date:20161109

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

Sorry for the late answer. I had to re-install dealii + trilinos.

jomivalen@Nalia ~/cfem/trilinos/lib $ ldd libepetra.so.12.6.2 | grep mpi
libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x7fb4ac8f7000)
libmpi.so.1 => /usr/lib/libmpi.so.1 (0x7fb4ac576000)

jomivalen@Nalia ~/thesis/dealii-8.4.1/build/lib $ ldd libdeal_II.g.so.8.4.1
| grep mpi
libmpicxx.so.12 =>
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpicxx.so.12
(0x7f75b64c3000)
libmpi.so.12 =>
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpi.so.12
(0x7f75b3855000)
libmpi_cxx.so.1 => /usr/lib/libmpi_cxx.so.1 (0x7f75ae037000)
libmpi.so.1 => /usr/lib/libmpi.so.1 (0x7f75adcb5000)

What does these results mean?. What should i do?

Thanks,
Joaquin

2016-11-09 18:56 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 03:52 PM, 'Joaquin M Valencia Bravo' via deal.II User Group
> wrote:
>
>>
>> In case of trilinos, I followed the next steps:
>> $  mkdir build
>> $  cd build
>> $
>>
>> cmake \
>> -DTrilinos_ENABLE_Sacado=ON \
>> -DTrilinos_ENABLE_MueLu:BOOL=ON \
>> -DTrilinos_ENABLE_Stratimikos=ON \
>> -DCMAKE_BUILD_TYPE=RELEASE \
>> -DCMAKE_CXX_FLAGS="-g -O3" \
>> -DCMAKE_C_FLAGS="-g -O3" \
>> -DCMAKE_FORTRAN_FLAGS="-g -O5" \
>> -DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
>> -DCMAKE_VERBOSE_MAKEFILE=FALSE \
>> -DTrilinos_VERBOSE_CONFIGURE=FALSE \
>> -DTPL_ENABLE_MPI=ON \
>> -DBUILD_SHARED_LIBS=ON \
>> -DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \
>>
>> $ make -j8 install
>>
>> In case of dealii, I followed the next steps:
>>
>> $ mkdir build
>>
>> $ cd build
>>
>> $ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
>> -DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \
>>
>> -DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../
>>
>> $ make -j8 install
>>
>> $ make test (failed)
>>
>
> That's interesting then. Can you try to do
>   ldd $HOME/share/trilinos/lib/libepetra.so.12.6.2
>   ldd /home/jomivalen/cfem/deal.II/lib/libdeal_II.g.so.8.4.1
> and in both cases see which MPI libraries they link to? For example, for
> me this yields the following:
>
> rilinos-12.8.1/lib> ldd libepetra.so.12.8.1 | grep mpi
> libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1
> (0x7f1107a5f000)
> libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12
> (0x7f110780b000)
> libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1
> (0x7f1107091000)
> libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12
> (0x7f1106dad000)
> libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12
> (0x7f1105d31000)
> libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13
> (0x7f1105a8e000)
> rilinos-12.8.1/lib> cd
> f/bangerth> cd p/deal.II/1/build/lib/
> build/lib> ldd libdeal_II.so.8.5.0-pre | grep mpi
> libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1
> (0x7f7e22f28000)
> libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12
> (0x7f7e22181000)
> libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1
> (0x7f7e152ff000)
> libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12
> (0x7f7e150ab000)
> libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12
> (0x7f7e148cf000)
> libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13
> (0x7f7e1462c000
>
> So they are the same.
>
>
> Best
>  W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/fo
> rum/dealii?hl=en
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>



-- 
Joaquin Valencia
Graduate Student

-- 
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread Wolfgang Bangerth

On 11/09/2016 03:52 PM, 'Joaquin M Valencia Bravo' via deal.II User 
Group wrote:


In case of trilinos, I followed the next steps:
$  mkdir build
$  cd build
$

cmake \
-DTrilinos_ENABLE_Sacado=ON \
-DTrilinos_ENABLE_MueLu:BOOL=ON \
-DTrilinos_ENABLE_Stratimikos=ON \
-DCMAKE_BUILD_TYPE=RELEASE \
-DCMAKE_CXX_FLAGS="-g -O3" \
-DCMAKE_C_FLAGS="-g -O3" \
-DCMAKE_FORTRAN_FLAGS="-g -O5" \
-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-DCMAKE_VERBOSE_MAKEFILE=FALSE \
-DTrilinos_VERBOSE_CONFIGURE=FALSE \
-DTPL_ENABLE_MPI=ON \
-DBUILD_SHARED_LIBS=ON \
-DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \

$ make -j8 install

In case of dealii, I followed the next steps:

$ mkdir build

$ cd build

$ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
-DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \

-DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../

$ make -j8 install

$ make test (failed)


That's interesting then. Can you try to do
  ldd $HOME/share/trilinos/lib/libepetra.so.12.6.2
  ldd /home/jomivalen/cfem/deal.II/lib/libdeal_II.g.so.8.4.1
and in both cases see which MPI libraries they link to? For example, for 
me this yields the following:


rilinos-12.8.1/lib> ldd libepetra.so.12.8.1 | grep mpi
libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1 
(0x7f1107a5f000)
libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12 
(0x7f110780b000)
libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1 
(0x7f1107091000)
libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12 
(0x7f1106dad000)
libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12 
(0x7f1105d31000)
libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13 
(0x7f1105a8e000)

rilinos-12.8.1/lib> cd
f/bangerth> cd p/deal.II/1/build/lib/
build/lib> ldd libdeal_II.so.8.5.0-pre | grep mpi
libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1 
(0x7f7e22f28000)
libmpi.so.12 => /usr/lib64/openmpi/lib/libmpi.so.12 
(0x7f7e22181000)
libmpi_usempi.so.1 => /usr/lib64/openmpi/lib/libmpi_usempi.so.1 
(0x7f7e152ff000)
libmpi_mpifh.so.12 => /usr/lib64/openmpi/lib/libmpi_mpifh.so.12 
(0x7f7e150ab000)
libopen-rte.so.12 => /usr/lib64/openmpi/lib/libopen-rte.so.12 
(0x7f7e148cf000)
libopen-pal.so.13 => /usr/lib64/openmpi/lib/libopen-pal.so.13 
(0x7f7e1462c000


So they are the same.

Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

Apparently I used the MPI by default for both of them.

In case of trilinos, I followed the next steps:
$  mkdir build
$  cd build
$

cmake \
-DTrilinos_ENABLE_Sacado=ON \
-DTrilinos_ENABLE_MueLu:BOOL=ON \
-DTrilinos_ENABLE_Stratimikos=ON \
-DCMAKE_BUILD_TYPE=RELEASE \
-DCMAKE_CXX_FLAGS="-g -O3" \
-DCMAKE_C_FLAGS="-g -O3" \
-DCMAKE_FORTRAN_FLAGS="-g -O5" \
-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-DCMAKE_VERBOSE_MAKEFILE=FALSE \
-DTrilinos_VERBOSE_CONFIGURE=FALSE \
-DTPL_ENABLE_MPI=ON \
-DBUILD_SHARED_LIBS=ON \
-DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \

$ make -j8 install

In case of dealii, I followed the next steps:

$ mkdir build

$ cd build

$ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
-DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \

-DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../

$ make -j8 install

$ make test (failed)

Thank you for your patience,

Joaquin


2016-11-09 18:47 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 03:44 PM, 'Joaquin M Valencia Bravo' via deal.II User Group
> wrote:
>
>>
>> cmake \
>> -D Trilinos_ENABLE_Sacado=ON \
>> -D Trilinos_ENABLE_MueLu:BOOL=ON \
>> -D Trilinos_ENABLE_Stratimikos=ON \
>> -D CMAKE_BUILD_TYPE=RELEASE \
>> -D CMAKE_CXX_FLAGS="-g -O3" \
>> -D CMAKE_C_FLAGS="-g -O3" \
>> -D CMAKE_FORTRAN_FLAGS="-g -O5" \
>> -D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
>> -D CMAKE_VERBOSE_MAKEFILE=FALSE \
>> -D Trilinos_VERBOSE_CONFIGURE=FALSE \
>> -D TPL_ENABLE_MPI=ON \
>> -D BUILD_SHARED_LIBS=ON \
>> -D CMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \
>>
>>
>> In case of deal.II, I followed the next steps:
>>  $   mkdir build
>>  $   cd build
>>  $   cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II ../
>>
>
> Does this build deal.II with MPI? If you enter the last command, it will
> provide you with a summary at the end that states whether MPI was used or
> not.
>
>
> Best
>  W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/fo
> rum/dealii?hl=en
> --- You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
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> pic/dealii/r4B-B-s6fO4/unsubscribe.
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> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Joaquin Valencia
Graduate Student

-- 
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

Apparently I used the same MPI by default for both of them.

In case of trilinos, I followed the next steps:
$  mkdir build
$  cd build
$

cmake \
-DTrilinos_ENABLE_Sacado=ON \
-DTrilinos_ENABLE_MueLu:BOOL=ON \
-DTrilinos_ENABLE_Stratimikos=ON \
-DCMAKE_BUILD_TYPE=RELEASE \
-DCMAKE_CXX_FLAGS="-g -O3" \
-DCMAKE_C_FLAGS="-g -O3" \
-DCMAKE_FORTRAN_FLAGS="-g -O5" \
-DTrilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-DCMAKE_VERBOSE_MAKEFILE=FALSE \
-DTrilinos_VERBOSE_CONFIGURE=FALSE \
-DTPL_ENABLE_MPI=ON \
-DBUILD_SHARED_LIBS=ON \
-DCMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \

$ make -j8 install

In case of dealii, I followed the next steps:

$ mkdir build

$ cd build

$ cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II \
-DTRILINOS_DIR=/home/jomivalen/thesis/trilinos-12.6.2 \

-DDEAL_II_WITH_TRILINOS=ON -DDEAL_II_WITH_MPI=ON ../

$ make -j8 install

$ make test (failed)

Thank you for your patience,

Joaquin


2016-11-09 18:31 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 03:30 PM, 'Joaquin M Valencia Bravo' via deal.II User Group
> wrote:
>
>>
>> I understand, but I don't know how to compile both of them with the same
>> version. Could you please tell me the steps to do that?
>>
>
> Well, how did you compile the two before? :-) Presumably you used some way
> to tell Trilinos which MPI to use, and some way to tell deal.II which MPI
> to use.
>
>
> Best
>  W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/fo
> rum/dealii?hl=en
> --- You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
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> pic/dealii/r4B-B-s6fO4/unsubscribe.
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> dealii+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Joaquin Valencia
Graduate Student

-- 
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread Wolfgang Bangerth

On 11/09/2016 03:44 PM, 'Joaquin M Valencia Bravo' via deal.II User 
Group wrote:


cmake \
-D Trilinos_ENABLE_Sacado=ON \
-D Trilinos_ENABLE_MueLu:BOOL=ON \
-D Trilinos_ENABLE_Stratimikos=ON \
-D CMAKE_BUILD_TYPE=RELEASE \
-D CMAKE_CXX_FLAGS="-g -O3" \
-D CMAKE_C_FLAGS="-g -O3" \
-D CMAKE_FORTRAN_FLAGS="-g -O5" \
-D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-D CMAKE_VERBOSE_MAKEFILE=FALSE \
-D Trilinos_VERBOSE_CONFIGURE=FALSE \
-D TPL_ENABLE_MPI=ON \
-D BUILD_SHARED_LIBS=ON \
-D CMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \


In case of deal.II, I followed the next steps:
 $   mkdir build
 $   cd build
 $   cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II ../


Does this build deal.II with MPI? If you enter the last command, it will 
provide you with a summary at the end that states whether MPI was used 
or not.


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

Apparently I used the same MPI by default for both of them.
In case of trilinos, I followed the next steps:
$   mkdir build
$   cd build
$

cmake \
-D Trilinos_ENABLE_Sacado=ON \
-D Trilinos_ENABLE_MueLu:BOOL=ON \
-D Trilinos_ENABLE_Stratimikos=ON \
-D CMAKE_BUILD_TYPE=RELEASE \
-D CMAKE_CXX_FLAGS="-g -O3" \
-D CMAKE_C_FLAGS="-g -O3" \
-D CMAKE_FORTRAN_FLAGS="-g -O5" \
-D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
-D CMAKE_VERBOSE_MAKEFILE=FALSE \
-D Trilinos_VERBOSE_CONFIGURE=FALSE \
-D TPL_ENABLE_MPI=ON \
-D BUILD_SHARED_LIBS=ON \
-D CMAKE_INSTALL_PREFIX:PATH=$HOME/share/trilinos \


In case of deal.II, I followed the next steps:
 $   mkdir build
 $   cd build
 $   cmake -DCMAKE_INSTALL_PREFIX=/home/jomivalen/cfem/deal.II ../
 $   make -j8 install
 $   make test

2016-11-09 18:31 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 03:30 PM, 'Joaquin M Valencia Bravo' via deal.II User Group
> wrote:
>
>>
>> I understand, but I don't know how to compile both of them with the same
>> version. Could you please tell me the steps to do that?
>>
>
> Well, how did you compile the two before? :-) Presumably you used some way
> to tell Trilinos which MPI to use, and some way to tell deal.II which MPI
> to use.
>
>
> Best
>  W.
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see https://groups.google.com/d/fo
> rum/dealii?hl=en
> --- You received this message because you are subscribed to a topic in the
> Google Groups "deal.II User Group" group.
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> pic/dealii/r4B-B-s6fO4/unsubscribe.
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>



-- 
Joaquin Valencia
Graduate Student

-- 
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread Wolfgang Bangerth

On 11/09/2016 03:30 PM, 'Joaquin M Valencia Bravo' via deal.II User 
Group wrote:


I understand, but I don't know how to compile both of them with the same
version. Could you please tell me the steps to do that?


Well, how did you compile the two before? :-) Presumably you used some 
way to tell Trilinos which MPI to use, and some way to tell deal.II 
which MPI to use.


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

--
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

I understand, but I don't know how to compile both of them with the same
version. Could you please tell me the steps to do that?

Thanks for your time,
Joaquin

2016-11-09 18:10 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 02:46 PM, 'Joaquin M Valencia Bravo' via deal.II User Group
> wrote:
>
>>
>> Which version of trilinos may I use in my case?. I followed the
>> instructions on page:
>>
>>
>> https://www.dealii.org/8.4.1/external-libs/trilinos.html
>>
>> although, it was for trilinos-12.0.1. Should I use the same version?.
>> What suggestions could you give me?
>>
>
> Joaquin,
> you ask the wrong question. The issue is not whether you should use
> Trilinos 12.0 or 12.4 or 12.6. The problem was that you compiled Trilinos
> *with one version* of MPI, and deal.II *with another version* of MPI. This
> is what you need to fix. You can continue the same version of Trilinos, as
> long as you install it with the same MPI as you use for deal.II.
>
> Best
>  W.
>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread Wolfgang Bangerth

On 11/09/2016 02:46 PM, 'Joaquin M Valencia Bravo' via deal.II User 
Group wrote:


Which version of trilinos may I use in my case?. I followed the
instructions on page:


https://www.dealii.org/8.4.1/external-libs/trilinos.html

although, it was for trilinos-12.0.1. Should I use the same version?.
What suggestions could you give me?


Joaquin,
you ask the wrong question. The issue is not whether you should use 
Trilinos 12.0 or 12.4 or 12.6. The problem was that you compiled 
Trilinos *with one version* of MPI, and deal.II *with another version* 
of MPI. This is what you need to fix. You can continue the same version 
of Trilinos, as long as you install it with the same MPI as you use for 
deal.II.


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread Timo Heister

12.4.x is probably tested the most, but 12.6.x should also work.

On Wed, Nov 9, 2016 at 4:46 PM, 'Joaquin M Valencia Bravo' via deal.II
User Group  wrote:
> Thank you for your response:
>
> Which version of trilinos may I use in my case?. I followed the instructions
> on page:
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.dealii.org_8.4.1_external-2Dlibs_trilinos.html=CwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=5kCI7s-1sdw2_x0AHqWqxtm7tXyDGPt9_hkjcPA0V5w=r3pGi_SAF_7iXX_JdSX3zI8VLMDkl9lVK8MxB0A96Dg=
>  
>
> although, it was for trilinos-12.0.1. Should I use the same version?. What
> suggestions could you give me?
>
> Sincerely,
> Joaquin
>
>
>
> 2016-11-09 15:51 GMT-04:00 Wolfgang Bangerth :
>>
>> On 11/09/2016 12:04 PM, 'Joaquin' via deal.II User Group wrote:
>>>
>>>
>>> I hope someone help me. I want to run step-40, so I need trilinos
>>> and petsc. First, I'm trying to interface trilinos-12.6.2 with
>>> deal.II-8.4.1. My computer has a gnu 4.8.4 compiler. Everything is
>>> ok until the "make test". The five step failed. I'm sending
>>> detailed.log and quicktests.log files.
>>>
>>>
>>>  Thanks in advance.
>>
>>
>> The error you show
>>
>> /usr/bin/ld: warning: libmpi.so.1, needed by
>> /home/jomivalen/thesis/trilinos-12.6.2/lib/libmuelu-adapters.so, may
>> conflict with libmpi.so.12
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `Teuchos::details::safeCommFree(int*)'
>> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
>> `Epetra_MpiComm::Epetra_MpiComm(int)'
>>
>> suggests that you build Trilinos with a different MPI implementation than
>> you used for deal.II. This is not going to work.
>>
>> Best
>>  W>
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>>www: 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.colostate.edu_-7Ebangerth_=CwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=5kCI7s-1sdw2_x0AHqWqxtm7tXyDGPt9_hkjcPA0V5w=DDoqQDSlaRZCnBuA5NkNxhLQZbtQxzqVwZFpv9Bi0dw=
>>  
>>
>>
>> --
>> The deal.II project is located at 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dealii.org_=CwIBaQ=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw=5kCI7s-1sdw2_x0AHqWqxtm7tXyDGPt9_hkjcPA0V5w=XUgLrNnqjyAXDgL6XQibLos-mj1smZZuzDr5LcsWu-8=
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>>  .
>
>
>
>
> --
> Joaquin Valencia
> Graduate Student
>
> --
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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin M Valencia Bravo' via deal.II User Group

Thank you for your response:

Which version of trilinos may I use in my case?. I followed the
instructions on page:


https://www.dealii.org/8.4.1/external-libs/trilinos.html

although, it was for trilinos-12.0.1. Should I use the same version?. What
suggestions could you give me?

Sincerely,
Joaquin



2016-11-09 15:51 GMT-04:00 Wolfgang Bangerth :

> On 11/09/2016 12:04 PM, 'Joaquin' via deal.II User Group wrote:
>
>>
>> I hope someone help me. I want to run step-40, so I need trilinos
>> and petsc. First, I'm trying to interface trilinos-12.6.2 with
>> deal.II-8.4.1. My computer has a gnu 4.8.4 compiler. Everything is
>> ok until the "make test". The five step failed. I'm sending
>> detailed.log and quicktests.log files.
>>
>>
>>  Thanks in advance.
>>
>
> The error you show
>
> /usr/bin/ld: warning: libmpi.so.1, needed by /home/jomivalen/thesis/trilino
> s-12.6.2/lib/libmuelu-adapters.so, may conflict with libmpi.so.12
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
> `Teuchos::details::safeCommFree(int*)'
> ../../lib/libdeal_II.g.so.8.4.1: undefined reference to
> `Epetra_MpiComm::Epetra_MpiComm(int)'
>
> suggests that you build Trilinos with a different MPI implementation than
> you used for deal.II. This is not going to work.
>
> Best
>  W>
>
> --
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/
>
>
> --
> The deal.II project is located at http://www.dealii.org/
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> rum/dealii?hl=en
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-- 
Joaquin Valencia
Graduate Student

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Re: [deal.II] Re: Question about Step 44 shape function gradient computations

2016-11-09 Thread Anup Basak

Hi all,

The attached pdf might be useful. There is some notational difference from
step44, but it is defined here.

Thanks,
Anup

On Wed, Nov 9, 2016 at 12:41 PM, Andrew McBride 
wrote:

> Dear Claire
>
> You might also be interested in the one-field version of step-44 in the
> code gallery https://dealii.org/developer/doxygen/deal.II/
> code_gallery_Quasi_static_Finite_strain_Compressible_Elasticity.html
>
> A
>
> On 9 Nov 2016, at 18:24, Claire  wrote:
>
> Dear Wolfgang and Jean-Paul,
>
> I will try to do my best to produce the document and give a contribution
> (even small) to the library.
> I am not sure when exactly I will be able to have time to make it though...
> The problem that I personally try to solve is simpler and does not require
> a three field formulation... I actually ask the question in the first place
> to satisfy my curiosity!
> However I'll be glad to think about it, it will certainly be a good way to
> practice and improve my derivation skills.
> But in that case I will accept your offer Jean-Paul, I will for sure use a
> documented derivation.
>
> Thank you very much by advance,
>
> Best,
>
> Claire
>
> Le mardi 8 novembre 2016 15:55:10 UTC+1, Wolfgang Bangerth a écrit :
>>
>> On 11/08/2016 01:36 AM, Jean-Paul Pelteret wrote:
>> >
>> > You're welcome. If you go through the formulation and still don't have
>> full
>> > clarity, then let me know. I do have this derivation documented
>> somewhere...
>>
>> Claire -- If, on the other hand, you do figure it out, write it up into a
>> one-page latex document that we'll be happy to help you convert into
>> something
>> we could add to the documentation of that tutorial program! If this issue
>> wasn't clear to you, it's likely also not going to be clear to others.
>>
>> Cheers
>>   W.
>>
>> --
>> 
>> Wolfgang Bangerth  email: bang...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>
> --
> The deal.II project is located at http://www.dealii.org/
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> forum/dealii?hl=en
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largeStrain_Anup.pdf
Description: Adobe PDF document

[deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin' via deal.II User Group



On Wednesday, November 9, 2016 at 2:58:32 PM UTC-4, Joaquin wrote:
>
> Dear all,
>
> I hope someone help me. I want to run step-40, so I need trilinos and 
> petsc. First, I'm trying to interface trilinos-12.6.2 with deal.II-8.4.1. 
> My computer has a gnu 4.8.4 compiler. Everything is ok until the "make 
> test". The five step failed. I'm sending detailed.log and quicktests.log 
> files.
>

 Thanks in advance.
Joaquín

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###
#
#  deal.II configuration:
#CMAKE_BUILD_TYPE:   DebugRelease
#BUILD_SHARED_LIBS:  ON
#CMAKE_INSTALL_PREFIX:   /home/jomivalen/cfem/dealII-8.4.1
#CMAKE_SOURCE_DIR:   /home/jomivalen/thesis/dealii-8.4.1
#(version 8.4.1)
#CMAKE_BINARY_DIR:   /home/jomivalen/thesis/dealii-8.4.1/build
#CMAKE_CXX_COMPILER: GNU 4.8.4 on platform Linux x86_64
#/usr/bin/c++
#CMAKE_C_COMPILER:   /usr/bin/cc
#CMAKE_Fortran_COMPILER: /usr/bin/gfortran
#CMAKE_GENERATOR:Unix Makefiles
#
#  Base configuration (prior to feature configuration):
#DEAL_II_CXX_FLAGS:-pedantic -fpic -Wall -Wextra 
-Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch 
-Woverloaded-virtual -Wno-long-long -Wno-deprecated-declarations 
-Wno-literal-suffix -std=c++11
#DEAL_II_CXX_FLAGS_RELEASE:-O2 -funroll-loops -funroll-all-loops 
-fstrict-aliasing
#DEAL_II_CXX_FLAGS_DEBUG:  -Og -ggdb -Wa,--compress-debug-sections
#DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic
#DEAL_II_LINKER_FLAGS_RELEASE: 
#DEAL_II_LINKER_FLAGS_DEBUG:   -ggdb
#DEAL_II_DEFINITIONS:  
#DEAL_II_DEFINITIONS_RELEASE:  
#DEAL_II_DEFINITIONS_DEBUG:DEBUG
#DEAL_II_USER_DEFINITIONS: 
#DEAL_II_USER_DEFINITIONS_REL: 
#DEAL_II_USER_DEFINITIONS_DEB: DEBUG
#DEAL_II_INCLUDE_DIRS  
#DEAL_II_USER_INCLUDE_DIRS:
#DEAL_II_BUNDLED_INCLUDE_DIRS: 
#DEAL_II_LIBRARIES:m
#DEAL_II_LIBRARIES_RELEASE:
#DEAL_II_LIBRARIES_DEBUG:  
#
#  Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION 
= ON):
#  ( DEAL_II_WITH_64BIT_INDICES = OFF )
#DEAL_II_WITH_ARPACK set up with external dependencies
#ARPACK_LINKER_FLAGS = 
#ARPACK_LIBRARIES = 
/usr/lib/libarpack.so;/usr/lib/liblapack.so;/usr/lib/libblas.so;gfortran;quadmath;m;c;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.so;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/release_mt/libmpi.so;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpigi.a;dl;rt;pthread
#DEAL_II_WITH_BOOST set up with bundled packages
#BOOST_CXX_FLAGS = -Wno-unused-local-typedefs
#BOOST_BUNDLED_INCLUDE_DIRS = 
/home/jomivalen/thesis/dealii-8.4.1/bundled/boost-1.56.0/include
#BOOST_LIBRARIES = rt
#  ( DEAL_II_WITH_BZIP2 = OFF )
#DEAL_II_WITH_CXX11 = ON
#  ( DEAL_II_WITH_CXX14 = OFF )
#  ( DEAL_II_WITH_HDF5 = OFF )
#DEAL_II_WITH_LAPACK set up with external dependencies
#LAPACK_LINKER_FLAGS = 
#LAPACK_LIBRARIES = 
/usr/lib/liblapack.so;/usr/lib/libblas.so;gfortran;quadmath;m;c
#DEAL_II_WITH_METIS set up with external dependencies
#METIS_VERSION = 5.1.0
#METIS_INCLUDE_DIRS = /usr/include
#METIS_USER_INCLUDE_DIRS = /usr/include
#METIS_LIBRARIES = 
/usr/lib/x86_64-linux-gnu/libmetis.so;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpifort.so;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/release_mt/libmpi.so;/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/lib/libmpigi.a;dl;rt;pthread
#DEAL_II_WITH_MPI set up with external dependencies
#MPI_VERSION = 2.0
#MPI_C_COMPILER = 
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/bin/mpicc
#MPI_CXX_COMPILER = 
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/bin/mpicxx
#MPI_Fortran_COMPILER = 
/home/jomivalen/intel/compilers_and_libraries_2016.1.150/linux/mpi/intel64/bin/mpif90
#MPI_CXX_FLAGS = 
#MPI_LINKER_FLAGS = 
#MPI_INCLUDE_DIRS =

[deal.II] Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

2016-11-09 Thread 'Joaquin' via deal.II User Group

Deal all,

I hope someone help me. I want to run step-40, so I need trilinos and 
petsc. First, I'm trying to interface trilinos-12.6.2 with deal.II-8.4.1. 
My computer has a gnu 4.8.4 compiler. Everything is ok until the "make 
test". The five step failed. 

-- 
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Re: [deal.II] Re: Question about Step 44 shape function gradient computations

2016-11-09 Thread Andrew McBride

Dear Claire

You might also be interested in the one-field version of step-44 in the code 
gallery 
https://dealii.org/developer/doxygen/deal.II/code_gallery_Quasi_static_Finite_strain_Compressible_Elasticity.html
 

A

> On 9 Nov 2016, at 18:24, Claire  wrote:
> 
> Dear Wolfgang and Jean-Paul,
> 
> I will try to do my best to produce the document and give a contribution 
> (even small) to the library.
> I am not sure when exactly I will be able to have time to make it though...
> The problem that I personally try to solve is simpler and does not require a 
> three field formulation... I actually ask the question in the first place to 
> satisfy my curiosity!
> However I'll be glad to think about it, it will certainly be a good way to 
> practice and improve my derivation skills. 
> But in that case I will accept your offer Jean-Paul, I will for sure use a 
> documented derivation.
> 
> Thank you very much by advance,
> 
> Best,
> 
> Claire
> 
> Le mardi 8 novembre 2016 15:55:10 UTC+1, Wolfgang Bangerth a écrit :
> On 11/08/2016 01:36 AM, Jean-Paul Pelteret wrote: 
> > 
> > You're welcome. If you go through the formulation and still don't have full 
> > clarity, then let me know. I do have this derivation documented 
> > somewhere... 
> 
> Claire -- If, on the other hand, you do figure it out, write it up into a 
> one-page latex document that we'll be happy to help you convert into 
> something 
> we could add to the documentation of that tutorial program! If this issue 
> wasn't clear to you, it's likely also not going to be clear to others. 
> 
> Cheers 
>   W. 
> 
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>  
> 
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
> 
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> https://groups.google.com/d/forum/dealii?hl=en 
> 
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Re: [deal.II] Re: Question about Step 44 shape function gradient computations

2016-11-09 Thread Claire

Dear Wolfgang and Jean-Paul,

I will try to do my best to produce the document and give a contribution 
(even small) to the library.
I am not sure when exactly I will be able to have time to make it though...
The problem that I personally try to solve is simpler and does not require 
a three field formulation... I actually ask the question in the first place 
to satisfy my curiosity!
However I'll be glad to think about it, it will certainly be a good way to 
practice and improve my derivation skills. 
But in that case I will accept your offer Jean-Paul, I will for sure use a 
documented derivation.

Thank you very much by advance,

Best,

Claire

Le mardi 8 novembre 2016 15:55:10 UTC+1, Wolfgang Bangerth a écrit :
>
> On 11/08/2016 01:36 AM, Jean-Paul Pelteret wrote: 
> > 
> > You're welcome. If you go through the formulation and still don't have 
> full 
> > clarity, then let me know. I do have this derivation documented 
> somewhere... 
>
> Claire -- If, on the other hand, you do figure it out, write it up into a 
> one-page latex document that we'll be happy to help you convert into 
> something 
> we could add to the documentation of that tutorial program! If this issue 
> wasn't clear to you, it's likely also not going to be clear to others. 
>
> Cheers 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>
>

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Re: [deal.II] I am trying to configure deal.II with mpi, and pass it to cmake as $cmake -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=~/dealII ../dealii-8.4.1/

2016-11-09 Thread Timo Heister

> CMake Error at /usr/local/lib/cmake/Trilinos/TrilinosConfig.cmake:174 (LIST):
>  list sub-command REMOVE_DUPLICATES requires list to be present.

This looks like cmake chokes on your Trilinos installation. It might
be that your cmake version is too old. You could also try disabling
trilinos or installing a newer version.


On Sun, Nov 6, 2016 at 11:26 AM, sudarshan kumar  wrote:
> Please  see the whole  output when i pass mpi on.
>
>
>
> -- This is CMake 2.8.12.2
> --
> -- Include /home/sudarshan/dealii-8.4.1/cmake/setup_external_macros.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_find_system_library.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_replace_flag.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_find_library.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_expand_instantiations.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_check_cxx_compiler_bug.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_setup_target.cmake
> -- Include /home/sudarshan/dealii-8.4.1/cmake/macros/macro_add_flags.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_add_library.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_configure_feature.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_insource_setup_target.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_clear_cmake_required.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_add_definitions.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_push_cmake_required.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_add_test.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_switch_library_preference.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_find_package.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_purge_feature.cmake
> -- Include /home/sudarshan/dealii-8.4.1/cmake/macros/macro_strip_flag.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_enable_if_supported.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_verbose_include.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_enable_if_links.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_filter_system_libraries.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_find_path.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_pickup_tests.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_enable_language_optional.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_query_git_information.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_set_if_empty.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_reset_cmake_required.cmake
> -- Include /home/sudarshan/dealii-8.4.1/cmake/macros/macro_to_string.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_add_dependencies.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_remove_duplicates.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_find_file.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_register_feature.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_deal_ii_package_handle.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_to_string_and_add_prefix.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_item_matches.cmake
> -- Include
> /home/sudarshan/dealii-8.4.1/cmake/macros/macro_check_mpi_interface.cmake
> --
> -- Include /home/sudarshan/dealii-8.4.1/cmake/setup_cached_variables.cmake
> --
> -- Include /home/sudarshan/dealii-8.4.1/cmake/setup_deal_ii.cmake
> --
> -- Include /home/sudarshan/dealii-8.4.1/cmake/setup_compiler_flags.cmake
> --
> -- Include /home/sudarshan/dealii-8.4.1/cmake/setup_compiler_flags_gnu.cmake
> -- Performing Test DEAL_II_HAVE_FLAG_pedantic
> -- Performing Test DEAL_II_HAVE_FLAG_pedantic - Success
> -- Performing Test DEAL_II_HAVE_FLAG_fpic
> -- Performing Test DEAL_II_HAVE_FLAG_fpic - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed
> -- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wall
> -- Performing Test DEAL_II_HAVE_FLAG_Wall - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wextra
> -- Performing Test DEAL_II_HAVE_FLAG_Wextra - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith
> -- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith - Success
> --

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

2016-11-09 Thread Daniel Arndt

Hamed,

Thanks for your help. I can reduce my problem to four 2D elements. I would 
> like to plot the system_matrix of sequential and parallel codes to compare 
> them but I am not sure how to do so.
> Can I loop over the elements of system_matrix and simply plot them?
>
All of the matrix classes also have a print method, see [1] for Trilinos.

Best,
Daniel

[1] 
https://www.dealii.org/8.4.0/doxygen/deal.II/classTrilinosWrappers_1_1SparseMatrix.html#a333dd1daec6398914395eeec7b83c520

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Re: [deal.II] Re: Convergence problem arising for large number of DoFs

2016-11-09 Thread Hamed Babaei

Dear Wolfgang,

Thanks for your help. I can reduce my problem to four 2D elements. I would 
like to plot the system_matrix of sequential and parallel codes to compare 
them but I am not sure how to do so.
Can I loop over the elements of system_matrix and simply plot them?

Thanks

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[deal.II] Cluster with Infiniband network

2016-11-09 Thread Ashkan Dorostkar

Hello all,

I am running a simulation of linear elasticity in the Lomonosov2 cluster 
(rank 41 in top 500) which has InfiniBand network. For problems larger than 
90 million unknowns openmpi just aborts the program with this message 

[n49422:9059] *** An error occurred in MPI_Allreduce
[n49422:9059] *** reported by process [3040346113,140733193388063]
[n49422:9059] *** on communicator MPI_COMM_WORLD
[n49422:9059] *** MPI_ERR_IN_STATUS: error code in status
[n49422:9059] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will 
now abort,
[n49422:9059] ***and potentially your MPI job)

This looks like a communication issue or a communication oversaturation. 
Does anyone have any experience with this?

Best,
Ashkan

P.S I use the following flag to avoid this issue but it doesn't work either

export OMPI_MCA_btl_openib_receive_queues="X,256,1024:X,65536,128"

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Re: [deal.II] small issues with assembly

2016-11-09 Thread Wolfgang Bangerth


On 11/09/2016 08:24 AM, Ashkan Dorostkar wrote:

void
dealii::TrilinosWrappers::VectorBase::add(dealii::TrilinosWrappers::VectorBase::size_type,
const size_type*, const double*)
The violated condition was:
!has_ghost_elements()
The name and call sequence of the exception was:
ExcGhostsPresent()
Additional Information:
You are trying an operation on a vector that is only allowed if the
vector has no ghost elements, but the vector you are operating on does
have ghost elements. Specifically, vectors with ghost elements are
read-only and cannot appear in operations that write into these vectors.

See the glossary entry on 'Ghosted vectors' for more information.

Stacktrace:
---
#0  1   libdeal_II.g.8.4.2.dylib0x000110560188
_ZN6dealii16TrilinosWrappers10VectorBase3addEjPKjPKd + 236: 1
libdeal_II.g.8.4.2.dylib0x000110560188
_ZN6dealii16TrilinosWrappers10VectorBase3addEjPKjPKd
#1  2   libdeal_II.g.8.4.2.dylib0x0001121830f0
_ZNK6dealii16ConstraintMatrix26distribute_local_to_globalINS_16TrilinosWrappers17BlockSparseMatrixENS2_3MPI11BlockVectorEEEvRKNS_10FullMatrixINT_10value_typeEEERKNS_6VectorINT0_10value_typeEEERKSt6vectorIjSaIjEERS7_RSD_bNS_8internal9bool2typeILb1EEE
+ 3124: 2   libdeal_II.g.8.4.2.dylib0x0001121830f0
_ZNK6*dealii16ConstraintMatrix26distribute_local_to_global*INS_16TrilinosWrappers17BlockSparseMatrixENS2_3MPI11BlockVectorEEEvRKNS_10FullMatrixINT_10value_typeEEERKNS_6VectorINT0_10value_typeEEERKSt6vectorIjSaIjEERS7_RSD_bNS_8internal9bool2typeILb1EEE
#2  3   gia 0x00010cb1a548
_ZN10GeoPhysics3gia8assembleEv + 13366: 3   gia
0x00010cb1a548 _ZN10GeoPhysics3gia8assembleEv
#3  4   gia 0x00010cb1bcfd
_ZN10GeoPhysics3gia3runEv + 421: 4   gia
0x00010cb1bcfd _ZN10GeoPhysics3gia3runEv

system_rhs is not touched anywhere between.


So if you output immediately before the call to 
distribute_local_to_global what

  system_rhs.has_ghost_elements()
says, what do you find?

Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] small issues with assembly

2016-11-09 Thread Ashkan Dorostkar

Here is a part of the stacktrace that shows where the issue arises

An error occurred in line <1357> of file 

 
in function
void 
dealii::TrilinosWrappers::VectorBase::add(dealii::TrilinosWrappers::VectorBase::size_type,
 
const size_type*, const double*)
The violated condition was: 
!has_ghost_elements()
The name and call sequence of the exception was:
ExcGhostsPresent()
Additional Information: 
You are trying an operation on a vector that is only allowed if the vector 
has no ghost elements, but the vector you are operating on does have ghost 
elements. Specifically, vectors with ghost elements are read-only and 
cannot appear in operations that write into these vectors.

See the glossary entry on 'Ghosted vectors' for more information.

Stacktrace:
---
#0  1   libdeal_II.g.8.4.2.dylib0x000110560188 
_ZN6dealii16TrilinosWrappers10VectorBase3addEjPKjPKd + 236: 1   
libdeal_II.g.8.4.2.dylib0x000110560188 
_ZN6dealii16TrilinosWrappers10VectorBase3addEjPKjPKd 
#1  2   libdeal_II.g.8.4.2.dylib0x0001121830f0 
_ZNK6dealii16ConstraintMatrix26distribute_local_to_globalINS_16TrilinosWrappers17BlockSparseMatrixENS2_3MPI11BlockVectorEEEvRKNS_10FullMatrixINT_10value_typeEEERKNS_6VectorINT0_10value_typeEEERKSt6vectorIjSaIjEERS7_RSD_bNS_8internal9bool2typeILb1EEE
 
+ 3124: 2   libdeal_II.g.8.4.2.dylib0x0001121830f0 _ZNK6
*dealii16ConstraintMatrix26distribute_local_to_global*
INS_16TrilinosWrappers17BlockSparseMatrixENS2_3MPI11BlockVectorEEEvRKNS_10FullMatrixINT_10value_typeEEERKNS_6VectorINT0_10value_typeEEERKSt6vectorIjSaIjEERS7_RSD_bNS_8internal9bool2typeILb1EEE
 
#2  3   gia 0x00010cb1a548 
_ZN10GeoPhysics3gia8assembleEv + 13366: 3   gia 
0x00010cb1a548 _ZN10GeoPhysics3gia8assembleEv 
#3  4   gia 0x00010cb1bcfd 
_ZN10GeoPhysics3gia3runEv + 421: 4   gia 
0x00010cb1bcfd _ZN10GeoPhysics3gia3runEv 

system_rhs is not touched anywhere between.

On Wednesday, November 9, 2016 at 6:13:47 PM UTC+3, Wolfgang Bangerth wrote:
>
> On 11/09/2016 02:40 AM, Ashkan Dorostkar wrote: 
> > constraints.distribute_local_to_global(cell_matrix,cell_rhs, 
> > 
> > local_dof_indices, 
> > 
> > system_matrix, 
> > 
> > system_rhs); 
> > 
> > 
> > constraints.distribute_local_to_global(cell_precond, 
> > 
> > local_dof_indices, 
> > 
> > system_precon); 
> > 
> > 
> > However at these two last lines the excution crashes with the message 
> > 
> > 
> > *You are trying an operation on a vector that is only allowed if the 
> > vector has no ghost elements, but the vector you are operating on does 
> > have ghost elements. Specifically, vectors with ghost elements are 
> > read-only and cannot appear in operations that write into these 
> vectors.* 
> > 
> > 
> > why is this happening. I am not creating the system_rhs with ghost 
> elements. 
>
> It's hard to tell without a complete example that shows the issue. Are 
> you sure the exception is triggered in the function you mention? Are you 
> sure that you don't modify system_rhs somewhere in between? 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Question about Step 44 shape function gradient computations

[deal.II] Re: Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

[deal.II] Interfacing dealii-8.4.1 with trilinos-12.6.2 - make test failed

Re: [deal.II] Re: Question about Step 44 shape function gradient computations

Re: [deal.II] Re: Question about Step 44 shape function gradient computations

Re: [deal.II] I am trying to configure deal.II with mpi, and pass it to cmake as $cmake -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=~/dealII ../dealii-8.4.1/

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

Re: [deal.II] Re: Convergence problem arising for large number of DoFs

[deal.II] Cluster with Infiniband network

Re: [deal.II] small issues with assembly

Re: [deal.II] small issues with assembly

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