaFVGridGeometryIN4Dune8GridViewINS3_25DefaultLeafGridViewTraitsINS3_6CpGridEEEEELb0ENS_31CCTpfaDefaultGridGeometryTraitsIS8_NS_19DefaultMapperTraitsIS8_NS3_35MultipleCodimMultipleGeomTypeMapperIS8_NS3_4Impl14MCMGFailLayoutEEESE_EEEEEENS_25CCTpfaGridVolumeVariablesINS_26TwoPCornerPointTestProblemINS_10Properties4TTag15TwoPCornerPointEEENS_19TwoPVolumeVariablesINS_25TwoPVolumeVariablesTraitsINS3_11FieldVectorIdLi2EEENS_12FluidSystems14TwoPImmiscibleIdNSS_10OnePLiquidIdNS_10Components9SimpleH2OIdEEEENSU_IdNSV_15TrichloroetheneIdEEEEEENS_20ImmiscibleFluidStateIdS12_EENS_12SolidSystems9OneCSolidIdNSV_8ConstantILi1EdEELb1EEENS_15InertSolidStateIdS19_EENS3_11FieldMatrixIdLi3ELi3EEENS_15TwoPModelTraitsILNS_15TwoPFormulationE0EEENS_31TwoPScvSaturationReconstructionILNS_20DiscretizationMethodE2ELb0EEEEEEELb0ENS_38CCTpfaDefaultGridVolumeVariablesTraitsISN_S1L_EEEENS_28CCTpfaGridFluxVariablesCacheISN_NS_44PorousMediu > mFluxVariablesCacheImplementationISM_LS1I_2EEENS_50PorousMediumFluxVariablesCacheFillerImplementationISM_LS1I_2EEELb0ENS_26CCTpfaDefaultGridFVCTraitsISN_S1R_S1T_EEEEEENS3_11BlockVectorISR_SaISR_EEEE16writeConforming_EdNS3_3VTK10OutputTypeE+0x1e85)[0x564e5a2a4275] > [mahmoud-Inspiron-N5110:29320] [ 5] > ./test_2p_cornerpoint(_ZN5Dumux15VtkOutputModuleINS_15FVGridVariablesINS_20CCTpfaFVGridGeometryIN4Dune8GridViewINS3_25DefaultLeafGridViewTraitsINS3_6CpGridEEEEELb0ENS_31CCTpfaDefaultGridGeometryTraitsIS8_NS_19DefaultMapperTraitsIS8_NS3_35MultipleCodimMultipleGeomTypeMapperIS8_NS3_4Impl14MCMGFailLayoutEEESE_EEEEEENS_25CCTpfaGridVolumeVariablesINS_26TwoPCornerPointTestProblemINS_10Properties4TTag15TwoPCornerPointEEENS_19TwoPVolumeVariablesINS_25TwoPVolumeVariablesTraitsINS3_11FieldVectorIdLi2EEENS_12FluidSystems14TwoPImmiscibleIdNSS_10OnePLiquidIdNS_10Components9SimpleH2OIdEEEENSU_IdNSV_15TrichloroetheneIdEEEEEENS_20ImmiscibleFluidStateIdS12_EENS_12SolidSystems9OneCSolidIdNSV_8ConstantILi1EdEELb1EEENS_15InertSolidStateIdS19_EENS3_11FieldMatrixIdLi3ELi3EEENS_15TwoPModelTraitsILNS_15TwoPFormulationE0EEENS_31TwoPScvSaturationReconstructionILNS_20DiscretizationMethodE2ELb0EEEEEEELb0ENS_38CCTpfaDefaultGridVolumeVariablesTraitsISN_S1L_EEEENS_28CCTpfaGridFluxVariablesCacheISN_NS_44PorousMediu > mFluxVariablesCacheImplementationISM_LS1I_2EEENS_50PorousMediumFluxVariablesCacheFillerImplementationISM_LS1I_2EEELb0ENS_26CCTpfaDefaultGridFVCTraitsISN_S1R_S1T_EEEEEENS3_11BlockVectorISR_SaISR_EEEE16writeConforming_EdNS3_3VTK10OutputTypeE+0x1e85)[0x564d5335f275] > [mahmoud-Inspiron-N5110:29321] [ 5] > ./test_2p_cornerpoint(+0x289732)[0x564d53279732] > [mahmoud-Inspiron-N5110:29321] [ 6] > ./test_2p_cornerpoint(+0x289732)[0x564e5a1be732] > [mahmoud-Inspiron-N5110:29320] [ 6] > ./test_2p_cornerpoint(main+0xb87)[0x564d532334b7] > [mahmoud-Inspiron-N5110:29321] [ 7] > ./test_2p_cornerpoint(main+0xb87)[0x564e5a1784b7] > [mahmoud-Inspiron-N5110:29320] [ 7] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fa9c8c8d0b3] > [mahmoud-Inspiron-N5110:29321] [ 8] > /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f61596180b3] > [mahmoud-Inspiron-N5110:29320] [ 8] > ./test_2p_cornerpoint(_start+0x2e)[0x564d532735ee] > [mahmoud-Inspiron-N5110:29321] *** End of error message *** > ./test_2p_cornerpoint(_start+0x2e)[0x564e5a1b85ee] > [mahmoud-Inspiron-N5110:29320] *** End of error message *** > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpirun noticed that process rank 1 with PID 0 on node mahmoud-Inspiron-N5110 > exited on signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > > Sorry for disturbing you and thanks in advance ! > > > Best Regards, > > Mahmoud Atef > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 2021-03-28 15:57 Timo Koch ha scritto: >> Hi Mahmoud, >> dumux is tested with OPM version: release/2020.04. >> Can you try this and see if the error persists? >> Also it might be necessary to add "-DUSE_MPI=ON” to your opts file. >> You might also need BLAS, LAPACK, Boost, SuiteSparse, Zoltan (see opm >> (optional) dependencies). >> This information is from >> https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/blob/master/bin/installexternal.sh >> You can also run "./dumux/bin/installexternal.sh opm” to download >> the opm modules in the matching version. >> Timo >>> On 28. Mar 2021, at 15:49, Mahmoud Atef Mahmoud Mohamed Aboelseoud >>> S277151 <[email protected]> wrote: >>> Hello Dumux team, >>> Sorry for re-sending this but I just hope someone can help me. >>> I hope you're all doing great. I want to use an eclipse grid for my >>> dumux problem. It was indicated in the handbook I should install >>> opm-grid module. I had only the minimum dumux setup along with the >>> dumux-course module. So I first installed opm-common (dependency of >>> opm-grid) using this command: >>> (dunecontrol --module=opm-common all) >>> and then I installed opm-grid using this command >>> (dunecontrol --module=opm-grid all) >>> They both installed successfully. The versions of opm-common and >>> opm-grid I used for the installation are the master versions in the >>> following repositories: >>> https://github.com/OPM/opm-common >>> https://github.com/OPM/opm-grid >>> To check that everything is OK before I start my own module with my >>> own eclipse grid, I first tried to build the dumux example with the >>> eclipse grid located in >>> dumux/test/porousmediumflow/2p/implicit/cornerpoint from its build >>> directory. However, I was faced with this error: The following cmake >>> condition is not met: HAVE-OPM-GRID >>> I then deleted all the build folders in all modules using these two >>> commands: >>> (rm -r d*/build-cmake) >>> (rm -r o*/build-cmake) >>> Then I ran dunecontrol again using this command: >>> (./dune-common/bin/dunecontrol --opts=dumux/cmake.opts all) >>> Again everything installed successfully. I tried to build the dumux >>> example with the eclipse grid again. It built successfully but when >>> I tried to run it using this command: >>> (./test_2p_cornerpoint params.input), I got the following error: >>> Reading parameters from file params.input. >>> Found PORO... >>> Found PERMX... >>> PERMZ not found, set equal to PERMX... >>> [mahmoud-Inspiron-N5110:120949] *** An error occurred in MPI_Barrier >>> [mahmoud-Inspiron-N5110:120949] *** reported by process >>> [1393164289,0] >>> [mahmoud-Inspiron-N5110:120949] *** on communicator MPI_COMM_WORLD >>> [mahmoud-Inspiron-N5110:120949] *** MPI_ERR_COMM: invalid >>> communicator >>> [mahmoud-Inspiron-N5110:120949] *** MPI_ERRORS_ARE_FATAL (processes >>> in this communicator will now abort, >>> [mahmoud-Inspiron-N5110:120949] *** and potentially your MPI job) >>> I have no clue what’s the problem. I have no problem building and >>> running other dumux examples. I just have the problem with this >>> example problem with the eclipse grid. >>> My OS is Ubuntu 20.04 LTS >>> My installed pre-requisites for dumux are the following: >>> - cmake version 3.16.3 >>> - gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 >>> - pkg-config version: 0.29.1 >>> - Open MPI version:4.0.3 >>> - paraview version 5.7.0 >>> - Python 3.8.5 >>> - git version 2.25.1 >>> My installed dune modules are: >>> 1) dumux Version: 3.2-git >>> 2) dune-common Version: 2.7.1 >>> 3) dune-geometry Version 2.7.1 >>> 4) dune-grid Version: 2.7.1 >>> 5) dune-istl Version: 2.7.1 >>> 6) dune-localfunctions Version: 2.7.1 >>> 7) dumux-course Version: 2018 >>> 8) opm-common Version: 2021.04-pre >>> 9) opm-grid Version: 2021.04-pre >>> Your help and advice to solve the issue are very highly appreciated. >>> Thanks in advance ! >>> Best Regards, >>> Mahmoud Atef >>> _______________________________________________ >>> DuMux mailing list >>> [email protected] >>> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux >> _______________________________________________ >> DuMux mailing list >> [email protected] >> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > _______________________________________________ > DuMux mailing list > [email protected] > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux _______________________________________________ DuMux mailing list [email protected] https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
