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
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