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tjhei / cracks

pfm-cracks: A Finite Element code for crack propagation
GNU General Public License v2.0
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Impossible to run examples except few of them #88

Closed Francyrad closed 1 year ago

Francyrad commented 1 year ago

Dear developers, I met several difficulties to make the script's example works. For example, I've been able to run only the following scripts:

parameters_sneddon_3d. prm parameters_sneddon_2d. prm

I hope to run other examples in the future, to understand hot the code works best regards Francesco

tjhei commented 1 year ago

What happens with other examples? What error message do you get? What is your deal.II version?

Francyrad commented 1 year ago

I use the version 9.4.2 (M1PRO, Apple silicon). Here it is what the terminal says:

mpirun -np 8 cracks parameters_hetero_3d.prm
Problem dimension: 3
Running on 8 cores
---------------------------------------------------------
TimerOutput objects finalize timed values printed to the
screen by communicating over MPI in their destructors.
Since an exception is currently uncaught, this
synchronization (and subsequent output) will be skipped
to avoid a possible deadlock.
---------------------------------------------------------

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

--------------------------------------------------------
An error occurred in line <902> of file </Users/francyrad/dealii-candi/tmp/unpack/deal.II-v9.4.2/source/grid/grid_in.cc> in function
    void dealii::GridIn<3, 3>::read_ucd(std::istream &, const bool) [dim = 3, spacedim = 3]
The violated condition was: 
    in.fail() == false
Additional information: 
    An input/output error has occurred. There are a number of reasons why
    this may be happening, both for reading and writing operations.

    If this happens during an operation that tries to read data: First,
    you may be trying to read from a file that doesn't exist or that is
    not readable given its file permissions. Second, deal.II uses this
    error at times if it tries to read information from a file but where
    the information in the file does not correspond to the expected
    format. An example would be a truncated file, or a mesh file that
    contains not only sections that describe the vertices and cells, but
    also sections for additional data that deal.II does not understand.

    If this happens during an operation that tries to write data: you may
    be trying to write to a file to which file or directory permissions do
    not allow you to write. A typical example is where you specify an
    output file in a directory that does not exist.

Stacktrace:
-----------
#0  2   libdeal_II.g.9.4.2.dylib            0x000000013a2031e4 _ZN6dealii6GridInILi3ELi3EE8read_ucdERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEEb + 3180: 2   libdeal_II.g.9.4.2.dylib            0x000000013a2031e4 _ZN6dealii6GridInILi3ELi3EE8read_ucdERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEEb 
#1  3   libdeal_II.g.9.4.2.dylib            0x000000013a1fc9e4 _ZN6dealii6GridInILi3ELi3EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE + 112: 3   libdeal_II.g.9.4.2.dylib            0x000000013a1fc9e4 _ZN6dealii6GridInILi3ELi3EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE 
#2  4   cracks                              0x00000001007a69ec _ZN25FracturePhaseFieldProblemILi3EE10setup_meshEv + 920: 4   cracks                              0x00000001007a69ec _ZN25FracturePhaseFieldProblemILi3EE10setup_meshEv 
#3  5   cracks                              0x000000010079e47c _ZN25FracturePhaseFieldProblemILi3EE22set_runtime_parametersEv + 2680: 5   cracks                              0x000000010079e47c _ZN25FracturePhaseFieldProblemILi3EE22set_runtime_parametersEv 
#4  6   cracks                              0x00000001006a7ee8 _ZN25FracturePhaseFieldProblemILi3EE3runEv + 148: 6   cracks                              0x00000001006a7ee8 _ZN25FracturePhaseFieldProblemILi3EE3runEv 
#5  7   cracks                              0x00000001006a4d7c main + 792: 7   cracks                              0x00000001006a4d7c main 
#6  8   dyld                                0x000000018fd4fe50 start + 2544: 8   dyld                                0x000000018fd4fe50 start 
--------------------------------------------------------

Aborting!
----------------------------------------------------
mpirun cracks parameters_threepoint.prm
Problem dimension: 2
Running on 10 cores
---------------------------------------------------------
TimerOutput objects finalize timed values printed to the
screen by communicating over MPI in their destructors.
Since an exception is currently uncaught, this
synchronization (and subsequent output) will be skipped
to avoid a possible deadlock.
---------------------------------------------------------

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

----------------------------------------------------
Exception on processing: 

--------------------------------------------------------
An error occurred in line <2000> of file </Users/francyrad/dealii-candi/tmp/unpack/deal.II-v9.4.2/source/grid/grid_in.cc> in function
    void dealii::GridIn<2, 2>::read_msh(std::istream &) [dim = 2, spacedim = 2]
The violated condition was: 
    in.fail() == false
Additional information: 
    An input/output error has occurred. There are a number of reasons why
    this may be happening, both for reading and writing operations.

    If this happens during an operation that tries to read data: First,
    you may be trying to read from a file that doesn't exist or that is
    not readable given its file permissions. Second, deal.II uses this
    error at times if it tries to read information from a file but where
    the information in the file does not correspond to the expected
    format. An example would be a truncated file, or a mesh file that
    contains not only sections that describe the vertices and cells, but
    also sections for additional data that deal.II does not understand.

    If this happens during an operation that tries to write data: you may
    be trying to write to a file to which file or directory permissions do
    not allow you to write. A typical example is where you specify an
    output file in a directory that does not exist.

Stacktrace:
-----------
#0  2   libdeal_II.g.9.4.2.dylib            0x000000013a2aa800 _ZN6dealii6GridInILi2ELi2EE8read_mshERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE + 6804: 2   libdeal_II.g.9.4.2.dylib            0x000000013a2aa800 _ZN6dealii6GridInILi2ELi2EE8read_mshERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE 
#1  3   libdeal_II.g.9.4.2.dylib            0x000000013a2a7e9c _ZN6dealii6GridInILi2ELi2EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE + 120: 3   libdeal_II.g.9.4.2.dylib            0x000000013a2a7e9c _ZN6dealii6GridInILi2ELi2EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE 
#2  4   cracks                              0x00000001007fcd14 _ZN25FracturePhaseFieldProblemILi2EE10setup_meshEv + 808: 4   cracks                              0x00000001007fcd14 _ZN25FracturePhaseFieldProblemILi2EE10setup_meshEv 
#3  5   cracks                              0x00000001007f3df0 _ZN25FracturePhaseFieldProblemILi2EE22set_runtime_parametersEv + 2680: 5   cracks                              0x00000001007f3df0 _ZN25FracturePhaseFieldProblemILi2EE22set_runtime_parametersEv 
#4  6   cracks                              0x000000010076e7e8 _ZN25FracturePhaseFieldProblemILi2EE3runEv + 148: 6   cracks                              0x000000010076e7e8 _ZN25FracturePhaseFieldProblemILi2EE3runEv 
#5  7   cracks                              0x000000010076ccf4 main + 656: 7   cracks                              0x000000010076ccf4 main 
#6  8   dyld                                0x000000018fd4fe50 start + 2544: 8   dyld                                0x000000018fd4fe50 start 
--------------------------------------------------------

Aborting!
----------------------------------------------------

--------------------------------------------------------
An error occurred in line <2000> of file </Users/francyrad/dealii-candi/tmp/unpack/deal.II-v9.4.2/source/grid/grid_in.cc> in function
    void dealii::GridIn<2, 2>::read_msh(std::istream &) [dim = 2, spacedim = 2]
The violated condition was: 
    in.fail() == false
Additional information: 
    An input/output error has occurred. There are a number of reasons why
    this may be happening, both for reading and writing operations.

    If this happens during an operation that tries to read data: First,
    you may be trying to read from a file that doesn't exist or that is
    not readable given its file permissions. Second, deal.II uses this
    error at times if it tries to read information from a file but where
    the information in the file does not correspond to the expected
    format. An example would be a truncated file, or a mesh file that
    contains not only sections that describe the vertices and cells, but
    also sections for additional data that deal.II does not understand.

    If this happens during an operation that tries to write data: you may
    be trying to write to a file to which file or directory permissions do
    not allow you to write. A typical example is where you specify an
    output file in a directory that does not exist.

Stacktrace:
-----------
#0  2   libdeal_II.g.9.4.2.dylib            0x000000028549e800 _ZN6dealii6GridInILi2ELi2EE8read_mshERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE + 6804: 2   libdeal_II.g.9.4.2.dylib            0x000000028549e800 _ZN6dealii6GridInILi2ELi2EE8read_mshERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE 
#1  3   libdeal_II.g.9.4.2.dylib            0x000000028549be9c _ZN6dealii6GridInILi2ELi2EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE + 120: 3   libdeal_II.g.9.4.2.dylib            0x000000028549be9c _ZN6dealii6GridInILi2ELi2EE4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEENS1_6FormatE 
#2  4   cracks                              0x000000010449cd14 _ZN25FracturePhaseFieldProblemILi2EE10setup_meshEv + 808: 4   cracks                              0x000000010449cd14 _ZN25FracturePhaseFieldProblemILi2EE10setup_meshEv 
#3  5   cracks                              0x0000000104493df0 _ZN25FracturePhaseFieldProblemILi2EE22set_runtime_parametersEv + 2680: 5   cracks                              0x0000000104493df0 _ZN25FracturePhaseFieldProblemILi2EE22set_runtime_parametersEv 
#4  6   cracks                              0x000000010440e7e8 _ZN25FracturePhaseFieldProblemILi2EE3runEv + 148: 6   cracks                              0x000000010440e7e8 _ZN25FracturePhaseFieldProblemILi2EE3runEv 
#5  7   cracks                              0x000000010440ccf4 main + 656: 7   cracks                              0x000000010440ccf4 main 
#6  8   dyld                                0x000000018fd4fe50 start + 2544: 8   dyld                                0x000000018fd4fe50 start 
--------------------------------------------------------

Aborting!
----------------------------------------------------

I get only these 2 kind of error. The line 902 error is the same for everyone except for the last that involve line 2000. Thank you for your help

tjhei commented 1 year ago 
void dealii::GridIn<3, 3>::read_ucd(std::istream &, const bool) [dim = 3, spacedim = 3]

... void dealii::GridIn<2, 2>::read_msh(std::istream &) [dim = 2, spacedim = 2]

This means that the mesh files are not found on your system. Did you move any files around? Do you have the necessary meshes in the meshes/ directory? see https://github.com/tjhei/cracks/tree/master/meshes

Francyrad commented 1 year ago

I'm sorry for my late response. Yes, i moved files because i believed that i could run my runs in a separate folder, like in aspect, then with just my "crack" and prm file. To avoid bugs, I reinstalled everything and now the simulations that i could not run works. Thank you!