Unsuccessful integration of p4est with dealii

[Kartik Jujare]

Hello,

I was wondering if anyone could help pinpoint any anomaly with my p4est and dealii integration. 

I was able to successfully install Petsc and run its own tests using my already installed mpich.

Next, I installed p4est which also seemed to install without problems.

Then dealii which also did not give me any problems.

I could not find any topics relating to this error. I'd be grateful if anyone could help solve this issue. Following is more information about my installations.

The problem came when I ran the following command after dealii installation

$ make test

The attachments:

detailed.log -- dealii

config.log -- p4est build directory

Here is the output from the terminal:

********************************************************************************************************************************************

ubuntu@dulcet:~/software/dealii-8.4.1/build$ make test

Scanning dependencies of target test

[100%] Running quicktests...

Test project /home/ubuntu/software/dealii-8.4.1/build/tests/quick_tests

    Start 1: step.debug

1/7 Test #1: step.debug .......................   Passed   20.28 sec

    Start 2: step.release

2/7 Test #2: step.release .....................   Passed   17.81 sec

    Start 3: affinity.debug

3/7 Test #3: affinity.debug ...................   Passed   12.33 sec

    Start 4: mpi.debug

4/7 Test #4: mpi.debug ........................   Passed   12.67 sec

    Start 5: tbb.debug

5/7 Test #5: tbb.debug ........................   Passed   11.19 sec

    Start 6: p4est.debug

6/7 Test #6: p4est.debug ......................***Failed   17.08 sec

Test p4est.debug: RUN

===============================   OUTPUT BEGIN  ===============================

Scanning dependencies of target kill-p4est.debug-OK

[  0%] Built target kill-p4est.debug-OK

[  0%] Built target expand_instantiations_exe

[  0%] Built target obj_opencascade.inst

[  1%] Built target obj_opencascade.debug

[  6%] Built target obj_boost_serialization.debug

[  6%] Built target obj_boost_system.debug

[ 13%] Built target obj_tbb.debug

[ 15%] Built target obj_muparser.debug

[ 20%] Built target obj_numerics.inst

[ 28%] Built target obj_numerics.debug

[ 37%] Built target obj_fe.inst

[ 47%] Built target obj_fe.debug

[ 49%] Built target obj_dofs.inst

[ 52%] Built target obj_dofs.debug

[ 55%] Built target obj_lac.inst

[ 66%] Built target obj_lac.debug

[ 67%] Built target obj_base.inst

[ 79%] Built target obj_base.debug

[ 83%] Built target obj_grid.inst

[ 86%] Built target obj_grid.debug

[ 88%] Built target obj_hp.inst

[ 89%] Built target obj_hp.debug

[ 91%] Built target obj_multigrid.inst

[ 93%] Built target obj_multigrid.debug

[ 94%] Built target obj_distributed.inst

[ 96%] Built target obj_distributed.debug

[ 96%] Built target obj_algorithms.inst

[ 98%] Built target obj_algorithms.debug

[ 98%] Built target obj_integrators.debug

[100%] Built target obj_matrix_free.inst

[100%] Built target obj_matrix_free.debug

[100%] Built target obj_meshworker.inst

[100%] Built target obj_meshworker.debug

[100%] Built target deal_II.g

Scanning dependencies of target p4est.debug

[100%] Building CXX object tests/quick_tests/CMakeFiles/p4est.debug.dir/p4est.cc.o

Linking CXX executable p4est.debug

[100%] Built target p4est.debug

Scanning dependencies of target p4est.debug.run

p4est.debug: RUN failed. Output:

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

make[7]: *** [tests/quick_tests/CMakeFiles/p4est.debug.run] Error 1

make[6]: *** [tests/quick_tests/CMakeFiles/p4est.debug.run.dir/all] Error 2

make[5]: *** [tests/quick_tests/CMakeFiles/p4est.debug.run.dir/rule] Error 2

make[4]: *** [p4est.debug.run] Error 2

p4est.debug: ******    RUN failed    *******

===============================    OUTPUT END   ===============================

Expected stage PASSED - aborting

CMake Error at /home/ubuntu/software/dealii-8.4.1/cmake/scripts/run_test.cmake:140 (MESSAGE):

  *** abort

    Start 7: step-petsc.debug

Errors while running CTest

7/7 Test #7: step-petsc.debug .................   Passed   16.50 sec

86% tests passed, 1 tests failed out of 7

Total Test time (real) = 107.88 sec

The following tests FAILED:

 6 - p4est.debug (Failed)

*******************************     WARNING     *******************************

Some of the tests failed!

Please scroll up or check the file tests/quick_tests/quicktests.log for the

error messages. If you are unable to fix the problems, see the FAQ or write

to the mailing list linked at http://www.dealii.org

The p4est test can fail if you are running an OpenMPI version before 1.5.

This is a known problem and the only work around is to update to a more

recent version or use a different MPI library like MPICH.

Built target test

********************************************************************************************************************************************

Thank you for your help.

Regards,

Kartik Jujare

[Timo Heister]

Hey Kartik,

I haven't seen an error like this before. A few ideas:
1. Can you check that p4est is using the same mpi libraries? You can
for example compare the output of "ldd libp4est.so | grep mpi" with
the one from the deal.II libs.
2. you can go into the tests/quicktests/ directory inside your build
directory and run the p4est test manually using mpirun. Maybe vary the
number of MPI ranks and/or try running in a debugger to see where
things are breaking.

> to the mailing list linked at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org&d=CwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=kJCrxRvG_tbq41NC8oZvBxxT3eVYqKmZ9KvjoogieJg&s=4gGLkxn4kqLMcvYIIhPXdKpxQV_3yMiA0mhdK5nb6Ew&e=

>
>
> The p4est test can fail if you are running an OpenMPI version before 1.5.
> This is a known problem and the only work around is to update to a more
> recent version or use a different MPI library like MPICH.
>
> Built target test
>
> ********************************************************************************************************************************************
>
> Thank you for your help.
>
> Regards,
> Kartik Jujare
>

> --
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Timo Heister
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[Kartik Jujare]

Hi Timo, 

Thank you for your reply.

I ran the commands as you instructed:

1)

ubuntu@dulcet:~/programfiles/p4est/FAST/lib$ ldd libp4est.so | grep mpi

libmpi.so.12 => /home/ubuntu/programfiles/mpich/lib/libmpi.so.12 (0x00007f281d956000)

ubuntu@dulcet:~/programfiles/dealii/lib$ ldd libdeal_II.so | grep mpi

libmpi.so.12 => /home/ubuntu/programfiles/mpich/lib/libmpi.so.12 (0x00007f2dbaea8000)

libmpifort.so.12 => /home/ubuntu/programfiles/mpich/lib/libmpifort.so.12 (0x00007f2db9e6e000)

2) It returned this when I tried to compile it this way. Is this the right way? I am running this on a remote virtual machine. I am trying to see how to resolve this compilation error.   

ubuntu@dulcet:~/software/dealii-8.4.1/tests/quick_tests$ mpicxx p4est.cc -o p4est -I/home/ubuntu/programfiles/dealii/include/

In file included from /home/ubuntu/programfiles/dealii/include/deal.II/base/logstream.h:23:0,

                 from p4est.cc:21:

/home/ubuntu/programfiles/dealii/include/deal.II/base/thread_local_storage.h:23:46: fatal error: tbb/enumerable_thread_specific.h: No such file or directory

 #  include <tbb/enumerable_thread_specific.h>

                                              ^

compilation terminated.

Thanks.

[Kartik Jujare]

Hi Timo,

I slightly remember that I had included -DDEAL_II_WITH_THREADS=OFF . This could be a cause of the problem right? If it could be should I reconfigure dealii with this option on?

Regards,

Kartik Jujare.

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[Kartik Jujare]

This is not the case. Still unable to figure out.

[Timo Heister]

Kartik,

> It returned this when I tried to compile it this way. Is this the right way?

No, don't compile it manually. You will be missing a large number of
preprocessor defines, include paths, etc.. If you run "make test", the
binaries should still exist. Just try to run them as is.

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>>>
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>>>
>>> --
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>>>
>>> --

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[Kartik Jujare]

Timo, 

Yes. My mistake. I was looking at the source folder instead of the installation folder.  But I guess getting this output does not make a lot of sense.

ubuntu@dulcet:~/software/dealii-8.4.1/build/tests/quick_tests$ mpirun -np 4 ./p4est.debug 

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

>> try running in a debugger

Will have to try this and I will come back with what I get. but I hope you mean using eclipse for it. Or are you referring to gdb and xterm. I am still a novice at debugging parallel codes. Would you be able to point to resources in this regard? 

Regards,

Kartik Jujare

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>>>
>>>
>>> --
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>>> http://www.math.clemson.edu/~heister/
>>>
>>> --

>>> The deal.II project is located at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_&d=CwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=qBfFDSWPW4ApDkpXc56B3mTfcJw6fjR-h--zNqhpXSg&s=xSad9dbz_W-ao7x0gYtrTM3nHWiZZIpjPUUwhQWBt2I&e=
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[Timo Heister]

> installation folder. But I guess getting this output does not make a lot of
> sense.
>
> ubuntu@dulcet:~/software/dealii-8.4.1/build/tests/quick_tests$ mpirun -np 4
> ./p4est.debug
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Does this also happen with 1 rank?

>>> try running in a debugger
> Will have to try this and I will come back with what I get. but I hope you
> mean using eclipse for it. Or are you referring to gdb and xterm. I am still
> a novice at debugging parallel codes. Would you be able to point to
> resources in this regard?

see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dealii_dealii_wiki_Frequently-2DAsked-2DQuestions-23how-2Ddo-2Di-2Ddebug-2Dmpi-2Dprograms&d=CwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=YN0JHrQA35iJTgejwPRe1gm5nGqklqgPm0wTTWjc0a8&s=zu4qxhp7eX0DAdKfncd0oL1f3zARknQWkFdAYvxnEFA&e=

[Kartik Jujare]

Hi Timo,

 
> ubuntu@dulcet:~/software/dealii-8.4.1/build/tests/quick_tests$ mpirun -np 4 
> ./p4est.debug 
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 

>>Does this also happen with 1 rank?

with $mpirun -np 1 ./p4est-debug 

it runs without error. It does not show any output. The control returns to the terminal. 

[Uwe Köcher]

Dear Kartik,

I cannot help you out in your specific problem, but have you tried out candi:

  https://github.com/dealii/candi

to download, compile and install deal.II with MPI + p4est (and other tools if

you like)?

Kind regards

  Uwe

[Kartik Jujare]

>>I cannot help you out in your specific problem, but have you tried out candi:

Thank You for your reply Uwe. I will try it and post any observations or solutions that I find probably in the next week.

Regards,

Kartik Jujare

[Kartik Jujare]

Dear Uwe, 

It seems that the candi script was able to install everything without a problem. Is there anyway I can verify the installation was a success? Could you please give me directions on how this could work?

Regards,

Kartik

On Saturday, December 10, 2016 at 5:29:49 PM UTC+1, Uwe Köcher wrote:

[Uwe Köcher]

Dear Kartik,

well, candi has users around the world - if it reports a successful installation, then everything should be fine.

But anyhow, you can go to each installation folder, e.g. deal.II, and try to run their specific test suite, if available.

Kind regards

  Uwe

[Kartik Jujare]

Thank you for your help.