An error occurred in line <1983> for nucleationModel_preferential, dendriticSolidification, and other applications

[gablerona]

Hi! I'm new to this.
After running mpirun -n 1 main
This is what I get:

An error occurred in line <1983> of file <../source/base/parameter_handler.cc> in function
    void dealii::ParameterHandler::scan_line(std::__cxx11::string, const string&, unsigned int)
The violated condition was: 
    entries->get_child_optional (get_current_full_path(subsection))
Additional information: 
    Line <44> of file <parameters.in: There is no such subsection to be entered: Refinement criterion: n
--------------------------------------------------------

Aborting!
----------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[42277,1],0]
  Exit code:    1

What could be the problem?

[david-montiel-t]

Hello, It looks like there is an issue in the mesh refinement settings. Did you modified any of the files of the preferentialNucleation application? If you did, can you send me the file(s) you modified? David

…

On Sun, Jun 14, 2020, 6:50 PM GabroxylicAcid ***@***.***> wrote: Hi! I'm new to this. After running mpirun -n 1 main This is what I get: An error occurred in line <1983> of file <../source/base/parameter_handler.cc> in function void dealii::ParameterHandler::scan_line(std::__cxx11::string, const string&, unsigned int) The violated condition was: entries->get_child_optional (get_current_full_path(subsection)) Additional information: Line <44> of file <parameters.in: There is no such subsection to be entered: Refinement criterion: n -------------------------------------------------------- Aborting! ---------------------------------------------------- ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[42277,1],0] Exit code: 1 What could be the problem? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#159>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA47FXWKII3PU4XN6Y23RWVHZRANCNFSM4N5U3WRQ> .

[gablerona]

Hello,

I have not modified anything as I'm trying to run the example applications first. Although, I was able to run cahnHilliard only.

Thanks.

Gab

[david-montiel-t]

Hello Gab, I found an issue with the compilation of the nucleationModel_preferential application. I will work on fixing it and let you know when it is ready. However, the dendriticSolidification (and other) applications work fine in my local installation. Can you let me know if you have the traditional installation or the Docker installation? Also have you made sure to download the most updated version of PRISMS-PF? Thank you, David

…

On Mon, Jun 15, 2020, 12:09 PM GabroxylicAcid ***@***.***> wrote: Hello, I have not modified anything as I'm trying to run the example applications first. Although, I was able to run cahnHilliard only. Thanks. Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA46REW33IXUGMZN5FHTRWZBTDANCNFSM4N5U3WRQ> .

[gablerona]

Hello David,

Thank you.

As for the dendriticSolidification, I have installed from Docker. I just learned of the PRISMS-PF two days ago and it seemed promising so I tried installing it. I had no issue in installing CMake, however, I had trouble installing deal.ii binary package as there was an issue with 9.2.0 in Mac OSX 10.14. So I tried installing from Docker same with PRISMS-PF.

Thank you!

Gab

[david-montiel-t]

Hello Gab, I think the issue is that the Docker container is slightly out of date. And when you bind to the host volume, you combine the outdated core library (from the Docker container) with the applications written for the new version of PRISMS-PF, which you have just cloned from the github repository, so there is a conflict. I suggest that you try the following steps. Assuming that you cloned the PRISMS-PF repository inside the folder ~/DockerWorkspace, launch the docker environment using the following line: *$ docker run -ti -v ~/DockerWorkspace/phaseField:/home/dealii/phaseField stvdwtt/prismspf:prismspf* Then inside PRISMS-PF Docker environment, go to the folder *phaseField *and compile the core library $ cmake . $ make -j 8 It may take a while (about 5 mins.) but after that you'll be using the most up-to-date version of PRISMS-PF. Then go to any application and re-compile (but first delete the file CMakeCache.txt if there is one) $ rm CMakeCache.txt $ cmake . $ make -j 8 Finally, run your code: $ mpirun -n 1 main This should work because you will be using the latest version of both the core library and the applications. Hope this helps. Let me know if you still have issues. The new Docker installation will be released very soon. David

…

On Mon, Jun 15, 2020 at 1:10 PM GabroxylicAcid ***@***.***> wrote: Hello David, Thank you. As for the dendriticSolidification, I have installed from Docker. I just learned of the PRISMS-PF two days ago and it seemed promising so I tried installing it. I had no issue in installing CMake, however, I had trouble installing deal.ii binary package as there was an issue with 9.2.0 in Mac OSX 10.14. So I tried installing from Docker same with PRISMS-PF. Thank you! Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA4Y2YHZPVD6LPPLOJQDRWZIYFANCNFSM4N5U3WRQ> .

[gablerona]

Hello David,

Thank you for the response.
I still get the same error. I tried your suggestion above:

Gabs-MacBook-Air:~ GabroxylicAcid$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications stvdwtt/prismspf:prismspf
dealii@716fbb19bc30:~/phaseField$ cmake .
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField
dealii@716fbb19bc30:~/phaseField$ make -j 8
[  2%] Linking CXX static library libprisms_pf.a
[  2%] Linking CXX static library libprisms_pf_debug.a
[ 51%] Built target prisms_pf
[100%] Built target prisms_pf_debug
dealii@716fbb19bc30:~/phaseField$ rm CMakeCache.txt
dealii@716fbb19bc30:~/phaseField$ cmake .
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField
dealii@716fbb19bc30:~/phaseField$ make -j 8
Scanning dependencies of target prisms_pf
Scanning dependencies of target prisms_pf_debug
[ 50%] Built target prisms_pf_debug
[100%] Built target prisms_pf
dealii@716fbb19bc30:~/phaseField$ cd applications/dendriticSolidification/
dealii@716fbb19bc30:~/phaseField/applications/dendriticSolidification$ cmake .
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField
[ 50%] Built target prisms_pf_debug
[100%] Built target prisms_pf
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField/applications/dendriticSolidification
dealii@716fbb19bc30:~/phaseField/applications/dendriticSolidification$ make debug
[100%] Switch CMAKE_BUILD_TYPE to Debug
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField
make[4]: Entering directory '/home/dealii/phaseField'
make[5]: Entering directory '/home/dealii/phaseField'
make[6]: Entering directory '/home/dealii/phaseField'
make[6]: Leaving directory '/home/dealii/phaseField'
[ 50%] Built target prisms_pf_debug
make[6]: Entering directory '/home/dealii/phaseField'
make[6]: Leaving directory '/home/dealii/phaseField'
[100%] Built target prisms_pf
make[5]: Leaving directory '/home/dealii/phaseField'
make[4]: Leaving directory '/home/dealii/phaseField'
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/phaseField/applications/dendriticSolidification
[ 50%] Linking CXX executable main
[100%] Built target main
Built target debug
dealii@716fbb19bc30:~/phaseField/applications/dendriticSolidification$ mpirun -n 1 main
Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/var/lib/docker/overlay2/l/X7MHTOP4KJ3Y7NKIYFZNWZGEKT:/var/lib/docker/overlay2/l/EIRFTDCJMYSH2GGLUMGOI7BKRG:/var/lib/docker/overlay2/l/B6TV6NHB4PHOIA3NTXBTVBIMLW:/var/lib/docker/overlay2/l/JZ22WAZX3VN7ZC2QX5DW6SF3UM:/var/lib/docker/overlay2/l/22J6TOEYGANN2MOOJLKC7C2JM2:/var/lib/docker/overlay2/l/TCO73GWMQKJDMGUAJH5QLZUG5P:/var/lib/docker/overlay2/l/UFGDJGM6QC3RTXT3RDYOWVHTQY:/var/lib/docker/overlay2/l/OA6EFXTUCC4OT66GBOQU7M54SM:/var/lib/docker/overlay2/l/GBFIURZF4VMDC'
Unexpected end of /proc/mounts line `QZDCRRORWEPQ3:/var/lib/docker/overlay2/l/HJ4S5JL6AQX5JBA2JVNO63FJMN:/var/lib/docker/overlay2/l/ZOYKFJWSMRVK7BUP55C6JUUNFV:/var/lib/docker/overlay2/l/FG3CPKWCL7FHPIHYQCRP7HBPGB:/var/lib/docker/overlay2/l/544DMBTVGX7DFBUHGRWJU6ICWU:/var/lib/docker/overlay2/l/ITXJYCV7VDGOBOCFNA7NPALCVM:/var/lib/docker/overlay2/l/W7LBW5YVVQNZWHZ7NHHPCJR3BR:/var/lib/docker/overlay2/l/U6JZBW75VO4PTOOH3SOLAVD4PJ:/var/lib/docker/overlay2/l/QOK6QPYOU6WM3HP6NHU27FDBBS:/var/lib/docker/overlay2/l/DYN5CVYETGYVWX4JAZ2J4C7H5A:/var/lib/do'
Using the input parameter file: parameters.in
Number of constants: 6
Number of post-processing variables: 0


----------------------------------------------------
PRISMS-PF: Exception on processing: 

--------------------------------------------------------
An error occurred in line <1983> of file <../source/base/parameter_handler.cc> in function
    void dealii::ParameterHandler::scan_line(std::__cxx11::string, const string&, unsigned int)
The violated condition was: 
    entries->get_child_optional (get_current_full_path(subsection))
Additional information: 
    Line <47> of file <parameters.in: There is no such subsection to be entered: Refinement criterion: phi
--------------------------------------------------------

Aborting!
----------------------------------------------------
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[10027,1],0]
  Exit code:    1
--------------------------------------------------------------------------
dealii@716fbb19bc30:~/phaseField/applications/dendriticSolidification$ 

Thank you.

Gab

[gablerona]

Hello David,

Is it an issue that I am still using deal.ii 9.0.0? or do I have to install the 9.2.0?

Thanks.

Gab

[david-montiel-t]

Hello Gab, Looks like you wrote the following line: docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications stvdwtt/prismspf:prismspf However, the line I suggested doesn't include "applications": *$ docker run -ti -v ~/DockerWorkspace/phaseField:/home/dealii/phaseField stvdwtt/prismspf:prismsp* Can you try again? David

…

On Mon, Jun 15, 2020, 3:40 PM GabroxylicAcid ***@***.***> wrote: Hello David, Thank you for the response. I still get the same error. I tried your suggestion above: Gabs-MacBook-Air:~ GabroxylicAcid$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications stvdwtt/prismspf:prismspf ***@***.***:~/phaseField$ cmake . -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField ***@***.***:~/phaseField$ make -j 8 [ 2%] Linking CXX static library libprisms_pf.a [ 2%] Linking CXX static library libprisms_pf_debug.a [ 51%] Built target prisms_pf [100%] Built target prisms_pf_debug ***@***.***:~/phaseField$ rm CMakeCache.txt ***@***.***:~/phaseField$ cmake . -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField ***@***.***:~/phaseField$ make -j 8 Scanning dependencies of target prisms_pf Scanning dependencies of target prisms_pf_debug [ 50%] Built target prisms_pf_debug [100%] Built target prisms_pf ***@***.***:~/phaseField$ cd applications/dendriticSolidification/ ***@***.***:~/phaseField/applications/dendriticSolidification$ cmake . -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField [ 50%] Built target prisms_pf_debug [100%] Built target prisms_pf -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField/applications/dendriticSolidification ***@***.***:~/phaseField/applications/dendriticSolidification$ make debug [100%] Switch CMAKE_BUILD_TYPE to Debug -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Using the deal.II-9.0.0 installation found at /home/dealii/dealii-v9.0.0 -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_query_git_information.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_setup_target.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake -- Include macro /home/dealii/dealii-v9.0.0/share/deal.II/macros/macro_deal_ii_add_test.cmake -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField make[4]: Entering directory '/home/dealii/phaseField' make[5]: Entering directory '/home/dealii/phaseField' make[6]: Entering directory '/home/dealii/phaseField' make[6]: Leaving directory '/home/dealii/phaseField' [ 50%] Built target prisms_pf_debug make[6]: Entering directory '/home/dealii/phaseField' make[6]: Leaving directory '/home/dealii/phaseField' [100%] Built target prisms_pf make[5]: Leaving directory '/home/dealii/phaseField' make[4]: Leaving directory '/home/dealii/phaseField' -- Configuring done -- Generating done -- Build files have been written to: /home/dealii/phaseField/applications/dendriticSolidification [ 50%] Linking CXX executable main [100%] Built target main Built target debug ***@***.***:~/phaseField/applications/dendriticSolidification$ mpirun -n 1 main Unexpected end of /proc/mounts line overlay / overlay rw,relatime,lowerdir=/var/lib/docker/overlay2/l/X7MHTOP4KJ3Y7NKIYFZNWZGEKT:/var/lib/docker/overlay2/l/EIRFTDCJMYSH2GGLUMGOI7BKRG:/var/lib/docker/overlay2/l/B6TV6NHB4PHOIA3NTXBTVBIMLW:/var/lib/docker/overlay2/l/JZ22WAZX3VN7ZC2QX5DW6SF3UM:/var/lib/docker/overlay2/l/22J6TOEYGANN2MOOJLKC7C2JM2:/var/lib/docker/overlay2/l/TCO73GWMQKJDMGUAJH5QLZUG5P:/var/lib/docker/overlay2/l/UFGDJGM6QC3RTXT3RDYOWVHTQY:/var/lib/docker/overlay2/l/OA6EFXTUCC4OT66GBOQU7M54SM:/var/lib/docker/overlay2/l/GBFIURZF4VMDC' Unexpected end of /proc/mounts line `QZDCRRORWEPQ3:/var/lib/docker/overlay2/l/HJ4S5JL6AQX5JBA2JVNO63FJMN:/var/lib/docker/overlay2/l/ZOYKFJWSMRVK7BUP55C6JUUNFV:/var/lib/docker/overlay2/l/FG3CPKWCL7FHPIHYQCRP7HBPGB:/var/lib/docker/overlay2/l/544DMBTVGX7DFBUHGRWJU6ICWU:/var/lib/docker/overlay2/l/ITXJYCV7VDGOBOCFNA7NPALCVM:/var/lib/docker/overlay2/l/W7LBW5YVVQNZWHZ7NHHPCJR3BR:/var/lib/docker/overlay2/l/U6JZBW75VO4PTOOH3SOLAVD4PJ:/var/lib/docker/overlay2/l/QOK6QPYOU6WM3HP6NHU27FDBBS:/var/lib/docker/overlay2/l/DYN5CVYETGYVWX4JAZ2J4C7H5A:/var/lib/do' Using the input parameter file: parameters.in Number of constants: 6 Number of post-processing variables: 0 ------------------------------ PRISMS-PF: Exception on processing: ------------------------------ An error occurred in line <1983> of file <../source/base/parameter_handler.cc> in function void dealii::ParameterHandler::scan_line(std::__cxx11::string, const string&, unsigned int) The violated condition was: entries->get_child_optional (get_current_full_path(subsection)) Additional information: Line <47> of file <parameters.in: There is no such subsection to be entered: Refinement criterion: phi Aborting! ------------------------------ Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------ mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[10027,1],0] Exit code: 1 ***@***.***:~/phaseField/applications/dendriticSolidification$ ` Thank you. Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA4YP72MBDZKFDEQPRGDRWZ2LZANCNFSM4N5U3WRQ> .

[david-montiel-t]

The version of deal.ii should not be an issue. Please refer my last email.

…

On Mon, Jun 15, 2020, 3:53 PM GabroxylicAcid ***@***.***> wrote: Hello David, Is it an issue that I am still using deal.ii 9.0.0? or do I have to install the 9.2.0? Thanks. Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA43MDYNDULOMN62JN4LRWZ33JANCNFSM4N5U3WRQ> .

[gablerona]

Hello David,

Thank you for pointing it out. I am currently trying it.
However, after
make -j 8
I have been encountering error like

[ 10%] Building CXX object CMakeFiles/prisms_pf.dir/src/matrixfree/utilities.cc.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
CMakeFiles/prisms_pf_debug.dir/build.make:206: recipe for target 'CMakeFiles/prisms_pf_debug.dir/src/matrixfree/computeLHS.cc.o' failed
make[2]: *** [CMakeFiles/prisms_pf_debug.dir/src/matrixfree/computeLHS.cc.o] Error 4
make[2]: *** Waiting for unfinished jobs....

It is still currently running. Is this something that I should be worried about? What could have went wrong?

Thanks.

Gab

[david-montiel-t]

Can you cancel the compilation and try with just "make" (without the "-j 8")? Like this: $ make That worked for me. David

…

On Mon, Jun 15, 2020 at 4:14 PM GabroxylicAcid ***@***.***> wrote: Hello David, Thank you for pointing it out. I am currently trying it. However, after make -j 8 I have been encountering error like g++: internal compiler error: Killed (program cc1plus) Please submit a full bug report, with preprocessed source if appropriate. See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions. CMakeFiles/prisms_pf_debug.dir/build.make:206: recipe for target 'CMakeFiles/prisms_pf_debug.dir/src/matrixfree/computeLHS.cc.o' failed make[2]: *** [CMakeFiles/prisms_pf_debug.dir/src/matrixfree/computeLHS.cc.o] Error 4 make[2]: *** Waiting for unfinished jobs.... It is still currently running. Is this something that I should be worried about? What could have went wrong? Thanks. Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA424ULE57MSPEW7UDODRWZ6JFANCNFSM4N5U3WRQ> .

[gablerona]

It did not work.

dealii@c80f3f91c95d:~/phaseField/applications/dendriticSolidification$ mpirun -n 1 main
Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/var/lib/docker/overlay2/l/IFK4P3L3MJUXHSNHQX47WKTXUQ:/var/lib/docker/overlay2/l/EIRFTDCJMYSH2GGLUMGOI7BKRG:/var/lib/docker/overlay2/l/B6TV6NHB4PHOIA3NTXBTVBIMLW:/var/lib/docker/overlay2/l/JZ22WAZX3VN7ZC2QX5DW6SF3UM:/var/lib/docker/overlay2/l/22J6TOEYGANN2MOOJLKC7C2JM2:/var/lib/docker/overlay2/l/TCO73GWMQKJDMGUAJH5QLZUG5P:/var/lib/docker/overlay2/l/UFGDJGM6QC3RTXT3RDYOWVHTQY:/var/lib/docker/overlay2/l/OA6EFXTUCC4OT66GBOQU7M54SM:/var/lib/docker/overlay2/l/GBFIURZF4VMDC'
Unexpected end of /proc/mounts line `QZDCRRORWEPQ3:/var/lib/docker/overlay2/l/HJ4S5JL6AQX5JBA2JVNO63FJMN:/var/lib/docker/overlay2/l/ZOYKFJWSMRVK7BUP55C6JUUNFV:/var/lib/docker/overlay2/l/FG3CPKWCL7FHPIHYQCRP7HBPGB:/var/lib/docker/overlay2/l/544DMBTVGX7DFBUHGRWJU6ICWU:/var/lib/docker/overlay2/l/ITXJYCV7VDGOBOCFNA7NPALCVM:/var/lib/docker/overlay2/l/W7LBW5YVVQNZWHZ7NHHPCJR3BR:/var/lib/docker/overlay2/l/U6JZBW75VO4PTOOH3SOLAVD4PJ:/var/lib/docker/overlay2/l/QOK6QPYOU6WM3HP6NHU27FDBBS:/var/lib/docker/overlay2/l/DYN5CVYETGYVWX4JAZ2J4C7H5A:/var/lib/do'
Using the input parameter file: parameters.in
Number of constants: 6
Number of post-processing variables: 0
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 945 on node c80f3f91c95d exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
dealii@c80f3f91c95d:~/phaseField/applications/dendriticSolidification$ 

Maybe I have to install everything again.

Gab

[david-montiel-t]

Yes, sorry. Could you start again followimg the procedure I described in my long email? Make sure you delete the files CMakeCache.txt (if existing) before you do $cmake . both in the core library (phaseField) and the application directory. Also type "make" to compile instead of "make -j 8" David

…

On Mon, Jun 15, 2020, 5:34 PM GabroxylicAcid ***@***.***> wrote: It did not work. ***@***.***:~/phaseField/applications/dendriticSolidification$ mpirun -n 1 main Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/var/lib/docker/overlay2/l/IFK4P3L3MJUXHSNHQX47WKTXUQ:/var/lib/docker/overlay2/l/EIRFTDCJMYSH2GGLUMGOI7BKRG:/var/lib/docker/overlay2/l/B6TV6NHB4PHOIA3NTXBTVBIMLW:/var/lib/docker/overlay2/l/JZ22WAZX3VN7ZC2QX5DW6SF3UM:/var/lib/docker/overlay2/l/22J6TOEYGANN2MOOJLKC7C2JM2:/var/lib/docker/overlay2/l/TCO73GWMQKJDMGUAJH5QLZUG5P:/var/lib/docker/overlay2/l/UFGDJGM6QC3RTXT3RDYOWVHTQY:/var/lib/docker/overlay2/l/OA6EFXTUCC4OT66GBOQU7M54SM:/var/lib/docker/overlay2/l/GBFIURZF4VMDC' Unexpected end of /proc/mounts line `QZDCRRORWEPQ3:/var/lib/docker/overlay2/l/HJ4S5JL6AQX5JBA2JVNO63FJMN:/var/lib/docker/overlay2/l/ZOYKFJWSMRVK7BUP55C6JUUNFV:/var/lib/docker/overlay2/l/FG3CPKWCL7FHPIHYQCRP7HBPGB:/var/lib/docker/overlay2/l/544DMBTVGX7DFBUHGRWJU6ICWU:/var/lib/docker/overlay2/l/ITXJYCV7VDGOBOCFNA7NPALCVM:/var/lib/docker/overlay2/l/W7LBW5YVVQNZWHZ7NHHPCJR3BR:/var/lib/docker/overlay2/l/U6JZBW75VO4PTOOH3SOLAVD4PJ:/var/lib/docker/overlay2/l/QOK6QPYOU6WM3HP6NHU27FDBBS:/var/lib/docker/overlay2/l/DYN5CVYETGYVWX4JAZ2J4C7H5A:/var/lib/do' Using the input parameter file: parameters.in Number of constants: 6 Number of post-processing variables: 0 -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 945 on node c80f3f91c95d exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- ***@***.***:~/phaseField/applications/dendriticSolidification$ Maybe I had to install everything again. Gab — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AD3FA4YCBMY7LMOL234NXXTRW2HWDANCNFSM4N5U3WRQ> .

[david-montiel-t]

Also, since you have not made any changes, you can also re-clone the repository. On Mon, Jun 15, 2020, 5:40 PM David Montiel Taboada <dmontiel@umich.edu> wrote:

…

Yes, sorry. Could you start again followimg the procedure I described in my long email? Make sure you delete the files CMakeCache.txt (if existing) before you do $cmake . both in the core library (phaseField) and the application directory. Also type "make" to compile instead of "make -j 8" David On Mon, Jun 15, 2020, 5:34 PM GabroxylicAcid ***@***.***> wrote: > It did not work. > > ***@***.***:~/phaseField/applications/dendriticSolidification$ mpirun -n 1 main > Unexpected end of /proc/mounts line `overlay / overlay rw,relatime,lowerdir=/var/lib/docker/overlay2/l/IFK4P3L3MJUXHSNHQX47WKTXUQ:/var/lib/docker/overlay2/l/EIRFTDCJMYSH2GGLUMGOI7BKRG:/var/lib/docker/overlay2/l/B6TV6NHB4PHOIA3NTXBTVBIMLW:/var/lib/docker/overlay2/l/JZ22WAZX3VN7ZC2QX5DW6SF3UM:/var/lib/docker/overlay2/l/22J6TOEYGANN2MOOJLKC7C2JM2:/var/lib/docker/overlay2/l/TCO73GWMQKJDMGUAJH5QLZUG5P:/var/lib/docker/overlay2/l/UFGDJGM6QC3RTXT3RDYOWVHTQY:/var/lib/docker/overlay2/l/OA6EFXTUCC4OT66GBOQU7M54SM:/var/lib/docker/overlay2/l/GBFIURZF4VMDC' > Unexpected end of /proc/mounts line `QZDCRRORWEPQ3:/var/lib/docker/overlay2/l/HJ4S5JL6AQX5JBA2JVNO63FJMN:/var/lib/docker/overlay2/l/ZOYKFJWSMRVK7BUP55C6JUUNFV:/var/lib/docker/overlay2/l/FG3CPKWCL7FHPIHYQCRP7HBPGB:/var/lib/docker/overlay2/l/544DMBTVGX7DFBUHGRWJU6ICWU:/var/lib/docker/overlay2/l/ITXJYCV7VDGOBOCFNA7NPALCVM:/var/lib/docker/overlay2/l/W7LBW5YVVQNZWHZ7NHHPCJR3BR:/var/lib/docker/overlay2/l/U6JZBW75VO4PTOOH3SOLAVD4PJ:/var/lib/docker/overlay2/l/QOK6QPYOU6WM3HP6NHU27FDBBS:/var/lib/docker/overlay2/l/DYN5CVYETGYVWX4JAZ2J4C7H5A:/var/lib/do' > Using the input parameter file: parameters.in > Number of constants: 6 > Number of post-processing variables: 0 > -------------------------------------------------------------------------- > mpirun noticed that process rank 0 with PID 945 on node c80f3f91c95d exited on signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > ***@***.***:~/phaseField/applications/dendriticSolidification$ > > Maybe I had to install everything again. > > Gab > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#159 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AD3FA4YCBMY7LMOL234NXXTRW2HWDANCNFSM4N5U3WRQ> > . >