Re: [deal.II] Minimal deal.ii application loads many surprising dynamic libraries on macos

[Matthias Maier]

Can one of you test the following for me?

 1/ reduce the main.cc to a single "int main() { return 0; }".

 2/ Force as needed:

diff --git a/examples/step-1/CMakeLists.txt b/examples/step-1/CMakeLists.txt
index 1a2602ee0d..aa3c6c60be 100644
--- a/examples/step-1/CMakeLists.txt
+++ b/examples/step-1/CMakeLists.txt
@@ -36,4 +36,5 @@ endif()
 
 deal_ii_initialize_cached_variables()
 project(${TARGET})
+string(APPEND DEAL_II_LINKER_FLAGS " -Wl,--as-needed")
 deal_ii_invoke_autopilot()


Does this link at all? If so, how many libraries are linked in?


MM


On Mon, Apr 22, 2024, at 06:25 CDT, "blais...@gmail.com" 
 wrote:

> Dear Jack,
> Interesting you took a look at this. I was always wondering why lethe takes 
> forever to start on my ARM M1 Mac compared to on a regular Linux desktop. 
> Seems you figured it out...
> However, I am unsure of the solution for this.
> Orthogonally to this, have you ever managed to have cmake ctest command 
> work correctly with dylib files under this setup?
> Best
> Bruno
>
>
> On Saturday, April 20, 2024 at 12:11:16 a.m. UTC+2 johnbc...@gmail.com 
> wrote:
>
>> Wolfgang,
>>
>> Thank you for the reply, I'm glad to see that the developers are keeping 
>> an eye on dependencies and startup time.
>>
>> In my case, I was actually careful to compile deal.ii ONLY against MPI, so 
>> there are only seven direct deps, mostly from my homebrew installation of 
>> openmpi. But after figuring out the correct tooling to do this on macos and 
>> digging a little more, it seems that openmpi's libhwloc is the culprit. 
>> Once it pulls in Foundation.framework and IOKit.framework, we are really 
>> off to the races.
>>
>> It appears that my ubuntu build in a docker container starts up in about 
>> half the time (also just built against MPI).
>>
>> -Jack
>>
>> On Friday, April 19, 2024 at 2:00:29 PM UTC-7 Wolfgang Bangerth wrote:
>>
>> On 4/18/24 23:29, Jack Coughlin wrote: 
>> > 
>> > As I say, I don't understand the issue well enough to know if there is 
>> > anything I or the deal.ii developers can do about it! In any case, 0.25s 
>> is a 
>> > very small price to pay for so much functionality and expressiveness. 
>>
>> Jack, 
>> I appreciate the qualification in the last sentence :-) 
>>
>> I don't have a Mac, so can't repeat the experiment and tell you what these 
>> ~100 libraries are, but I've looked into this on my Linux laptop. There, 
>> libdeal_II.g.so directly references the following 54 libraries: 
>>
>> Part of Trilinos: 
>> libnox.so.13 
>> libamesos2.so.13 
>> libtacho.so.13 
>> libml.so.13 
>> libifpack.so.13 
>> libamesos.so.13 
>> libaztecoo.so.13 
>> libtrilinosss.so.13 
>> libtpetra.so.13 
>> libtpetraclassicnodeapi.so.13 
>> libepetraext.so.13 
>> libzoltan.so.13 
>> libepetra.so.13 
>> libkokkoskernels.so.13 
>> libteuchoscomm.so.13 
>> libteuchosparameterlist.so.13 
>> libteuchoscore.so.13 
>> libkokkoscore.so.13 
>> libsuperlu_dist.so.5 
>>
>> HDF5: 
>> libhdf5.so.103 
>>
>> Part of OpenCASCADE: 
>> libTKBool.so.11 
>> libTKBRep.so.11 
>> libTKernel.so.11 
>> libTKG3d.so.11 
>> libTKGeomAlgo.so.11 
>> libTKGeomBase.so.11 
>> libTKMath.so.11 
>> libTKMesh.so.11 
>> libTKShHealing.so.11 
>> libTKTopAlgo.so.11 
>> libTKXSBase.so.11 
>> libTKIGES.so.11 
>> libTKSTEP.so.11 
>> libTKSTL.so.11 
>>
>> PETSc and SLEPc: 
>> libslepc.so.3.16 
>> libpetsc.so.3.16 
>> libmetis.so 
>>
>> MPI: 
>> libmpi_cxx.so.40 
>> libmpi.so.40 
>>
>> SUNDIALS: 
>> libsundials_idas.so.4 
>> libsundials_arkode.so.4 
>> libsundials_kinsol.so.5 
>> libsymengine.so.0.8 
>>
>> BLAS and LAPACK: 
>> liblapack.so.3 
>> libblas.so.3 
>>
>> p4est: 
>> libp4est.so.0 
>> libsc.so.0 
>>
>> System and compiler libraries: 
>> libgmp.so.10 
>> libz.so.1 
>> libm.so.6 
>> libstdc++.so.6 
>> libgcc_s.so.1 
>> libc.so.6 
>> ld-linux-x86-64.so.2 
>>
>> These are all libraries from which deal.II directly utilizes 
>> functionality. It 
>> is so many because some of the packages we rely on (notably Trilinos and 
>> OpenCASCADE) split their functionality into many separate libraries for 
>> reasons unknown to me. 
>>
>> Beyond these 54, every executable then pulls in another 27 libraries. 
>> These 
>> are libraries that, directly or indirectly, one of the 57 above 
>> references. 
>> For me, these are: 
>>
>> More from Trilinos: 
>> libgaleri-epetra.so.13 
>> libHYPRE-2.23.0.so 
>> libkokkoscontainers.so.13 
>> libteuchosnumerics.so.13 
>> libteuchosparser.so.13 
>> libteuchosremainder.so.13 
>> libthyracore.so.13 
>> libtriutils.so.13 
>>
>> More from OpenCASCADE: 
>> libTKBO.so.11 
>> libTKG2d.so.11 
>> libTKPrim.so.11 
>> libTKSTEP209.so.11 
>> libTKSTEPAttr.so.11 
>> libTKSTEPBase.so.11 
>>
>> More from PETSc: 
>> libparmetis.so 
>>
>> More from MPI: 
>> libmpi_mpifh.so.40 
>> libopen-pal.so.40 
>> libopen-rte.so.40 
>>
>> More compiler libraries: 
>> libgfortran.so.5 
>> libgomp.so.1 
>> libhwloc.so.15 
>> libquadmath.so.0 
>>
>> Unclear to me: 
>> libevent_core-2.1.so.7 
>> 

Re: [deal.II] CMAKE Warnig: no source or binary provided

[Matthias Maier]

The problem is that you do not have a working compiler installed. If
this is an Ubuntu try to run:

  $ sudo apt install gcc g++ gdb make ninja-build

to get a working toolchain. You might also be interested in the clang
toolchain:

  $ sudo apt install clang-format clangd clang


Best,
Matthias



On Fri, Apr 19, 2024, at 19:23 CDT, Adnan  wrote:

> Thanks for the reply.
> please find the fotos attached.
> i am confused about how to give the path and what should i do to correct.
> Everytime i was making mistake.
> Mit freundlichen Grüßen
> Adnan Khan
>
> *Climate is important. Be kind to our environment!!! *
>
>
> On Sat, Apr 20, 2024 at 12:55 AM Wolfgang Bangerth 
> wrote:
>
>> On 4/19/24 15:56, Adnan wrote:
>> >
>> > Fixing CMake was unable to find a build program corresponding to "Unix
>> Makefiles".
>> > CMAKE_MAKE:PROGRAm ist not set.
>> > You probably need to select a different build tool.
>> > CMAKE_CXX_Compiler not set after enablelanguage.
>>
>> Adnan:
>> can you remove everything in your build directory, run cmake again, and if
>> you
>> get the same error again, show us *exactly* the command line you are using?
>>
>> 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/forum/dealii?hl=en
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>> .
>>

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[deal.II] You're welcome to join the deal.II chat on matrix!

[Matthias Maier]

Dear all,

After almost 6 years we have decommissioned our developer slack channel
and migrated to matrix.

Long story short, you can now find all of us developers on matrix in our
shiny new deal.II space (#dealii:matrix.org) at

  https://matrix.to/#/#dealii:matrix.org

There, we have a general chat (#dealii-general:matrix.org) for all
deal.II related questions and a lounge (#dealii-lounge:matrix.org) for
not so on-topic chat :-)

A good web-based client for matrix is https://app.element.io/

Best,
Matthias
on behalf of the deal.II developer team

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Re: [deal.II] Installation on Arm

[Matthias Maier]

Can you install tbb externally and link against that one?

I am not surprised that our bundled tbb doesn't compile - it has never
been tested on non x86/amd64.

Best,
Matthias



On Thu, Nov 30, 2023, at 23:23 CST, Jai  wrote:

> Hello ,
> I am installing dealii-9.5.0 on ARM. while running the make command i am 
> getting the following error. I used the following cmake command:
>  cmake  -DCMAKE_INSTALL_PREFIX=/abc/dealii-9.5.0/build1 
> -DDEAL_II_WITH_MPI=ON -DPETSC_DIR=/home/abc/petsc 
>
> Error:
> dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12: 
> error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
>   329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
>   |^~~
> dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/tools_api/ittnotify_config.h:329:12: 
> error: ‘__TBB_machine_fetchadd4’ was not declared in this scope
>   329 | return __TBB_machine_fetchadd4(ptr, 1) + 1L;
>   |^~~
> collect2: error: ld returned 1 exit status
> make[2]: *** 
> [cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/build.make:97: 
> bin/expand_instantiations] Error 1
> make[1]: *** [CMakeFiles/Makefile2:1522: 
> cmake/scripts/CMakeFiles/expand_instantiations_exe.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
> make[1]: *** [CMakeFiles/Makefile2:1782: 
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/all] Error 2
> make[1]: *** [CMakeFiles/Makefile2:1808: 
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_release.dir/all] Error 2
> [ 15%] Built target bundled_muparser_debug
> [ 15%] Built target bundled_boost_iostreams_debug
> [ 15%] Built target bundled_boost_iostreams_release
> [ 15%] Built target bundled_muparser_release
> [ 15%] Built target bundled_boost_serialization_debug
> [ 15%] Built target bundled_kokkos_debug
> [ 15%] Built target bundled_boost_serialization_release
> [ 15%] Built target bundled_kokkos_release
> make: *** [Makefile:136: all] Error 2
> Thank You.

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Re: [deal.II] A question on licenses

[Matthias Maier]

[Standard bla bla: I am not a lawyer]

Generally speaking, yes.

If you happen to use deal.II with any of the GPL only derivatives (such
as GMSH, or more importantly, P4est) then the "effective" license for
deal.II would be GPL [1,2,3].

But generally this is only of concern if you

 - distribute deal.II in binary form. In this case the effective license
   of deal.II is GPL (and not LGPL) and you have to abide to the rules
   of the more restrictive license (by making all source code of deal.II
   and all GPL dependencies available).

 - distribute your own project based on deal.II in binary form. In this
   case the GPL license would apply to deal.II and your project and
   would require you to make your source code available to *everyone who
   received your binary program*.

 * In general you are neither required to publish your project, nor to
   make source code available except in the case(s) outlined above.

Best,
Matthias



[1] This has funny consequences: If one of the dependencies is licensed
under GPL-2 only and another one is GPL-3 only then you would be unable
to the resulting library/executable in binary form... the licenses are
incompatible.



[2] Sometimes a GPL only project contains a "linkage exception" to work
around this issue. And sure enough GMSH has one:

  Gmsh is provided under the terms of the GNU General Public License
  (GPL), Version 2 or later, with the following exception:

The copyright holders of Gmsh give you permission to combine Gmsh
with code included in the standard release of Netgen (from Joachim
Sch"oberl), METIS (from George Karypis at the University of
Minnesota), OpenCASCADE (from Open CASCADE S.A.S) and ParaView
(from Kitware, Inc.) under their respective licenses. You may copy
and distribute such a system following the terms of the GNU GPL for
Gmsh and the licenses of the other code concerned, provided that
you include the source code of that other code when and as the GNU
GPL requires distribution of source code.

Note that people who make modified versions of Gmsh are not
obligated to grant this special exception for their modified
versions; it is their choice whether to do so. The GNU General
Public License gives permission to release a modified version
without this exception; this exception also makes it possible to
release a modified version which carries forward this exception.


I have no idea why the GMSH authors haven't used one of the standard
linkage exceptions that would apply to everyone and decided on this very
specific wording...





On Wed, Sep 13, 2023, at 04:29 CDT, Simon Sticko  wrote:

> Hi.
>
> The function
>
> GridIn::read_msh
>
> uses the Gmsh-api internally to read a mesh from file.  However, Gmsh is
> distributed under GPL and not LGPL.
>
> Does this mean that one can not use this function if one wants to use
> deal.II under LGPL?
>
> Best,
> Simon

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Re: [deal.II] try catch of "ExcDereferenceInvalidCell"

[Matthias Maier]

Have you considered looking into our FEPointEvaluation [1] and related
"nonmatching" facilities?

I have the feeling that we already provide the right data structures for
your interpolation/evaluation needs - in particular with an efficient
and fast implementation. An example usage can be found in step-19.

Best,
Matthias

[1]  https://www.dealii.org/current/doxygen/deal.II/classFEPointEvaluation.html

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Re: [deal.II] try catch of "ExcDereferenceInvalidCell"

[Matthias Maier]

I am a bit confused.


In optimized release mode the `Assert` are reduced to a nnop and will
not abort (or throw an exception). For user-visible/induced runtime
errors we have `AssertThrow` which will throw an exception (and not
abort a program). In summary:

 - we use `Assert(...)` in the library to check for logical error
   conditions in *debug* mode. These are optimized out in optimized
   release mode.

   The reasoning behind this is that these asserts are "static", logical
   mistakes in the library / user code.

 - we use `AssertThrow(...)` to check for error conditions in *debug*
   and *release* mode. These checks are always run and used to validate
   user-controlled input.

   (and catchable to do something in case such an error is encountered).

So I am not sure how you would ever use an `Assert(...)` in optimized
release mode (where you want to run your program to get any
performance).


Regarding the additional if statement: If this is performance critical I
suggest to not use the c++ exception mechanism in this way. Stack
unwinding is very, very slow.


On the other hand, if you have a very unlikely error path and handled in
an if-statement (c++20 style):

if (/* error condition */) [[unlikely]] {
  // ... handle error
}

then we have often made the observation that this leads to very acceptable
performance - even in hot execution paths.


Best,
Matthias




On Thu, Aug  3, 2023, at 12:25 CDT, Simon Wiesheier  
wrote:

> Let me please clarify my last concerns in this regard:
>
> The operations
> GridTools::find_active_cell_around_point and
> feValues.reinit
> are executed at quadrature point level and performance
> is really important in our application.
>
> The reason why I wanted to use an
> try/catch block is to surrogate the use of an if-statement.
> Consider these two variants:
>
> Variant 1:
>
> disable_abort_on_exception();
> try
> {
>feValues.reinit(cell,...);
> }
> catch(dealii::Exception Base exception & )
> {
>Assert(checkSecondRunTimeCondition, ...)
>// do something
> }
>
> Variant 2:
>
> if(cell->state()==-1)
> {
> Assert(checkSecondRunTimeCondition, ...)
>// do something
> }
> else
> {
>  feValues.reinit(cell,...);
> }
>
> As you can see, there are two conditions I have to check at every
> quadrature point.
> Clearly, Variant 2 implements an if-requests and is probably not the way to
> go.
>
>
> 1. So with regard to performance, would you prefer Variant 1
> (as the try/catch introduces less overhead compared to the if-statement)?
> 2. If so, is the call of "disable_abort_on_exception()" good
> coding practice or would you refrain from doing so?
> In the main function of our program, we have a try/catch with
> catch(dealii::ExceptionBase exception &).
> Given that, in my opinion  "disable_abort_on_exception()"
> should cause any undue behavior.
>
> Best,
> Simon
>
>
> Am Do., 3. Aug. 2023 um 14:21 Uhr schrieb Wolfgang Bangerth <
> bange...@colostate.edu>:
>
>> On 8/2/23 15:58, Simon Wiesheier wrote:
>> >
>> > Does that make sense?
>> > Or do you see a better solution, like checking
>> > cell->status() right after GridTools::find_active_cell_around_point?
>>
>> This. If the function you call returns an error code in the form of an end
>> iterator, just test for that rather than doing something with this
>> iterator
>> and wait to see what happens. It is always worth checking errors as early
>> as
>> possible.
>>
>> Best
>>   W.
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>>
>> --
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>> .
>>

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Re: [deal.II] adding openmp in CMakeLists.txt

[Matthias Maier]

 - Most of your find package calls have to come after the project(...)
   call. deal.II is a bit special - we call find_package(deal.II) before
   project() so that the compiler is configured to be the same as the
   one used for deal.II.

  - Also you only need to call target_link_libraries() with the imported
libraries. This will set up everything:

  - You cannot use the "PUBLIC" keyword with target_link_libraries at
the moment in combination with DEAL_II_INVOKE_AUTOPILOT... :-(

  - I am guessing a bit because you have not quoted the full
CMakeLists.txt.

but the following should work:


set(TARGET "cook_membrane")

set(TARGET_SRC
  gcmma/GCMMASolver.cpp
  mma/MMASolver.cpp
  cook_membrane.cpp
  )

find_package(deal.II 9.3.0 REQUIRED
  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
  )

DEAL_II_INITIALIZE_CACHED_VARIABLES()
project(${TARGET})
DEAL_II_INVOKE_AUTOPILOT()

find_package(Eigen3 REQUIRED)
find_package(OpenMP REQUIRED)

target_link_libraries(${TARGET} Eigen3::Eigen OpenMP::OpenMP_CXX)

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Re: [deal.II] Compiling release 9.5.0

[Matthias Maier]

I can reproduce. Thanks a lot for the bug report!

We will track this issue here

  https://github.com/dealii/dealii/issues/15724

We will have a new point release very soon...

For background: we have a regression testsuite variant that should check
that we can indeed compile successfully with all bundled
dependencies. But it turns out that the testsuite is misconfigured :-(

In the meantime you can either disable tbb with "-DDEAL_II_WITH_TBB=off"
when configuring deal.II (which also means no thread/task support), or
install tbb with your distribution package manager
(apt install libtbb-dev on debian/ubuntu)
and use the external one.

Best,
Matthias



On Tue, Jul 11, 2023, at 21:25 CDT, Jack Urombo  wrote:

> Here is the detailed log.
>
> On Sat, 8 Jul 2023 at 17:37, Matthias Maier  wrote:
>
>> Hi,
>>
>> Would you mind to also send us the "detailed.log" file located in your
>> build directory?
>>
>> Best,
>> Matthias
>>
>>
>>
>> On Sat, Jul  8, 2023, at 03:16 CDT, jack urombo  wrote:
>>
>> > The new release has this error on compiling.
>> >
>> > [ 10%] Building CXX object
>> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
>> > ena.cpp.o
>> > In file included from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
>> > cheduler_common.h:43,
>> > from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
>> > cheduler.h:24,
>> > from
>> > /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
>> > rena.cpp:23:
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
>> > 0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’
>> > changes meaning o
>> > f ‘task’ [-Wchanges-meaning]
>> >  266 | tbb::task& task() {return
>> > *reinterpret_cast(this+1);}
>> >  |^~~~
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
>> > : note: used here to mean ‘class tbb::task’
>> >  225 | task* next_offloaded;
>> >  | ^~~~
>> > /home/
>> ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7
>> :
>> > note: declared here
>> >   33 | class task;
>> >  |   ^~~~
>> > make[2]: ***
>> > [bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90:
>> > bund
>> > led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o]
>> Error
>> > 1
>> > make[1]: *** [CMakeFiles/Makefile2:1782:
>> > bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
>> > bug.dir/all] Error 2
>> > make: *** [Makefile:136: all] Error 2
>> >
>> >
>> >
>> > --
>> >
>> >
>> >
>> >
>> > The information in this message is confidential and legally
>> > privileged.
>> > It is intended solely for the addressee(s). Access to this message
>> > by
>> > anyone else is unauthorized. If received in error, please accept our
>> > apologies
>> > and notify the sender immediately. You must also delete the
>> > original message
>> > from your machine. If you are not the intended recipient,
>> > any use, disclosure,
>> > copying, distribution or action taken in reliance of
>> > it, is prohibited and may
>> > be unlawful. The information, attachments,
>> > opinions or advice contained in this
>> > email are not the views or opinions of
>> > Harare Institute of Technology, its
>> > subsidiaries or affiliates. Although
>> > this email and any attachments are
>> > believed to be free of any virus or
>> > other defects which might affect any
>> > computer or IT system into which they
>> > are received, no responsibility is
>> > accepted by Harare Institute of
>> > Technology and/or its subsidiaries for any loss
>> > or damage arising in any
>> > way from the receipt or use thereof.
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
>> ---
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Re: [deal.II] illegal instruction 4

[Matthias Maier]

Do you have an M1 or M2 CPU?

If yes, would you mind trying out the shiny new  venture arm64 dmg?

  https://github.com/dealii/dealii/releases

Best,
Matthias



On Sun, Jul  9, 2023, at 18:41 CDT, "andre...@gmail.com"  
wrote:

> Hello, 
>
> I've installed deal.ii on my macbook pro running macOS 13.4.1. I installed 
> deal.ii using the version 9.4.0 dmg file. 
>
> I have been able to run cmake and make on step-33 but when I run make run I 
> get the following error:
>
> make[3]: *** [CMakeFiles/run] Illegal instruction: 4
>
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>
> Does anyone know what is going wrong?
>
> 
>
> Here is the full output:
>
> bash-3.2$ cmake ..
>
> -- Using the deal.II-9.4.0 installation found at 
> /Applications/deal.II.app/Contents/Resources/Libraries
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_add_test.cmake
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_initialize_cached_variables.cmake
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_pickup_tests.cmake
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_query_git_information.cmake
>
> -- Include macro 
> /Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/macros/macro_deal_ii_setup_target.cmake
>
> -- The C compiler identification is AppleClang 14.0.3.14030022
>
> -- The CXX compiler identification is Clang 13.0.1
>
> -- Detecting C compiler ABI info
>
> -- Detecting C compiler ABI info - done
>
> -- Check for working C compiler: 
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
>  
> - skipped
>
> -- Detecting C compile features
>
> -- Detecting C compile features - done
>
> -- Detecting CXX compiler ABI info
>
> -- Detecting CXX compiler ABI info - done
>
> -- Check for working CXX compiler: 
> /Applications/deal.II.app/Contents/Resources/spack/opt/spack/mpich-3.4.2-7776/bin/mpic++
>  
> - skipped
>
> -- Detecting CXX compile features
>
> -- Detecting CXX compile features - done
>
> -- Autopilot invoked
>
> ###
>
> #
>
> #  Project  step-33  set up with  deal.II-9.4.0  found at
>
> #  /Applications/deal.II.app/Contents/Resources/Libraries
>
> #
>
> #  CMAKE_BUILD_TYPE:  Debug
>
> #
>
> #  You can now run
>
> #   $ make- to compile and link the program
>
> #   $ make run- to (compile, link and) run the program
>
> #
>
> #   $ make sign   - to sign the executable with the supplied 
> OSX developer key
>
> #
>
> #   $ make debug  - to switch the build type to 'Debug'
>
> #   $ make release- to switch the build type to 'Release'
>
> #
>
> #   $ make edit_cache - to change (cached) configuration variables
>
> #   and rerun the configure and generate phases 
> of CMake
>
> #
>
> #   $ make strip_comments - to strip the source files in this
>
> #   directory off their comments; this is 
> irreversible
>
> #   $ make clean  - to remove the generated executable as well 
> as
>
> #   all intermediate compilation files
>
> #   $ make runclean   - to remove all output generated by the 
> program
>
> #   $ make distclean  - to clean the directory from _all_ generated
>
> #   files (includes clean, runclean and the 
> removal
>
> #   of the generated build system)
>
> #   $ make info   - to view this message again
>
> #
>
> #  Have a nice day!
>
> #
>
> ###
>
> -- Configuring done
>
> -- Generating done
>
> -- Build files have been written to: 
> /Users/andrewdavis/Documents/boltzmann/code/build
>
> bash-3.2$ make -j5
>
> [ 50%] Building CXX object CMakeFiles/step-33.dir/step-33.cc.o
>
> [100%] *Linking CXX executable step-33*
>
> [100%] Built target step-33
>
> bash-3.2$ make run
>
> *Consolidate compiler generated dependencies of target step-33*
>
> [ 66%] Built target step-33
>
> [100%] *Run step-33 with Debug configuration*
>
> make[3]: *** [CMakeFiles/run] Illegal instruction: 4
>
> make[2]: *** [CMakeFiles/run.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/run.dir/rule] Error 2
>
> make: *** [run] Error 2
>
> bash-3.2$ 

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Re: [deal.II] Compiling release 9.5.0

[Matthias Maier]

Hi,

Would you mind to also send us the "detailed.log" file located in your
build directory?

Best,
Matthias



On Sat, Jul  8, 2023, at 03:16 CDT, jack urombo  wrote:

> The new release has this error on compiling.
>
> [ 10%] Building CXX object 
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/ar
> ena.cpp.o 
> In file included from 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> cheduler_common.h:43, 
> from 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/s
> cheduler.h:24, 
> from 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/tbb/a
> rena.cpp:23: 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:266:2
> 0: error: declaration of ‘tbb::task& tbb::internal::task_prefix::task()’ 
> changes meaning o
> f ‘task’ [-Wchanges-meaning] 
>  266 | tbb::task& task() {return 
> *reinterpret_cast(this+1);} 
>  |^~~~ 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:225:9
> : note: used here to mean ‘class tbb::task’ 
>  225 | task* next_offloaded; 
>  | ^~~~ 
> /home/ju.rom.bo/downloads/dealii-9.5.0/bundled/tbb-2018_U2/src/../include/tbb/task.h:33:7:
> note: declared here 
>   33 | class task; 
>  |   ^~~~ 
> make[2]: *** 
> [bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/build.make:90: 
> bund
> led/tbb-2018_U2/src/CMakeFiles/bundled_tbb_debug.dir/tbb/arena.cpp.o] Error 
> 1 
> make[1]: *** [CMakeFiles/Makefile2:1782: 
> bundled/tbb-2018_U2/src/CMakeFiles/bundled_tbb_de
> bug.dir/all] Error 2 
> make: *** [Makefile:136: all] Error 2
>
>
>
> -- 
>
>
>
>
> The information in this message is confidential and legally
> privileged. 
> It is intended solely for the addressee(s). Access to this message
> by 
> anyone else is unauthorized. If received in error, please accept our 
> apologies
> and notify the sender immediately. You must also delete the 
> original message
> from your machine. If you are not the intended recipient, 
> any use, disclosure,
> copying, distribution or action taken in reliance of 
> it, is prohibited and may
> be unlawful. The information, attachments, 
> opinions or advice contained in this
> email are not the views or opinions of 
> Harare Institute of Technology, its
> subsidiaries or affiliates. Although 
> this email and any attachments are
> believed to be free of any virus or 
> other defects which might affect any
> computer or IT system into which they 
> are received, no responsibility is
> accepted by Harare Institute of 
> Technology and/or its subsidiaries for any loss
> or damage arising in any 
> way from the receipt or use thereof.

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[deal.II] deal.II 9.5.0 release candidate 1

[Matthias Maier]

Dear all,

We have tagged a first release candidate for the upcoming deal.II 9.5.0 release.
You can find the sources and a generated offline documentation here:

  https://github.com/dealii/dealii/releases/tag/v9.5.0-rc1

Alternatively, you can switch to the dealii-9.5 branch in your local git 
repository

  git remote update
  git checkout v9.5.0-rc1

It would be great if you could test it on your machine with your typical 
configuration!
If no further regressions show up, we will release Friday July 7. The release
progress is tracked in the following GitHub issue:

  https://github.com/dealii/dealii/issues/15383

Thanks!

Matthias
on behalf of the deal.II developer team

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Re: [deal.II] linking dealii (compiled with MPI) to MATLAB engine results in segmentation fault

[Matthias Maier]

In the debugger after you ran with the command »r« could you please try
to generate a back trace with »bt«?

(gdb) r
...
(gdb) bt
...

Best,
Matthias



On Thu, Jun 22, 2023, at 17:12 CDT, Mathieu  wrote:

> See ldd.txt for the output of 
> $ ldd ./step-1
> and gdb.txt for the output of
> $ gdb ./step-1
>
> Does this help?
>
>
>
> Matthias Maier schrieb am Donnerstag, 22. Juni 2023 um 23:28:16 UTC+2:
>
>> The most likely issue will be a "symbol clash" either due to ABI
>> incompatible versions of the same external shared library linked into
>> the executable, or due to the matlab shared library you are linking
>> against containing these.
>>
>> Can you send us the output of $ ldd executable (for a faulty one)?
>>
>> Furthermore, have you tried running the startup in a debugger such as
>> gdb? If possible, the stacktrace for the segfault will be very
>> illuminating:
>>
>> $ gdb executable
>> > run
>> > bt
>>
>> Best,
>> Matthias
>>
>>
>>
>> On Thu, Jun 22, 2023, at 14:46 CDT, Mathieu  wrote:
>>
>> > Thanks Matthias for clarification. 
>> > But as I said, I do not have this problem using the default compiler on 
>> my 
>> > system. 
>> >
>> > Since I have no experience with a debugger, I let valgrind run on the 
>> > program:
>> > valgrind --tool=memcheck --leak-check=full --track-origins=yes ./step-1
>> > (see the attachment for the output). 
>> >
>> > From the memcheck, I can not deduce anything that would bring me closer 
>> to 
>> > the bottom.
>> > Do you have any suggestions based on the memcheck?
>> > I could imagine there is a mismatch between some deal.II dependencies 
>> (TBB 
>> > ?) and the 
>> > corresponding versions shipped with matlab.
>> >
>> > Best,
>> > Math
>> >
>> >
>> >
>> > Matthias Maier schrieb am Donnerstag, 22. Juni 2023 um 20:14:02 UTC+2:
>> >
>> >
>> > On Thu, Jun 22, 2023, at 04:13 CDT, Mathieu  wrote: 
>> >
>> >> Good point to narrow down the problem. 
>> >> I modified step-1 so that the main function only calls matlab via 
>> >> callFevalsqrt(). 
>> >> This works fine, even if I use the mpi compiler mentioned in my 
>> original 
>> >> post. 
>> >> However, if I just add a second line in the main function, 
>> >> dealii::Triangulation<2> triangulation, 
>> >> I run again into the segfault. 
>> >
>> > What happens when you include this statement in yourr main function is 
>> > that your main.cc compilation unit now contains a symbol to the deal.II 
>> > library. The linker will then keep libdeal_ii.so as a shared object 
>> > dependency. If you do not actually use any symbol from the deal.II 
>> > library itself then the linker might drop the shared object altogether 
>> > and the final result is as if you never linked to deal.II in the first 
>> > place. You can verify this by running "ldd" on the executable: 
>> >
>> > $ ldd executable 
>> > libdeal_II.so. => /usr/lib64/libdeal_II.so 
>> >
>> > Best, 
>> > Matthias 
>>

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Re: [deal.II] linking dealii (compiled with MPI) to MATLAB engine results in segmentation fault

[Matthias Maier]

The most likely issue will be a "symbol clash" either due to ABI
incompatible versions of the same external shared library linked into
the executable, or due to the matlab shared library you are linking
against containing these.

Can you send us the output of $ ldd executable  (for a faulty one)?

Furthermore, have you tried running the startup in a debugger such as
gdb? If possible, the stacktrace for the segfault will be very
illuminating:

  $ gdb executable
  > run
  > bt

Best,
Matthias



On Thu, Jun 22, 2023, at 14:46 CDT, Mathieu  wrote:

> Thanks Matthias for clarification. 
> But as I said, I do not have this problem using the default compiler on my 
> system. 
>
> Since I have no experience with a debugger, I let valgrind run on the 
> program:
> valgrind --tool=memcheck --leak-check=full --track-origins=yes ./step-1
> (see the attachment for the output). 
>
> From the memcheck, I can not deduce anything that would bring me closer to 
> the bottom.
> Do you have any suggestions based on the memcheck?
> I could imagine there is a mismatch between some deal.II dependencies (TBB 
> ?) and the 
> corresponding versions shipped with matlab.
>
> Best,
> Math
>
>
>
> Matthias Maier schrieb am Donnerstag, 22. Juni 2023 um 20:14:02 UTC+2:
>
>
> On Thu, Jun 22, 2023, at 04:13 CDT, Mathieu  wrote: 
>
>> Good point to narrow down the problem. 
>> I modified step-1 so that the main function only calls matlab via 
>> callFevalsqrt(). 
>> This works fine, even if I use the mpi compiler mentioned in my original 
>> post. 
>> However, if I just add a second line in the main function, 
>> dealii::Triangulation<2> triangulation, 
>> I run again into the segfault. 
>
> What happens when you include this statement in yourr main function is 
> that your main.cc compilation unit now contains a symbol to the deal.II 
> library. The linker will then keep libdeal_ii.so as a shared object 
> dependency. If you do not actually use any symbol from the deal.II 
> library itself then the linker might drop the shared object altogether 
> and the final result is as if you never linked to deal.II in the first 
> place. You can verify this by running "ldd" on the executable: 
>
> $ ldd executable 
> libdeal_II.so. => /usr/lib64/libdeal_II.so 
>
> Best, 
> Matthias 

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Re: [deal.II] linking dealii (compiled with MPI) to MATLAB engine results in segmentation fault

[Matthias Maier]

On Thu, Jun 22, 2023, at 04:13 CDT, Mathieu  wrote:

> Good point to narrow down the problem.
> I modified step-1 so that the main function only calls matlab via 
> callFevalsqrt().
> This works fine, even if I use the mpi compiler mentioned in my original 
> post. 
> However, if I just add a second line in the main function,
> dealii::Triangulation<2> triangulation,
> I run again into the segfault. 

What happens when you include this statement in yourr main function is
that your main.cc compilation unit now contains a symbol to the deal.II
library. The linker will then keep libdeal_ii.so as a shared object
dependency. If you do not actually use any symbol from the deal.II
library itself then the linker might drop the shared object altogether
and the final result is as if you never linked to deal.II in the first
place. You can verify this by running "ldd" on the executable:

  $ ldd executable
  libdeal_II.so. => /usr/lib64/libdeal_II.so

Best,
Matthias

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Re: [deal.II] cmake_minimum_required

[Matthias Maier]

Did you accidentally run "cmake ." in "examples/" instead of
"examples/step-4"?

Best,
Matthias



On Sat, Jul 30, 2022, at 05:32 CDT, Felix Felix  wrote:

> Hi, 
>
> I am currently still learning how to use dealii libraries. 
> Just recently I was trying to use step-4 examples. 
>
> so i did the usual by inputing: " cmake . " within the directory. 
>
> What happened was I received this: 
> "
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *CMake Warning (dev) in CMakeLists.txt:  No project() command is present. 
>  The top-level CMakeLists.txt file must  contain a literal, direct call to 
> the project() command.  Add a line of  code such as
> project(ProjectName)  near the top of the file, but after 
> cmake_minimum_required().  CMake is pretending there is a 
> "project(Project)" command on the first  line.This warning is for project 
> developers.  Use -Wno-dev to suppress it.CMake Warning (dev) in 
> CMakeLists.txt:  No cmake_minimum_required command is present.  A line of 
> code such ascmake_minimum_required(VERSION 3.16)  should be added at 
> the top of the file.  The version specified may be lower  if you wish to 
> support older CMake versions for this project.  For more  information run 
> "cmake --help-policy CMP".This warning is for project developers.  Use 
> -Wno-dev to suppress it.-- Configuring done-- Generating done-- Build files 
> have been written to: /home/felixelf/dealdottwo/dealii/examples/step-4 "*
>
> and then when I key in " make " nothing seems to happen. 
> Would someone kindly guide me to what I am supposed to do here? 
> I am not very familiar with cmake myself so I'm learning by doing 
> everything at the moment. 
>
> Kind regards, 
> Felix 

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Re: [deal.II] Re: dealii-9.4.0 release candidate 1

[Matthias Maier]

Dear Alberto,

On Thu, Jun 30, 2022, at 06:55 CDT, Alberto Salvadori 
 wrote:

> I wonder if this release is  fully compatible with Apple M1 (and M2 as 
> well) or not. 

It depends a bit on what "fully compatible" should imply - in general,
yes, deal.II should just compile and work fine on Apple M1 processors.

I cannot guarantee that all external dependencies work, though - we also
do not have a regression tester set up for Apple M1.

Best,
Matthias

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[deal.II] deal.II Version 9.4.0 contributors, thank you!

[Matthias Maier]

Dear all,

I would like to follow up on the announcement of this release by publicly
saying again how much we appreciate the many contributions from those who
have sent it code, bug reports, fixed grammar and typos, or have helped in
any other way. Many thanks!

The ChangeLog lists at least the following people to whom thanks are due
(though I am certain that I am forgetting someone):

  Pasquale Africa,
  Tyler Anderson,
  Francesco Andreuzzi,
  Mathias Anselmann,
  Maximilian Bergbauer,
  Manaswinee Bezbaruah,
  Bruno Blais,
  Till Budde,
  Fabian Castelli,
  Praveen Chandrashekar,
  Huimin Chen,
  Cu Cui,
  Ivo Dravins,
  Marco Feder,
  Niklas Fehn,
  Corbin Foucart,
  Johannes Friedlein,
  Sebastian Fuchs,
  Daniel Garcia-Sanchez,
  Nicola Giuliani,
  Alexander Grayver,
  Diane Guignard,
  Jake Harmon,
  Sean Ingimarson,
  Pengfei Jia,
  Sebastian Kinnewig,
  Uwe Köcher,
  Katharina Kormann,
  Paras Kumar,
  Wenyu Lei,
  Alberto F. Martin,
  Nils Much,
  Lucas Myers,
  Justin O'Connor,
  Judith Pauen,
  Vachan Potluri,
  Raghunandan Pratoori,
  Sebastian Proell,
  Ce Qin,
  Reza Rastak,
  Jose E. Roman,
  Raphael Schoof,
  Magdalena Schreter,
  Konrad Simon,
  Simon Sticko,
  Daniel Sun,
  Kuljit S. Virk,
  Michał Wichrowski,
  Niklas Wik,
  Jiaqi Zhang.


Matthias,
on behalf of the deal.II developer team.

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[deal.II]

[Matthias Maier]

Version 9.4.0 of deal.II, the object-oriented finite element library awarded the
J. H. Wilkinson Prize for Numerical Software, has been released. It is
available for free under an Open Source license from the deal.II homepage at

   https://www.dealii.org/

The major changes of this release are:

 - Advances in simplex- and mixed-mesh support
 - Repartitioning of distributed meshes
 - Advances in matrix-free infrastructure
 - Advances in multigrid infrastructure
 - CutFEM support
 - Experimental integration of the Computational Geometry Algorithms Library 
(CGAL)
 - Performance improvements in the particle infrastructure
 - Improvements to unstructured communication
 - Three new tutorial programs (steps 81, 82, and 85) and one new code gallery 
program

For more information see:
  - The preprint at https://www.dealii.org/deal94-preprint.pdf
  - The list of changes at

https://www.dealii.org/developer/doxygen/deal.II/changes_between_9_3_3_and_9_4_0.html

The main features of deal.II are:
  - Extensive documentation and 83 fully-functional example programs
  - Support for dimension-independent programming
  - Locally refined adaptive meshes
  - Multigrid support
  - A zoo of different finite elements
  - Fast linear algebra
  - Built-in support for shared memory and distributed parallel computing,
scaling from laptops to clusters with 100,000+ processor cores
  - Interfaces to Trilinos, PETSc, METIS, UMFPACK and other external software
  - Output for a wide variety of visualization platforms.

Matthias,
on behalf of the deal.II developer team and many contributors.

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[deal.II] dealii-9.4.0 release candidate 1

[Matthias Maier]

Dear all,

We have tagged a first release candidate for the upcoming deal.II 9.4.0 release.
You can find the sources and a generated offline documentation here:

  https://github.com/dealii/dealii/releases/tag/v9.4.0-rc1

Alternatively, you can switch to the dealii-9.4 branch in your local git 
repository

  git remote update
  git checkout v9.4.0-rc1

It would be great if you could test it on your machine with your typical 
configuration!
If no further regressions show up, we will release Friday June 24. The release
progress is tracked in the following GitHub issue:

  https://github.com/dealii/dealii/issues/13574

Thanks!

Matthias
on behalf of the deal.II developer team

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[deal.II] Publications based on deal.II

[Matthias Maier]

All,

as you may know, we try to list all publications based on deal.II at
 http://dealii.org/publications.html
We use this list to justify the effort we spend on writing this software, both
to our universities as well as the funding agencies that support its
development.

In anticipation of the next release, we would like to update this page. If you
have (or know of) a publication that uses deal.II for numerical results and
that isn't already listed, please let us know so we can put it on there. For
this purpose, publications also include MSc, Diploma or PhD theses, or
anything else that may seem appropriate.

We've made the process of submitting entries much simpler than in the past.
Here are a number of ways you can let us know:

* Open a new issue via
  https://github.com/dealii/publication-list/issues/new and just copy-paste
  either a bibtex entry, or just the reference information

* If you want to save us a bit of work, follow the process here:
  https://github.com/dealii/publication-list/blob/master/README.md

* Or email the information directly to me or one of the other principal
  developers.

Thanks!

Matthias
on behalf of the deal.II developer team

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[deal.II] Release preparations

[Matthias Maier]

All,

we would like to start the release process for deal.II 9.4.0 soon. Please
let us know if you have any last minute things that need to be addressed
(bugs, documentation issues, configuration problems, etc.).

If you are running the current development version, please update your local
working copy and test if everything compiles, especially if you are running a
less common configuration (mac, old compilers, etc.).

Thanks!

Matthias
on behalf of the deal.II developer team

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Re: [deal.II] compile dealii with intel oneAPI

[Matthias Maier]

Hi,

Something went wrong with your setup - your error message suggests that
tbb had been set up from the bundled directory and you end up mixing
bundled tbb with external oneapi tbb, which cannot work.

Would you mind sending us the detailed.log file found in your build
directory? It contains a listing of the entire configuration including
all libraries.

Best,
Matthias



On Thu, May 12, 2022, at 05:30 CDT, 陈敏  wrote:

> Hi, everyone
> I compile the deal.ii-9.3.3 with the intel oneAPI version 2022.1.1.119
> (intel compiler, intel MPI, intel mkl and intel TBB). And I compiled it
> with the ReleaseAndDebug version. so in the dir of the installed deal.ii,
> there are examples of step-X.release and step-X.debug. I can run the
> step-9.release and step-9.debug right and get the results, but if I compile
> the step-9.cc like
>
> mkdir build
> cd build
> cmake ..
>  make
>
>
> there are some error:
>
> In file included from
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_machine.h:117,
>  from
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/atomic.h:32,
>  from
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:24,
>  from
> /home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
>  from
> /home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/tbb_stddef.h:409:14:
> error: expected type-specifier before ‘split’
>   409 | operator split() const { return split(); }
>   |  ^
> In file included from
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/pipeline.h:25,
>  from
> /home/tfblab/dealii_9_3_3/include/deal.II/base/work_stream.h:34,
>  from
> /home/tfblab/dealii_9_3_3/examples/step-9/step-9.cc:52:
> /home/tfblab/dealii_9_3_3/include/deal.II/bundled/tbb/task.h:139:9: error:
> reference to ‘task_group_context’ is ambiguous
>   139 | task_group_context& my_context;
>
>
> The detailed error log is attached
> It seems that I compile the step-9 with bundled tbb, but I compile dealii
> with the intel oneAPI TBB actually, and the step-9.release can run right.
> So why is there the error?
>
> Best,
> Chen

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Re: [deal.II] AVX and AVX512 instruction detection

[Matthias Maier]

Hi Bruno,

You'll have to explicitly enable the instruction set with your
CXXFLAGS. For example, by compiling via

  $ cmake -DDEAL_II_CXX_FLAGS="-march=native" [...]

Best,
Matthias



On Wed, Apr 20, 2022, at 06:50 CDT, "blais...@gmail.com" 
 wrote:

> Dear all,
> I hope you are well.
>
> I was wondering if there was anything specific that had to be done to 
> enable deal.II to leverage AVX and AVX512 instructions on intel processors?
>
> By default, it seems that on my intel machine, these vectorization 
> instructions are not detected, e.g.:
> -- Performing Test DEAL_II_HAVE_SSE2
> -- Performing Test DEAL_II_HAVE_SSE2 - Success
> -- Performing Test DEAL_II_HAVE_AVX
> -- Performing Test DEAL_II_HAVE_AVX - Failed
> -- Performing Test DEAL_II_HAVE_AVX512
> -- Performing Test DEAL_II_HAVE_AVX512 - Failed
> -- Performing Test DEAL_II_HAVE_ALTIVEC
> -- Performing Test DEAL_II_HAVE_ALTIVEC - Failed
>
>
> However, I can see that avx  is a supported set of instruction on my 
> processor by looking at /proc/cpuinfo.
>
> Is there something I am missing that needs to be done to enable full 
> support of vectorization instruction?
>
> Best :)
> Bruno

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Re: [deal.II] Re: Error loading petsc shared library in step-40 when distributing cell matrix and rhs separately

[Matthias Maier]

Can you find any petsc library under /usr or /usr/local ?

 $ find /usr -iname "libpetsc*"

Similarly, would you mind checking how many petsc installation you have
in your home directory?

 $ find $HOME -iname "libpetsc*"

Best,
Matthias

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Re: [deal.II] Store data from a Tensor<1, dim> to a Vector

[Matthias Maier]

Dear Judy,

On Tue, Dec  7, 2021, at 11:45 CST, Judy Lee  wrote:

> cell_x(i) += fe_values.shape_value(i, q_index) * x(i);

Here, you are multiplying a scalar (fe_values.shape_value(i, q_index))
and a rank-1 tensor (x(i)), which results in a rank-1 tensor.

The error message says that you cannot store this rank-1 tensor in
cell_x(i), which is a scalar (vector).

I don't know whether this is what you want to do, but in 1D you can
simply take the first value of your rank-1 tensor to transform the
expression into a scalar:

  cell_x(i) += fe_values.shape_value(i, q_index) * x(i)[0];

However, this is not a good "dimension independent" approach, meaning
the moment you try to solve in 2D or 3D you will have to modify your
code.

Best,
Matthias

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Re: [deal.II] Please help me on running deal.ii on Ubuntu subsystem on Win10

[Matthias Maier]

Hi,

What about you simply install the binary deal.II package for Ubuntu
20.04 from here:

  https://launchpad.net/~ginggs/+archive/ubuntu/deal.ii-9.3.0-backports

  Simply follow the instructions on how to add the PPA, then install all
  necessary libraries and tools via:

  $ sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make g++


Best,
Matthias

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Re: [deal.II] Compiled example programs fail with segfault

[Matthias Maier]

Hi,

On Thu, Sep 23, 2021, at 07:57 CDT, "'develo...@googlemail.com' via deal.II 
User Group"  wrote:

> Hei,
> I did some testing now, with different compilers. I did not get a segfault 
> for GCC 11.2, but it segfaults with ICC 2021.3.0. I attached the 
> detailed.log-files for both deal.II-versions.

> Could the issue be that some libraries which have been compiled with
> GCC are linked into my executable, even when being compiled with ICC?

That shouldn't be an issue. The Intel compiler tries to be ABI compliant
with the GCC compiler, so it is perfectly fine to link against libraries
compiled with GCC - in fact, Intel is using the C++ standard library
(libstdc++) shipped by GCC.

But, would you mind quickly checking compilation and execution with ICC
again *without* the "-march=native -mavx2" that you have set somewhere
(CXXFLAGS?)? (After configure and before you can check 'detailed.log"
quickly whether the flags still show up in the line DEAL_II_CXX_FLAGS.)

We had issues with ICC miscompiling with "-march=native" in the past.

Best,
Matthias

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Re: [deal.II] Compiled example programs fail with segfault

[Matthias Maier]

Would you mind sharing your `detailed.log` (in the build directory) with
us?

Best,
Matthias



On Wed, Sep 22, 2021, at 15:13 CDT, "'Roland Richter' via deal.II User Group" 
 wrote:

> Hei, the interesting point is that I'm installing deal.II directly using
> cmake/make/make install on that machine (after it's my development
> machine), there is no cross-compilation or something similar involved.
>
>
> ons. 22. sep. 2021, 20:37 skrev Wolfgang Bangerth :
>
>> On 9/21/21 11:16 PM, 'develo...@googlemail.com' via deal.II User Group
>> wrote:
>> > I am currently trying to run some example programs with a down-scaled
>> > version of deal.II (i.e. no additional external libraries, internal
>> boost).
>> > I freshly compiled deal.II with the intel-compiler without issues, but
>> > when compiling and running any program which links to deal.II (including
>> > the example programs) the program directly crashes with a segfault.
>> > Running it in gdb results in
>> > /(gdb) backtrace
>> > #0 0x7fffd22edceein ??() from /usr/lib64/libstdc++.so.6
>> > #1 0x7fffd49a3259in start_thread() from /usr/lib64/libpthread.so.0
>> > #2 0x7fffd19532b3in clone() from /usr/lib64/libc.so.6/
>> > What could be the reason, and how can I narrow the issue down?
>>
>> One problem we often see is when running an executable compiled on one
>> platform on a different processor. So the question here would be how you
>> installed deal.II?
>>
>> Best
>>   W.
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
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>>

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Re: [deal.II] Step-69 : Parallel execution on 4 nodes

[Matthias Maier]

> I tried commenting out the call to check-pointing as you suggested and was 
> able to run the code on 4 node (each with 4 cores) and it finished very 
> quickly.

Did it write out vtu files during this run? (They are written using MPI-IO)

Best,
Matthias

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Re: [deal.II] Step-69 : Parallel execution on 4 nodes

[Matthias Maier]

Hi Nicholas,

On Fri, Sep  3, 2021, at 12:49 CDT, Nicholas Yue  wrote:

> Hi
>
> It seems to be consistently failing when writing the checkpoint file(s)
>
> Are there special flags I need to setup up for some form of parallel IO 
> that may be happening ?

> [...]

> Additional information: 
> deal.II encountered an error while calling an MPI function.
> The description of the error provided by MPI is "MPI_ERR_FILE: invalid
> file".
> The numerical value of the original error code is 30.

This is interesting. It seems that MPI IO is failing.

Do you write into a distributed file system that is replicated among nodes?

Would you mind testing running the code with checkpointing disabled,
something like:


diff --git a/examples/step-69/step-69.cc b/examples/step-69/step-69.cc
index 4a801f97ba..4b7c9a2f63 100644
--- a/examples/step-69/step-69.cc
+++ b/examples/step-69/step-69.cc
@@ -2595,7 +2595,7 @@ namespace Step69
 
 if (t > output_cycle * output_granularity)
   {
-checkpoint(U, base_name, t, output_cycle);
+// checkpoint(U, base_name, t, output_cycle);
 output(U, base_name, t, output_cycle);
 ++output_cycle;
   }


I am interested in seeing whether the solution output (into vtu) works.


Best,
Matthias

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[deal.II] Finite Element Software deal.II Version 9.3.0 released

[Matthias Maier]

Version 9.3.0 of deal.II, the object-oriented finite element library awarded the
J. H. Wilkinson Prize for Numerical Software, has been released. It is
available for free under an Open Source license from the deal.II homepage at

   https://www.dealii.org/

The major changes of this release are:

  - Ten new tutorial programs: step-19 introduces particle methods,
and step-68 uses these for tracking locations in a flow
field. step-66 is a matrix-free geometric multigrid solver for a
nonlinear problem. step-71 and step-72 illustrate automatic and
symbolic differentiation. step-77 demonstrates deal.II's SUNDIALS
interfaces to solve a nonlinear problem. step-74 shows the SIPG
approach to discontinuous Galerkin methods. step-76 is an explicit
integrator for the Euler equations. step-78 solves the
Black-Scholes equations, and step-79 solves a topology
optimization problem.

  - Experimental support for simplex and mixed meshes.

  - Improved flexibility of the particle infrastructure.

  - Support for global-coarsening multigrid algorithms.

  - Advances in the matrix-free infrastructure.

  - Usage of MPI-3.0 shared-memory features to reduce memory footprint.

  - Improved support for evaluation and integration at arbitrary points.

  - More than 210 other new features, improvements, and bugfixes.

For more information see:
  - The preprint at https://www.dealii.org/deal93-preprint.pdf
  - The list of changes at

https://www.dealii.org/developer/doxygen/deal.II/changes_between_9_2_0_and_9_3_0.html

The main features of deal.II are:
  - Extensive documentation and 76 fully-functional example programs
  - Support for dimension-independent programming
  - Locally refined adaptive meshes
  - Multigrid support
  - A zoo of different finite elements
  - Fast linear algebra
  - Built-in support for shared memory and distributed parallel computing,
scaling from laptops to clusters with 100,000+ processor cores
  - Interfaces to Trilinos, PETSc, METIS, UMFPACK and other external software
  - Output for a wide variety of visualization platforms.

Matthias Maier and Peter Munch,
on behalf of the deal.II developer team and many contributors.

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Re: [deal.II] Make test fail after installation

[Matthias Maier]

Hi,

It looks like your deal.II installation picked up a gmsh binary and
configured deal.II with support for gmsh. This is done by calling the
binary and if it is not compiled/installed with the correct set of
features the test might fail.

If you don't plan to use the gmsh interface in deal.II you can safely
ignore the test failure.

Best,
Matthias


On Mon, Jun 28, 2021, at 15:03 CDT, Sou Ren  wrote:

> Hello there,
>
> I am new to deal.ii and I am currently at installation stage.
> To install the code I followed mostly the tutorial given here 
>  and I also had 
> a look at this page  . There are 
> slight differences but I don't think it makes huge difference at the end.
>
> Here is my problem I downloaded the code and unpacked it then following the 
> instructions on the video I compiled and installed the code. But for the 
> test part I did not implement the "cd examples/step-1" command and instead 
> I ran the "make test" command.
> seven out of eight tests were run successfully but the last one failed 
> giving the following error :
>
> Test project 
> /home/sourena/Documents/Homework/Pro/dealii-9.3.0/build/tests/quick_tests
> Start 1: step.debug
> Start 2: step.release
> Start 3: affinity.debug
> Start 4: tbb.debug
> 1/8 Test #2: step.release .   Passed   67.30 sec
> Start 5: lapack.debug
> 2/8 Test #4: tbb.debug    Passed   72.39 sec
> Start 6: umfpack.debug
> 3/8 Test #3: affinity.debug ...   Passed   72.55 sec
> Start 7: boost_zlib.debug
> 4/8 Test #1: step.debug ...   Passed   84.15 sec
> Start 8: gmsh.debug
> 5/8 Test #5: lapack.debug .   Passed   23.66 sec
> 6/8 Test #7: boost_zlib.debug .   Passed   29.22 sec
> 7/8 Test #6: umfpack.debug    Passed   37.05 sec
> 8/8 Test #8: gmsh.debug ...***Failed   31.21 sec
> make[7]: *** 
> [tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/build.make:57: 
> tests/quick_tests/CMakeFiles/gmsh.debug.run] Error 1
> make[6]: *** [CMakeFiles/Makefile2:9279: 
> tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/all] Error 2
> make[5]: *** [CMakeFiles/Makefile2:9286: 
> tests/quick_tests/CMakeFiles/gmsh.debug.run.dir/rule] Error 2
> make[4]: *** [Makefile:3830: gmsh.debug.run] Error 2
> Test gmsh.debug: RUN
>
> What's wrong?

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Re: [deal.II] Re: Unable to Build Dealii on WSL Ubuntu 18.04

[Matthias Maier]

If you are happy with version 9.2 you could also add the following PPA:

  https://launchpad.net/~ginggs/+archive/ubuntu/deal.ii-9.2.0-backports

and then simply install via

  sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make g++

See https://github.com/dealii/dealii/issues/11529

This version of deal.II-9.2.0 comes enabled with the most common
external libraries. We are in the process of releasing 9.3.0 very soon
and hope to have an updated PPA in the very near future (~1month).

Best,
Matthias



On Tue, May 25, 2021, at 14:51 CDT, SANKET KULKARNI 
 wrote:

> Hello,
> I am not able to figure out how to resolve this issue since I am naive in
> the Linux environment. Please can you help with this? My CMake command is
> working fine. But the make install command is showing errors.
>
> On Mon, May 24, 2021 at 2:19 PM Marc Fehling  wrote:
>
>> Sanket,
>>
>> you need to specify an installation directory with a cmake parameter as
>> explained here .
>>
>> `/PATH/TO/DEALII/INSTALLATION` is just a placeholder.
>>
>> Best,
>> Marc
>>
>> On Monday, May 24, 2021 at 12:06:02 PM UTC-6 sanketku...@gmail.com wrote:
>>
>>> Hello,
>>>
>>> Error after "make install".
>>>
>>> Regards,
>>> Sanket Kulkarni
>>>
>>> On Fri, May 21, 2021 at 7:21 PM Marc Fehling  wrote:
>>>
 Hi Sanket,

 Yes, you need to install g++.

 For ubuntu, I would encourage you to install a group of essential
 compilation packages via

 ```

 sudo apt install build-essential

 ```

 It contains the necessary compilers and a few more important tools.
 Best,
 Marc


 On 5/21/21 5:10 PM, SANKET KULKARNI wrote:

 Hello,
 I am attaching the screenshot. Do i need to install g++

 On Fri, May 21, 2021 at 7:00 PM Marc Fehling  wrote:

> Hi Sanket,
>
> what do you get if you type in `g++` in your console?
>
> Marc
>
>
> On 5/21/21 4:58 PM, SANKET KULKARNI wrote:
>
> Thank for your email, I tried installing and building it again but I
> guess the issue still exists.
>
> On Fri, May 21, 2021 at 4:45 PM Marc Fehling  wrote:
>
>> Hello,
>>
>> from your error message it appears to me that you have an `openmpi`
>> wrapper installed on your system which doesn't know anything about the
>> `gcc` compilers. Are you sure you have them installed?
>>
>> Marc
>>
>> On Friday, May 21, 2021 at 12:15:56 PM UTC-6 sanketku...@gmail.com
>> wrote:
>>
>>> Hello,
>>> I am trying to build environment for dealii install but i am not able
>>> to build it.
>>>
>>> I am facing error while downloading. p4est file. Attaching the error
>>> with this file.
>>> Also,can you send me updated manual of downloading Dealii.
>>>
>>>
>>>
>>>
>>> --
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>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>> 
>> .
>>
> --
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> 
> .
>
> --
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Re: [deal.II] MPI libraries

[Matthias Maier]

Hi Victor,

Please find attached a patch that disables the MPI sanity checks we put
in place. With that you should be able to configure without bailing out
in these sanity checks.

That said, I would recommend to try the debug and release versions of
the library against respective debug / release versions of MPI and
PETSc, etc.

The easiest way to achieve this is to compile deal.II by explicitly
setting -DCMAKE_BUILD_TYPE=Debug (or Release) and create separate
modules.

Best,
Matthias


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diff --git a/cmake/configure/configure_2_metis.cmake b/cmake/configure/configure_2_metis.cmake
index e644e725a3..c58ab3d8b5 100644
--- a/cmake/configure/configure_2_metis.cmake
+++ b/cmake/configure/configure_2_metis.cmake
@@ -36,7 +36,6 @@ MACRO(FEATURE_METIS_FIND_EXTERNAL var)
   SET(${var} FALSE)
 ENDIF()
 
-CHECK_MPI_INTERFACE(METIS ${var})
   ENDIF()
 ENDMACRO()
 
diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake
index da61cf9104..7c38f15827 100644
--- a/cmake/configure/configure_2_trilinos.cmake
+++ b/cmake/configure/configure_2_trilinos.cmake
@@ -162,8 +162,6 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var)
   SET(${var} FALSE)
 ENDIF()
 
-CHECK_MPI_INTERFACE(TRILINOS ${var})
-
 #
 # Check which optional features of trilinos are installed.
 #
diff --git a/cmake/configure/configure_3_petsc.cmake b/cmake/configure/configure_3_petsc.cmake
index 901557528e..2471a0f510 100644
--- a/cmake/configure/configure_3_petsc.cmake
+++ b/cmake/configure/configure_3_petsc.cmake
@@ -113,7 +113,6 @@ MACRO(FEATURE_PETSC_FIND_EXTERNAL var)
   SET(${var} FALSE)
 ENDIF()
 
-CHECK_MPI_INTERFACE(PETSC ${var})
   ENDIF()
 ENDMACRO()
 
diff --git a/cmake/configure/configure_hdf5.cmake b/cmake/configure/configure_hdf5.cmake
index 0a67ddc43c..4bb99ff64b 100644
--- a/cmake/configure/configure_hdf5.cmake
+++ b/cmake/configure/configure_hdf5.cmake
@@ -40,7 +40,6 @@ MACRO(FEATURE_HDF5_FIND_EXTERNAL var)
   SET(${var} FALSE)
 ENDIF()
 
-CHECK_MPI_INTERFACE(HDF5 ${var})
   ENDIF()
 ENDMACRO()
 
diff --git a/cmake/configure/configure_p4est.cmake b/cmake/configure/configure_p4est.cmake
index cc9c3c0016..2d90f1572d 100644
--- a/cmake/configure/configure_p4est.cmake
+++ b/cmake/configure/configure_p4est.cmake
@@ -71,7 +71,6 @@ MACRO(FEATURE_P4EST_FIND_EXTERNAL var)
   SET(${var} FALSE)
 ENDIF()
 
-CHECK_MPI_INTERFACE(P4EST ${var})
   ENDIF()
 ENDMACRO()
 
diff --git a/cmake/configure/configure_scalapack.cmake b/cmake/configure/configure_scalapack.cmake
index 1eefac4d12..0591a770f8 100644
--- a/cmake/configure/configure_scalapack.cmake
+++ b/cmake/configure/configure_scalapack.cmake
@@ -25,7 +25,6 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
 
   IF(SCALAPACK_FOUND)
 SET(${var} TRUE)
-CHECK_MPI_INTERFACE(SCALAPACK ${var})
 
 IF (${var})
   CLEAR_CMAKE_REQUIRED()

Re: [deal.II] Re: Error in p4est installation using deal.II suggested script

[Matthias Maier]

Yes, it install p4est alongside trilinos, petsc, and most of the
supported dependencies.

Give it a try!

Matthias



On Fri, Mar 12, 2021, at 13:31 CST, Kishore Nori  
wrote:

> Dear Matthias,
>
> No, I haven't tried this way, seems easier, thank you very much!
> Would it also install p4est? If not, can I use this way after installing
> p4est?
>
> Best wishes,
>
> Kishore
>
> On Sat, Mar 13, 2021 at 12:51 AM Matthias Maier  wrote:
>
>> For Ubuntu 20.04:
>>
>> Have you tried to use the ppa package found here?
>>
>>   https://launchpad.net/~ginggs/+archive/ubuntu/deal.ii-9.2.0-backports
>>
>> Doing this and running
>>
>>   sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make g++
>>
>> should install all necessary dependencies (and a functional deal.II
>> 9.2.0). If you want to use the development version, just install version
>> 9.2.0 on the system and then configure and compile the library by hand.
>>
>> Best,
>> Matthias
>>
>>
>>
>> see: https://github.com/dealii/dealii/issues/11529
>>
>>
>> On Fri, Mar 12, 2021, at 12:55 CST, Kishore Nori <
>> kishore.nori...@gmail.com> wrote:
>>
>> > Dear Bruno,
>> >
>> > Thank you for the suggestion, but unfortunately, this as well leads to
>> > exactly the same error report as above.
>> > I get the same error report even when I run it as a super user. (I
>> forgot
>> > to mention that I am running this on Ubuntu 20.04)
>> >
>> > Thanking you,
>> >
>> > Best wishes,
>> >
>> > Kishore
>> >
>> > On Saturday, March 13, 2021 at 12:15:13 AM UTC+5:30 bruno.t...@gmail.com
>> > wrote:
>> >
>> >> Kishore,
>> >>
>> >> Can you try the following command:
>> >> $  bash ./p4est-setup.sh p4est-2.2.tar.gz /home/kishore/bin
>> >>
>> >> Best,
>> >>
>> >> Bruno
>> >> On Friday, March 12, 2021 at 11:41:21 AM UTC-5 kishore...@gmail.com
>> wrote:
>> >>
>> >>> Hi everyone,
>> >>>
>> >>> Hope you are doing well!
>> >>>
>> >>> I  am new to deal.II and I am trying to install p4est before I install
>> >>> deal.II, I found this script on the deal.II website (
>> >>> https://www.dealii.org/current/external-libs/p4est.html) for
>> installing
>> >>> p4est with optimisations and settings relevant for deal.II, but I am
>> >>> getting an error while installing through this procedure, the
>> following are
>> >>> the run time updates, when executing: $ ./p4est-setup.sh
>> p4est-2.2.tar.gz
>> >>> ~/bin/
>> >>>
>> >>> CFLAGS_FAST: -O2 -qopenmp
>> >>> CFLAGS_DEBUG: -O0 -g -qopenmp
>> >>>
>> >>> This script tries to unpack, configure and build the p4est library.
>> >>> Build FAST: /home/kishore/p4est-build/FAST
>> >>> Build DEBUG: /home/kishore/p4est-build/DEBUG
>> >>> Install FAST: /home/kishore/bin//FAST
>> >>> Install DEBUG: /home/kishore/bin//DEBUG
>> >>> Checking environment: CFLAGS P4EST_CFLAGS_FAST P4EST_CFLAGS_DEBUG
>> >>> Unpack directory: /home/kishore/p4est-2.2
>> >>> Unpacking... done
>> >>> See output in files .../config.output and .../make.output
>> >>>
>> >>> Build FAST version in /home/kishore/p4est-build/FAST
>> >>> configure: error: unsafe srcdir value: '/home/kishore/p4est-2.2'
>> >>> Error: Error in configure
>> >>>
>> >>> May I get pointers on fixing this?
>> >>>
>> >>> Thank you very much,
>> >>>
>> >>> yours sincerely,
>> >>>
>> >>> Kishore
>> >>>
>> >>>
>>
>> --
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>>

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Re: [deal.II] Acoustic simulation

[Matthias Maier]

On Tue, Feb  9, 2021, at 12:22 CST, Wolfgang Bangerth  
wrote:

> On 2/9/21 8:34 AM, Matthias Maier wrote:
>> We do not have PMLs directly available in deal.II as a building block,
>> but it is straightforward for you to write one for your needs.
>
> But step-62 uses PML boundary conditions!

Even better!

Forgot about that one :-D

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Re: [deal.II] Acoustic simulation

[Matthias Maier]

Dear Anne,

We do not have PMLs directly available in deal.II as a building block,
but it is straightforward for you to write one for your needs.

I have written one for the time-harmonic Maxwell's equations (for 2D) a
while ago. It is very unpolished code, but have a look at:

  
https://github.com/tamiko/rspa-2019/blob/master/loki/grendel/perfectly_matched_layer.template.h
  
https://github.com/tamiko/rspa-2019/blob/master/loki/grendel/maxwell_problem.template.h#L192

More generally, step-6 covers nonconstant (material) coefficients:

  
https://www.dealii.org/current/doxygen/deal.II/step_6.html#Nonconstantcoefficients

Best,
Matthias



On Tue, Feb  9, 2021, at 08:18 CST, Anne  wrote:

> Hi,
>
> I would like use deal.II for acoustic simulations. Do we have PML available 
> in deal.II?
>
> Thanks

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Re: [deal.II] Install and running deal.II with latest debian package

[Matthias Maier]

All,

I have created an issue on github to track some much needed updates to
our documentation :-)

https://github.com/dealii/dealii/issues/11529

Best,
Matthias



On Thu, Jan 14, 2021, at 00:47 CST, Matthias Maier  wrote:

> Dear Matt,
>
> You need to compile and link your source code with all include
> directives ( -I  ) and external libraries. It is easiest to simply
> use the CMake configuration that we ship with the examples.
>
> I guess you installed the deal.II package via apt? If so, simply install
> the doc package and required dependencies and toolchain:
>
>   sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make
>
> and (as user) copy the first example step to a convenient location:
>
>   cp -r /usr/share/doc/libdeal.ii-doc/examples/step-1 .
>   cd step-1
>   cmake .
>   make
>   make run
>
> Best,
> Matthias
>
>
>
> On Wed, Jan 13, 2021, at 23:22 CST, Matthew Rich  wrote:
>
>> Hi, 
>>
>> I am new to deal.II and I wanted to mess with the tutorials. I am running 
>> the mint LDE distro of linux and just installed the package. per the 
>> website. On step one when you are just creating a mesh, I am getting an 
>> error regrading Sacado.h which appears to be a solver package external to 
>> deal.II. I was expecting the package management to cover all dependencies, 
>> so I am not sure how to proceed. I searched this group and no one else 
>> seems to have this error. 
>>
>> to get this error I simply touched a file called example1.cpp  and cut and 
>> pasted all the code from the tutorial in there. 
>>
>> initially tried compiling with g++ but that failed looking for mpi.h. I 
>> then switched mpiCC where I get *fatal error: Sacado.hpp: No such file or 
>> directory*. 
>>
>> I am not sure if I need to install something else to get off the ground. 
>>
>> Any help would be much appreciated. 
>>
>> Matt

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Re: [deal.II] Install and running deal.II with latest debian package

[Matthias Maier]

Dear Matt,

You need to compile and link your source code with all include
directives ( -I  ) and external libraries. It is easiest to simply
use the CMake configuration that we ship with the examples.

I guess you installed the deal.II package via apt? If so, simply install
the doc package and required dependencies and toolchain:

  sudo apt install libdeal.ii-dev libdeal.ii-doc cmake make

and (as user) copy the first example step to a convenient location:

  cp -r /usr/share/doc/libdeal.ii-doc/examples/step-1 .
  cd step-1
  cmake .
  make
  make run

Best,
Matthias



On Wed, Jan 13, 2021, at 23:22 CST, Matthew Rich  wrote:

> Hi, 
>
> I am new to deal.II and I wanted to mess with the tutorials. I am running 
> the mint LDE distro of linux and just installed the package. per the 
> website. On step one when you are just creating a mesh, I am getting an 
> error regrading Sacado.h which appears to be a solver package external to 
> deal.II. I was expecting the package management to cover all dependencies, 
> so I am not sure how to proceed. I searched this group and no one else 
> seems to have this error. 
>
> to get this error I simply touched a file called example1.cpp  and cut and 
> pasted all the code from the tutorial in there. 
>
> initially tried compiling with g++ but that failed looking for mpi.h. I 
> then switched mpiCC where I get *fatal error: Sacado.hpp: No such file or 
> directory*. 
>
> I am not sure if I need to install something else to get off the ground. 
>
> Any help would be much appreciated. 
>
> Matt

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Re: [deal.II] Using external libraries with deal.II

[Matthias Maier]

Hi,

No, the problem is much simpler. You have to reorganize your
CMakeLists.txt so that you search for your libraries and add them to
your link interface after the PROJECT() call and after the
DEAL_II_INVOKE_AUTOPILOT CALL(). It is simplest to put everything last:


  # The default CMakeLists.txt file does the following:

  FIND_PACKAGE(deal.II 9.1 QUIET [...])# finds deal.II configuration

  DEAL_II_INITIALIZE_CACHED_VARIABLES()# sets compiler and other cached 
variables
  PROJECT(${TARGET})   # initializes compiler toolchain

  DEAL_II_INVOKE_AUTOPILOT()   # defines executable target with the 
name stored in
   # variable "${TARGET}"


  # NOW, you can search for your external libraries:

  FIND_PACKAGE(Eigen3 REQUIRED)
  FIND_PACKAGE(Spectra REQUIRED)

  # and NOW you can add them to the target. (Simply use the variable
  # ${TARGET} where you already stored the name of the project):

  TARGET_LINK_LIBRARIES(${TARGET} Spectra::Spectra)



Best,
Matthias

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Re: [deal.II] initial values of different-type data

[Matthias Maier]

You have to be a bit careful - unfortunately, C++ has one of the most
convoluted rules when objects are zero initialized or not.

As a rule of thumb:

* whenever you are working with a plain "double", "float", "int",
  etc. it is best to explicitly initialize the variable (because C++ in
  most cases does not initialize the variable for you):

  unsigned int i = 0;
  double d = 0.;
  float f = 0.;

* in case of a "container" like std::vector, dealii::Vector,
  dealii::Tensor elements are default initialized:

  dealii::Tensor<1, dim> t; // zeroes elements
  dealii::Vector V;
  V.reinit(10);  // zeroes elements

  std::vector v;
  v.resize(10);  // zeroes elements

I do not understand your second question :-(

Best,
Matthias


On Wed, Dec  9, 2020, at 09:43 CST, Chenyi LUO  wrote:

> Hi dealii developers,
>
> I would like to ask(confirm)whether zero is the initial value of
> different-type data, e.g. for  double, int, Vector and Tensor. For
> example, if I just define double x;. Does x have an initial value of 0.0?
>
> Moreover, in my task, I set initial values of a variable, e.g. "a",  to
> be one in the whole domain. When I assemble the residual vector, I need
> to first compute the value of "a" at quadrature points (which turns out
> not exactly 1.0). Consequently, when I compute, e.g. "3*a^4-2*a^3+a^2",
> the answer is not zero. Is it avoidable?
>
> Best,
>
> Chenyi

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Re: [deal.II] Linear Operator

[Matthias Maier]

Dear Nikki,

A "linear operator" in deal.II is an object that linearly transforms a
vector into another one, i.e., it has a vector space as domain of
definition and a vector space as range space. 

In your case M.matrix_scalar_product(u,u) is  (u^T M u), this is a
quadratic operation, not a linear one. You cannot represent this
operation with a linear operator. Did you intend to simply scale with
that value?

Best,
Matthias


On Mon, Oct 26, 2020, at 13:40 CDT, Nikki Holtzer  
wrote:

> Hello all,
>
> I am struggling to turn a matrix scalar product into a linear operator. I 
> currently have:
>
> temp = M.matrix_scalar_product(u,u);
>
>
> and I need to turn 'temp' into a linear operator. 
>
> I have tried turning 'M' into a linear operator first  and then  performing 
> the multiplication and have also tried something like 
> linear_operator(temp). Neither has compiled.
>
> Thank you in advance!

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke  
wrote:

> HI Matthias,
>
> thanks for your input -- you might be onto something RE ld
>
> We use a wrapper script for ld:
> ```
> blaschke@cori06:~> which ld
> /global/common/cori/software/altd/2.0/bin/ld
> ```
> which is managed by the ALTD module (Automatic Library Tracking Database). 
> Using the system linker (which is what cmake is picking up) isn't usually a 
> problem, but in this case it might be. I checked Aaditya's loaded modules 
> and ALTD is in there, so CMake should be picking it up. How does CMake 
> detect the linker? Is it just a question of adding `-DCMAKE_LINKER=$(which 
> ld)`?

Yes, setting CMAKE_LINKER would be an option. But typically CMake just
invokes the compiler wrapper which should do the right thing...

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

On Wed, Aug 26, 2020, at 13:01 CDT, Aaditya Lakshmanan  
wrote:

> Hi, 
>   zlib(version 1.2.11) was already loaded as a module in all my previous 
> compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I 
> am not sure why the path to zlib libraries is picked up from /usr . Thanks 
> for the suggestion.

This is probably simply a faulty zlib module shipped with zlib. In order
to force cmake to pick up the correct library it might be easiest to use
"CMAKE_PREFIX_PATH" like so:

  -DCMAKE_PREFIX_PATH=/path/to/the/zlib/module/

If that doesn't help then you can specify zlib by hand:

  -DDEAL_II_WITH_ZLIB=ON -DZLIB_INCLUDE_DIRS=/[...]/include 
-DZLIB_LIBRARIES=/[...]/libz.so

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

Thanks.

This looks mostly good.

In particular, the Lapack CMake module seems to pick up "AtpSigHandler"
and "AtpSigHCommData":

 55 #DEAL_II_WITH_LAPACK set up with external dependencies  
 
 56 #LAPACK_WITH_64BIT_BLAS_INDICES = OFF   
 
 57 #LAPACK_LINKER_FLAGS =  
 
 58 #LAPACK_INCLUDE_DIRS =  
 
 59 #LAPACK_USER_INCLUDE_DIRS = 
 
 60 #LAPACK_LIBRARIES = 
/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_intel_lp64.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel6

4/libmkl_intel_thread.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_core.so;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64/libiom

p5.so;-lm;-ldl;hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5hl_fortran;hdf5_fortran;mpich_intel;mpichf90_intel;ifport;ifcoremt;imf;m;ipgo;irc;pthread;svml;gcc;gcc_s;irc_s;dl
;c

One thing is peculiar: 

108 #DEAL_II_WITH_ZLIB set up with external dependencies
 
109 #ZLIB_VERSION = 1.2.11  
 
110 #ZLIB_INCLUDE_DIRS = /usr/include   
 
111 #ZLIB_LIBRARIES = /usr/lib64/libz.so 

This library does not reside under /global and I doubt it has the right
architecture. Would you mind disabling zlib support for the time being
(-DDEAL_II_WITH_ZLIB=OFF)? Or reconfigure such that the correct zlib
library is picked up?

Maybe this explains why the system linker /usr/bin/ld is used instead of
one from the toolchain under /opt/cray/pe/craype/2.6.2/bin ...

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

On Tue, Aug 25, 2020, at 00:07 CDT, Johannes Blaschke  
wrote:

> But I am available to work with you directly -- however I cannot debug this 
> on my own (as the cmake setup is pretty huge!).

Please have a look at the file `detailed.log` found in the build
directory. It spells out the compiler, all compile flags and the full
configured link interface. Do you see anything odd there?

Aaditya, Johannes: Another point to check quickly is whether CMake
itself does the right thing. Would you mind adding the following three
lines to the main CMakeLists.txt file and examining the output?

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ab24b8f477..dce1dcac08 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -95,6 +95,10 @@ 
VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_cached_variables.cmake)
 PROJECT(deal.II CXX C)
 ENABLE_LANGUAGE_OPTIONAL(Fortran)
 
+message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
+message("Link libraries:   ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
+message(FATAL_ERROR "exit")
+
 VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)
 
 VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_compiler_flags.cmake)


I expect that the AtpSigHandler library should be listed there.

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

Would you mind quickly sending us the file `detailed.log` that you can
find in the build directory? This would help us a lot.

On Mon, Aug 24, 2020, at 16:40 CDT, Aaditya Lakshmanan  
wrote:

> [100%] Built target obj_fe_debug
> [100%] Linking CXX shared library ../lib/libdeal_II.g.so
> /usr/bin/ld: cannot find -lAtpSigHandler
> /usr/bin/ld: cannot find -lAtpSigHCommData

This implies that the linker (in this case "/usr/bin/ld" was invoked)
was not able to find the library "AtpSigHandler". So, your compiler
toolchain seems to do the right thing by adding

  -lAtpSigHandler -lAtpSigHCommData

to the link line but the linker does not know the correct library
location (which would typically be specified by -L<...>). This begs the
question whether "/usr/bin/ld" is actually the correct linker.


> The problem is that somewhere in the cmake files it's missing:
> ```
> find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
> target_link_libraries( ${ATP_SIGHANDLER_LIBRARY})
> ```

It looks like that these two commands might work around the problem by
letting cmake add a "-L<...>" to the command line. You can give this a
shot with the following changes to source/CMakeLists.txt:


diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index a6d85d8b68..86ca17d073 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -158,10 +158,12 @@ FOREACH(build ${DEAL_II_BUILD_TYPES})
   )
   ENDIF()
 
+  find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)
 
   TARGET_LINK_LIBRARIES(${DEAL_II_BASE_NAME}${DEAL_II_${build}_SUFFIX}
 ${DEAL_II_LIBRARIES_${build}}
 ${DEAL_II_LIBRARIES}
+${ATP_SIGHANDLER_LIBRARY}
 )
 
   FILE(MAKE_DIRECTORY



But I would rather prefer to figure out why our cmake configurations
(probably?) selects the wrong linker. In any case, please show us the
full contents of detailed.log

Best,
Matthias

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Re: [deal.II] deal.ii Installation : expand_instantiations Error

[Matthias Maier]

Hi,

CMake's cross compilation features are unfortunately a bit limited. To
work around this you have to create an executable
"expand_instantiations" separately by doing for example the following in
the source directory:

  $ mkdir build-executable
  $ cd build-executable
  $ cmake ..
  $ make expand_instantiations_exe

After that export the executable to your path:

  $ export PATH="$PWD/bin:$PATH"

when you now run "expand_instantiations" in your command prompt you
should get a help message:

  $ expand_instantiations
  Usage:
expand_instantiations class_list_files < in_file > out_file

If all that works out switch to the actual build directory (in the same
terminal) and compile.

This should take care of the following error:

  > /bin/sh: expand_instantiations: command not found
  > make[2]: *** 

Best,
Matthias



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[deal.II] Finite Element Software deal.II Version 9.2.0 released

[Matthias Maier]

Version 9.2.0 of deal.II, the object-oriented finite element library awarded the
J. H. Wilkinson Prize for Numerical Software, has been released. It is
available for free under an Open Source license from the deal.II homepage at

   https://www.dealii.org/

The major changes of this release are:

  - Seven new tutorial programs: step-47 solves the biharmonic equation;
step-50 demonstrates algebraic and geometric multigrid methods for
large, parallel computations on adaptively refined meshes, and
compares matrix-based and matrix-free implementations; step-58
solves the nonlinear Schroedinger equation; step-65 illustrates
working with complex geometries and curved domains; step-67 and
step-69 implementing different approaches for the Euler equations
in compressible gas dynamics; step-70 illustrates flow around a
moving obstacle.

  - Substantial improvements to the Python interfaces, including
Jupyter versions of the step-49 and step-53 tutorial program.

  - A new triangulation class (parallel::fullydistributed::Triangulation)
that completely distributes a triangulation, rather than keeping
the coarse mesh available on all processors.

  - The DataOut and related classes now fully support outputting
complex-valued solution vectors, including complex-valued vector
and tensor fields.

  - A number of fixes throughout the library for problems with more
than 2^32 (=4 billion) unknowns.

  - Improvements to the support for particle based methods as well as
to parallel hp-adaptive finite element methods.

  - More than 320 other new features, improvements, and bugfixes.

For more information see
  - the preprint at https://www.dealii.org/deal92-preprint.pdf
  - the list of changes at

https://www.dealii.org/developer/doxygen/deal.II/changes_between_9_1_1_and_9_2_0.html

The main features of deal.II are:
  - Extensive documentation and 66 fully-functional example programs
  - Support for dimension-independent programming
  - Locally refined adaptive meshes
  - Multigrid support
  - A zoo of different finite elements
  - Fast linear algebra
  - Built-in support for shared memory and distributed parallel computing,
scaling from laptops to clusters with 100,000+ processor cores
  - Interfaces to Trilinos, PETSc, METIS, UMFPACK and other external software
  - Output for a wide variety of visualization platforms.

Martin Kronbichler and Matthias Maier,
on behalf of the deal.II developer team and many contributors.

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Re: [deal.II] Building DEAL. II with an external dylib

[Matthias Maier]

On Thu, May 14, 2020, at 06:19 CDT, Yang Liu  wrote:

The  /usr/local/hlibpro-2.8.1/lib/libhpro.dylib  dynamic library
probably sets an incorrect rpath ("/lib/libhpro.dylib" instead of the
full path).

 - You might try to export the directory in DYLD_LIBRARY_PATH:

   export DYLD_LIBRARY_PATH="/usr/local/hlibpro-2.8.1/lib/:${DYLD_LIBRARY_PATH}"

 - Alternatively, you can try to add the directory to the rpath of the
 executable by specifying something like this (in CMakeLists.txt):

  SET_TARGET_PROPERTIES(step-6 PROPERTIES
BUILD_RPATH "/usr/local/hlibpro-2.8.1/lib/"
)  

Best,
Matthias

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[deal.II] dealii-9.2.0 release candidate 1

[Matthias Maier]

Dear all,

We have tagged a first release candidate for the upcoming deal.II 9.2.0
release. you can find the sources and a generated offline documentation
here:

  https://github.com/dealii/dealii/releases/tag/v9.2.0-rc1

Alternatively, you can switch to the dealii-9.2 branch in your local git
repository

  git remote update
  git checkout v9.2.0-rc1

It would be great if you could test it in your machine with your typical
configuration! If no further regressions show up we will release
Wednesday May 20. The release progress is tracked in the following
github issue:

  https://github.com/dealii/dealii/issues/10072

Thanks!

Matthias
on behalf of the deal.II developer team

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Re: [deal.II] Dealii & trilinos

[Matthias Maier]

On Fri, May  1, 2020, at 15:59 CDT, Victor Eijkhout  
wrote:

> I'm using trilinos 12.18.1
>
> This is the most error-like statement that I can find. Other files attached.

The actual error message (and why configure fails) is here:


12442 -- Include 
/admin/build/admin/rpms/frontera/BUILD/dealii-9.1.1/cmake/configure/configure_2_trilinos.cmake
12443 CMake Error at 
/home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/ShyLU/ShyLUConfig.cmake:156
 (INCLUDE):
12444   INCLUDE could not find load file:   
   
12445   
   
12446 
/home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/ShyLU/../ShyLU_Node/ShyLU_NodeConfig.cmake
12447 Call Stack (most recent call first):  
   
12448   
/home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/Trilinos/TrilinosConfig.cmake:130
 (INCLUDE)
12449   cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
   
12450   cmake/modules/FindTRILINOS.cmake:38 (FIND_PACKAGE)  
   
12451   cmake/macros/macro_find_package.cmake:27 (_FIND_PACKAGE)
   
12452   cmake/configure/configure_2_trilinos.cmake:22 (FIND_PACKAGE)
   
12453   /tmp/dealii-build/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1 
(FEATURE_TRILINOS_FIND_EXTERNAL)
12454   cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE)   
   
12455   cmake/macros/macro_configure_feature.cmake:237 (EVALUATE_EXPRESSION)
   
12456   cmake/configure/configure_2_trilinos.cmake:303 (CONFIGURE_FEATURE)  
   
12457   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)   
   
12458   CMakeLists.txt:124 (VERBOSE_INCLUDE)
   


This implies that the CMake configuration that gets installed by
Trilinos is broken. 

The file

  
/home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/ShyLU/ShyLUConfig.cmake

contains an include on line 156

  INCLUDE("${CMAKE_CURRENT_LIST_DIR}/../ShyLU_Node/ShyLU_NodeConfig.cmake")

pointing to a nonexistant file

  
/home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/ShyLU/../ShyLU_Node/ShyLU_NodeConfig.cmake


Why you did end up in this situation I cannot tell. The lazy approach
for making deal.II configure is to manually fix the cmake file by
commenting out the include.

As a quick smoke test:

  $ cd test
  $ cat CMakeLists.txt
  CMAKE_MINIMUM_REQUIRED(VERSION 3.0)
  PROJECT(test CXX)
  find_package(Trilinos REQUIRED)
  $ cmake .
  $

has to configure. Otherwise the Trilinos configuration is broken.

MM

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Re: [deal.II] Instalation

[Matthias Maier]

On Mon, Apr 27, 2020, at 17:21 CDT, Wilmar Alves Cruvinel Lima 
 wrote:

> As I have GNU im my Linux I uncompressed with the command:
>
> administrador@administrador-desktop:~$ *tar -xvf dealii-9.1.1.tar.gz*
>
> It function correctly and the directory   dealii-9.1.1  was populated.
>
> Next step was:
>
> *mkdir build
> cd build*
>
> and
>
> *cmake -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II*
>
> but I get:
>
> administrador@administrador-desktop:~/build$ cmake 
> -DCMAKE_INSTALL_PREFIX=/path/to/install/dir ../deal.II
> CMake Error: The source directory "/home/administrador/deal.II" does not 
> exist.
> Specify --help for usage, or press the help button on the CMake GUI.
>
> What can I do to solve it?

When you do

  mkdir build
  cd build

then the relative path is just ../

  cmake -DCMAKE_INSTALL_PREFIX= ../
  
You will also have to replace  (including the < >) with a
desired target directory, for example   ~/dealii-9.1.1-installed

  cmake -DCMAKE_INSTALL_PREFIX=~/dealii-9.1.1-installed ../

That way you will end up with a directory "dealii-9.1.1-installed" next
to the directory "dealii-9.1.1" in your home directory.

Best,
MM

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Re: [deal.II] "libpthreads"?

[Matthias Maier]

On Fri, Apr 24, 2020, at 11:44 CDT, Victor Eijkhout  
wrote:

>> On , 2020Apr24, at 09:47, Matthias Maier 
>> mailto:tam...@43-1.org>> wrote:
>>
>>  I have attached a new patch for 9.1.1
>
> I think that did it. I’m now compiling.

Fingers crossed!

Would you mind sending me the `detailed.log` file?

That way I can verify my suspicion that our renaming of "-lpthread" to
"-pthread" is indeed the problem. :-)

Best,
Matthias

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Re: [deal.II] "libpthreads"?

[Matthias Maier]

On Fri, Apr 24, 2020, at 09:00 CDT, Victor Eijkhout  
wrote:

> On , 2020Apr22, at 16:46, Matthias Maier 
> mailto:tam...@43-1.org>> wrote:
>
> patch -p1 < remove_pthread_workarounds.patch
>
> %% screen output
>
> patching file cmake/configure/configure_1_threads.cmake
> Hunk #1 FAILED at 38.
> Hunk #2 succeeded at 64 (offset -10 lines).
> 1 out of 2 hunks FAILED -- saving rejects to file 
> cmake/configure/configure_1_threads.cmake.rej

Ah, this is 9.1.1! Mea Culpa.

You don't need the failing hunk - the snippet of cmake configuration in
question was added after the 9.1.1 release. Nevertheless, I have
attached a new patch for 9.1.1. (the second patch works
without modification)

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diff --git a/cmake/configure/configure_1_threads.cmake b/cmake/configure/configure_1_threads.cmake
index b4de2cc2cc..d23af9b49f 100644
--- a/cmake/configure/configure_1_threads.cmake
+++ b/cmake/configure/configure_1_threads.cmake
@@ -64,21 +64,6 @@ MACRO(SETUP_THREADING)
 
   MARK_AS_ADVANCED(pthread_LIBRARY)
 
-  #
-  # Change -lphtread to -pthread for better compatibility on non linux
-  # platforms:
-  #
-  IF("${CMAKE_THREAD_LIBS_INIT}" MATCHES "-lpthread")
-CHECK_CXX_COMPILER_FLAG("-pthread"
-  DEAL_II_HAVE_FLAG_pthread
-  )
-IF(DEAL_II_HAVE_FLAG_pthread)
-  STRING(REPLACE "-lpthread" "-pthread" CMAKE_THREAD_LIBS_INIT
-"${CMAKE_THREAD_LIBS_INIT}"
-)
-ENDIF()
-  ENDIF()
-
   ADD_FLAGS(THREADS_LINKER_FLAGS "${CMAKE_THREAD_LIBS_INIT}")
 
   #

Re: [deal.II] "libpthreads"?

[Matthias Maier]

Hi Victor,

Would you mind testing something for me quickly?

We have a bit of code floating around in

  ./cmake/configure/configure_1_threads.cmake

that might create an issue (depending on icc and cmake version I guess).
Would you mind modifying the file as in the attached diff output? Simply
copy the patch file into the source directory of deal.II and run

  $ patch -p1 < remove_pthread_workarounds.patch

If that doesn't help, then my next request would be to see the full
terminal output of the cmake invocation.

Also, it seems that cmake barfs at the final sanity check where we check
whether we can compile a simply hello world program with our final
compile configuration. You can disable this check temporarily by
applying remove_sanity_checks.patch (that removes the corresponding
check from cmake./setup_finalize.cmake). cmake should then run through
without a problem creating a file 'detailed.log'. I would like to see
this one. (You can try to compile the library from here - but either the
final link of the library or linking any program against the library
will likely fail).

Best,
Matthias

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diff --git a/cmake/configure/configure_1_threads.cmake b/cmake/configure/configure_1_threads.cmake
index dea761738a..e8b4be0818 100644
--- a/cmake/configure/configure_1_threads.cmake
+++ b/cmake/configure/configure_1_threads.cmake
@@ -38,15 +38,7 @@ MACRO(SETUP_THREADING)
 
 RESET_CMAKE_REQUIRED()
 
-#
-# The FindThreads macro returned a linker option instead of the actual
-# library name in earlier versions. We still require the linker option,
-# so we fix the corresponding variable.
-#  - See: https://gitlab.kitware.com/cmake/cmake/issues/19747
-#
-IF(CMAKE_THREAD_LIBS_INIT AND NOT "${CMAKE_THREAD_LIBS_INIT}" MATCHES "^-l")
-  STRING(PREPEND CMAKE_THREAD_LIBS_INIT "-l")
-ENDIF()
+MESSAGE(STATUS "CMAKE_THREAD_LIBS_INIT: ${CMAKE_THREAD_LIBS_INIT}")
 
   ELSE()
 
@@ -74,21 +66,6 @@ MACRO(SETUP_THREADING)
 
   MARK_AS_ADVANCED(pthread_LIBRARY)
 
-  #
-  # Change -lphtread to -pthread for better compatibility on non linux
-  # platforms:
-  #
-  IF("${CMAKE_THREAD_LIBS_INIT}" MATCHES "-lpthread")
-CHECK_CXX_COMPILER_FLAG("-pthread"
-  DEAL_II_HAVE_FLAG_pthread
-  )
-IF(DEAL_II_HAVE_FLAG_pthread)
-  STRING(REPLACE "-lpthread" "-pthread" CMAKE_THREAD_LIBS_INIT
-"${CMAKE_THREAD_LIBS_INIT}"
-)
-ENDIF()
-  ENDIF()
-
   ADD_FLAGS(THREADS_LINKER_FLAGS "${CMAKE_THREAD_LIBS_INIT}")
 
   #
diff --git a/cmake/setup_finalize.cmake b/cmake/setup_finalize.cmake
index 515d999157..51b929695c 100644
--- a/cmake/setup_finalize.cmake
+++ b/cmake/setup_finalize.cmake
@@ -79,72 +79,6 @@ FOREACH(_suffix ${DEAL_II_LIST_SUFFIXES})
   ENDIF()
 ENDFOREACH()
 
-#
-# Sanity check: Can we compile with the final setup?
-#
-
-FOREACH(build ${DEAL_II_BUILD_TYPES})
-
-  MACRO(_check_linker_flags)
-CHECK_COMPILER_SETUP(
-  "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_${build}}"
-  "${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_${build}}"
-  DEAL_II_HAVE_USABLE_FLAGS_${build}
-  ${DEAL_II_LIBRARIES} ${DEAL_II_LIBRARIES_${build}}
-  )
-  ENDMACRO()
-
-  MACRO(_drop_linker_flag _linker_flag _replacement_flag _variable)
-MESSAGE(STATUS
-  "Unable to compile a simple test program. "
-  "Trying to drop \"${_linker_flag}\" from the linker flags."
-  )
-FOREACH(_flags
-DEAL_II_LINKER_FLAGS DEAL_II_LINKER_FLAGS_${build}
-BASE_LINKER_FLAGS BASE_LINKER_FLAGS_${build}
-)
-  STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
-${_flags} "${${_flags}}"
-)
-ENDFOREACH()
-SET(${_variable} FALSE CACHE INTERNAL "" FORCE)
-SET(${_variable} FALSE)
-  ENDMACRO()
-
-  _check_linker_flags()
-
-  IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build} AND DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
-SET(_replacement "")
-IF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-  SET(_replacement "-fuse-ld=gold")
-ENDIF()
-_drop_linker_flag(
-  "-fuse-ld=lld" ${_replacement}
-  DEAL_II_COMPILER_HAS_FUSE_LD_LLD
-  )
-_check_linker_flags()
-  ENDIF()
-
-  IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build} AND DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-_drop_linker_flag(
-  "-fuse-ld=gold" ""
-  DEAL_II_COMPILER_HAS_FUSE_LD_GOLD
-  )
-_check_linker_flags()
-  ENDIF()
-
-  IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build})
-MESSAGE(FATAL_ERROR "
-  Configuration error: Cannot compile a test program with the final set of
-  

Re: [deal.II] deal ii 9.1.1. installation fails

[Matthias Maier]

On Tue, Apr 21, 2020, at 16:06 CDT, Wolfgang Bangerth  
wrote:

> On 4/21/20 5:24 AM, Stefan Knauf wrote:
>>
>> I used the following command:
>>
>> cmake -DDEAL_II_WITH_MPI=ON
>> -DP4ESTDIR=/home/stefan/p4est-2.2/local/lib -DDEAL_WITH_P4EST=ON
>> -DDEAL_WITH_TRILINOS=ON ../sources/dealii-9.1.1/ ../install/
>> command
>>
>> I have attached the cmake output and error log.
>> Any help would be appreciated.
>
> I *believe* that this comes from the following error message:
>   No rule to make target '/usr/lib/x86_64-linux-gnu/libptscotch.so', needed by
>   'cmTC_d4d5a'.  Stop.
> I don't know where it pulls that in, but it may be from the Trilinos
> dependency. Does it work if you switch Trilinos detection off?

detailed.log should shed some light on what dependency pulled in libptscotch.so

Best,
Matthias

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Re: [deal.II] Peter Munch appointed Principal Developer of deal.II

[Matthias Maier]

Congratulations!



On Sat, Apr 11, 2020, at 12:03 CDT, Wolfgang Bangerth  
wrote:

> All,
> it's my pleasure to announce that we have appointed Peter Munch of the
> Technical University of Munich as a member of the Principal Developers
> of deal.II! Happy coding, Peter!
> Best
>  Wolfgang
>
> -- 
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
>www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Compiler linking

[Matthias Maier]

If you want to use binary packages I highly recommend to use the PPA
here in order to get the newest version:

  https://launchpad.net/~ginggs/+archive/ubuntu/deal.ii-backports

After that make sure that you actually install the developer
version. All in one:

  sudo add-apt-repository ppa:ginggs/deal.ii-backports
  sudo apt-get update
  sudo apt-get install libdeal.ii-dev

After that, a simple  $ cmake .  should be enough to configure the
example steps.

Best,
Matthias


On Mon, Mar  9, 2020, at 23:29 CDT, Robert Kopp  
wrote:

> I downloaded the source code for deal.II in Ubuntu, which contains the 
> example files. (I'm a beginner.) I noted, however, that a binary is 
> available for Ubuntu (18.04) and installed that, instead of compiling the 
> library. Then I attempted to run step-1.cc from the source code package, 
> after determining that the library was in /usr/include:
>
> (base) robert@robert-desktop:~/deal/dealii-9.1.1/examples/step-1$ cmake 
> -DDEAL_II_DIR=/usr/include/deal.II .
> CMake Error at CMakeLists.txt:30 (MESSAGE):
>   
>
>   *** Could not locate a (sufficiently recent) version of deal.II.  ***
>
>   
>
>   You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake
>
>   or set an environment variable "DEAL_II_DIR" that contains this path.
>
>
> -- Configuring incomplete, errors occurred!
>
> It's not clear to me why this doesn't work, but it doesn't work that way on 
> Debian either. Any advice would be appreciated.

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Re: [deal.II] Math symbols not displayed correctly in debian package documentation for deal.ii

[Matthias Maier]

Now I understand what happend.

The Debian package downloads the current offline documentation tarball
in which we use mathjax for formula rendering. Unfortunately, all
external links/resources in the documentation are getting removed in the
debian package (otherwise the package QA system detects a "privacy
breach" in the documentation and the package gets rejected).

This hasn't been a problem with the older tarballs in which we still
used latex to directly generate images.

I will try to resolve this in the near future by specifically creating
an "offline" documentation tarball. (You will need that one for reading
the documentation offline without internet anyway.)

I will keep you posted.

Best,
Matthias



On Wed, Jan  8, 2020, at 10:27 CST, Matthias Maier  wrote:

> Dear Gerald,
>
> Thanks a lot for pointing out this issue. I will have a look into it.
>
> Best,
> Matthias
>
>
>
> On Wed, Jan  8, 2020, at 03:40 CST, Gerald Marewo  wrote:
>
>> Dear all,
>>
>> I have noticed that unlike the online documentation (deal.ii 8.4.2) which 
>> behaves well, the documentation that comes with the Debian package 
>> (libdeal.ii-doc) on Debian stretch does not display the math symbols 
>> correctly. Instead it displays the LaTeX code as it is. Once in a while I 
>> need to read the documentation offline.
>>
>> Could you please assist me with solving this problem?
>>
>> Regards.
>>
>> Gerald.

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Re: [deal.II] Math symbols not displayed correctly in debian package documentation for deal.ii

[Matthias Maier]

Dear Gerald,

Thanks a lot for pointing out this issue. I will have a look into it.

Best,
Matthias



On Wed, Jan  8, 2020, at 03:40 CST, Gerald Marewo  wrote:

> Dear all,
>
> I have noticed that unlike the online documentation (deal.ii 8.4.2) which 
> behaves well, the documentation that comes with the Debian package 
> (libdeal.ii-doc) on Debian stretch does not display the math symbols 
> correctly. Instead it displays the LaTeX code as it is. Once in a while I 
> need to read the documentation offline.
>
> Could you please assist me with solving this problem?
>
> Regards.
>
> Gerald.

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Re: [deal.II] Tensor<1, dim> initialization

[Matthias Maier]

On Sun, Jan  5, 2020, at 07:15 CST, "A.Z Ihsan"  wrote:

> Tensor<1, 3> b();

If you write this then you declare a function "b" returning a
Tensor<1,3>. Declare the tensor without the parentheses:

  Tensor<1, 3> b;

You can access individual elements of the tensor via operator[]:

  b[0] = 1;
  b[1] = 1;
  b[2] = 0;

And you can do meaningful mathematical tensor operations. Including,
scaling a tensor

  auto a = 5. * b;

Adding two tensors together:

  auto c = a + b;

Taking the inner product:

  auto k = a * b;

etc.

Best,
Matthias

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Re: [deal.II] Re: cmake with library and executables

[Matthias Maier]

On Fri, Dec 20, 2019, at 13:07 CST, Konrad Simon  wrote:

> ###
> ###
> ADD_CUSTOM_TARGET(debug
>   COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR}
>   COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
>   COMMENT "Switch CMAKE_BUILD_TYPE to Debug"
>   )
>
> ADD_CUSTOM_TARGET(release
>   COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR}
>   COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all
>   COMMENT "Switch CMAKE_BUILD_TYPE to Release"
>   )
> ###
> ###

Do you get the jobserver warning while running "make release" or "make
debug" with "-j8"?

If so - that's because you cannot recursively call into make with the
jobserver feature that way.

We have fixed the example steps a while ago but probably never updated
the documentation regarding these two custom targets. It is best to
simply have:

ADD_CUSTOM_TARGET(debug
  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR}
  COMMENT "Switch CMAKE_BUILD_TYPE to Debug"
  )

ADD_CUSTOM_TARGET(release
  COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR}
  )

and then

  $ make release
  $ make -j8

or

  $ make debug
  $ make -j8

Best,
Matthias

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Re: [deal.II] Re: Is a call to compress() required after scale()?

[Matthias Maier]

On Mon, Nov 25, 2019, at 00:23 CST, vachan potluri 
 wrote:

> I was able to reproduce this behaviour with the following code (also 
> attached); the CMakeLists file is also attached. The code hangs after 
> printing 'Scaled variable 0'.

The problem is the communication pattern:

 90 for(auto : dof_handler.active_cell_iterators()){   
 
 91 if(!(cell->is_locally_owned())) continue;   
 
 92 
 
 93 cell->get_dof_indices(dof_ids); 
 
 97 for(uint var=0; var<4; var++){  
 
101 vecs[var].compress(VectorOperation::insert);
 
102 }   
 
106 for(uint var=0; var<4; var++){  
 
110 vecs[var].compress(VectorOperation::add);   
 
111 }   
 
115 for(uint var=0; var<4; var++){  
 
119 vecs[var].compress(VectorOperation::add);   
 
120 }   
 
121 } // loop over owned cells 

The call to compress is a collective operation - that requires all MPI
ranks to participate. But here you are iterating over active cells of a
distributed triangulation. If the number of locally owned cell is not
perfectly divisible by three the program will hang...

All your MPI communication should look like this:

  for (auto : dof_handler.active_cell_iterators()) {
// do something
  } /* end of for loop */

  [...].compress(...) // communicate

Best,
Matthias

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

Very happy to hear that :-)

I'd also love to get some feedback (in case you encounter some missing
functionality - the user base of this particular feature has just
increased from about 2 to 3 ^^)

Best,
Matthias



On Thu, Aug 15, 2019, at 06:53 CDT, Bruno Blais  wrote:

> Dear Matthias,
> I follow your repository and it works perfectly.
> Thanks, I managed to go down from 11 executables to 3... :)!
> Best
> Bruno
>
>
> On Wednesday, 14 August 2019 20:04:03 UTC-4, Matthias Maier wrote:
>>
>>
>> On Wed, Aug 14, 2019, at 18:58 CDT, Bruno Blais > > wrote: 
>>
>> > Dear Matthias, 
>> > If I understand correctly, the only constraint of working this way is 
>> that 
>> > all tests for a single executable must be grouped in a single folder, 
>> and 
>> > that a single folder can test a single executable? 
>> > That's perfect. I will try that tomorrow. 
>>
>> Exactly. 
>>
>> > If I manage to make that work, it is exactly what I was looking for. 
>>
>> Perfect! 
>>
>> Best, 
>> Matthias 
>>

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

On Wed, Aug 14, 2019, at 18:58 CDT, Bruno Blais  wrote:

> Dear Matthias,
> If I understand correctly, the only constraint of working this way is that 
> all tests for a single executable must be grouped in a single folder, and 
> that a single folder can test a single executable?
> That's perfect. I will try that tomorrow.

Exactly.

> If I manage to make that work, it is exactly what I was looking for.

Perfect!

Best,
Matthias

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

On Wed, Aug 14, 2019, at 18:57 CDT, Matthias Maier  wrote:

> On Wed, Aug 14, 2019, at 18:55 CDT, Matthias Maier  wrote:
>
>> [...]
>
> This is actually explained here:
>
>   https://www.dealii.org/current/users/testsuite.html

AND I apparently created a demo repository showcasing all of that:

https://github.com/tamiko/dealii-demo

o_O

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

Wolfgang,

there was a little bit of CMake development behind your back *cough*
*cough* (Luca wanted to have the feature Bruno was asking about).

Best,
Matthias



On Wed, Aug 14, 2019, at 18:16 CDT, Wolfgang Bangerth  
wrote:

> Bruno,
>
>> I am re-implementing some tests on our solvers (following 
>> https://www.dealii.org/developer/developers/testsuite.html#layoutaddtests)
>> Right now, it is really easy to test individual applications with a 
>> combination of executable + output + prm file.
>> We also test with various number of processors.
>> 
>> However, I was wondering if there was way to test a single executable 
>> with more than one .prm file and corresponding output files
>> Ex: test.1.prm test.1.output, test.2.prm, test.2.output where test would 
>> be the executable in question.
>> 
>> Is that something that is feasible in the current framework?
>> If not, what would be your advice on the way to proceed? I could make 
>> identical executables that instantiate the same class, but that 
>> increases linking time for no reasons.
>
> We've generally put the test in a function in the .cc file where that 
> function takes a filename as argument. The main() function then just 
> calls the function with each of the .prm files we have, and the output 
> file will simply contain all of the output of all .prm files 
> concatenated. If you add a .prm file, you'd have to adjust the main() 
> function and the .output file.
>
> This might not be the very most elegant solution, but it's worked 
> reasonably well so far. The idea of the same executable (several .cc 
> files all #includeing the same .h file that contains the test code) of 
> course also works -- in the big picture, compile time and link time for 
> tests are not negligible, but also not a terrible burden.
>
> Best
>   W.
>
>
> -- 
> 
> Wolfgang Bangerth  email: bange...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

On Wed, Aug 14, 2019, at 18:55 CDT, Matthias Maier  wrote:

> [...]

This is actually explained here:

  https://www.dealii.org/current/users/testsuite.html

:-D

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Re: [deal.II] Testing with CTest : Testing the same executable with more than one ".prm" and ".output" combination

[Matthias Maier]

On Wed, Aug 14, 2019, at 13:38 CDT, Bruno Blais  wrote:

> Hello all,
> I am re-implementing some tests on our solvers (following 
> https://www.dealii.org/developer/developers/testsuite.html#layoutaddtests)
> Right now, it is really easy to test individual applications with a 
> combination of executable + output + prm file.
> We also test with various number of processors.
>
> However, I was wondering if there was way to test a single executable with 
> more than one .prm file and corresponding output files
> Ex: test.1.prm test.1.output, test.2.prm, test.2.output where test would be 
> the executable in question.
>
> Is that something that is feasible in the current framework?

For example:

Having in .../tests

  test_1.prm
  test_1.output
  test_2.prm
  test_2.output

with the following tests/CMakeLists.txt file:

  SET(TEST_TARGET my_executable)
  DEAL_II_PICKUP_TESTS()

will define two tests in which the target "my_executable" is run with
the corresponding parameter file. For this two work, you will need to
have an executable target somewhere else, for example under src:

src/CMakeLists.txt:

  ADD_EXECUTABLE(my_executable )
  DEAL_II_SETUP_TARGET(my_executable)

If you want to run more than one executable, you will need multiple
subdirectories (one for each executable).

Best,
Matthias

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Re: [deal.II] Create a LinearOperator with a function instead of a matrix

[Matthias Maier]

A short comment:

On Tue, Jul 16, 2019, at 11:18 CDT, Matthias Maier  wrote:

> struct LeftVector {
> };

> struct RightVector {
> };

These two classes are of course just decoration (showing the minimal
interface a vector has to possess). There is usually no need to define
custom Vector clases.

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Re: [deal.II] Create a LinearOperator with a function instead of a matrix

[Matthias Maier]

Hi,

the following example (which is a simplified version of test
lac/linear_operator_01) should get you started. In short: Simply create
an empty LinearOperator object (with the appropriate template
parameters) and populate the corresponding std::function objects.

Best,
Matthias



#include 
#include 

using namespace dealii;

struct LeftVector {
  typedef double value_type;
  value_type value;

  LeftVector =(value_type new_value)
  {
value = new_value;
return *this;
  }
  LeftVector *=(value_type scale)
  {
value *= scale;
return *this;
  }
  LeftVector /=(value_type scale)
  {
value /= scale;
return *this;
  }
  LeftVector +=(const LeftVector )
  {
value += u.value;
return *this;
  }
  int size() const
  {
return 1;
  }
  std::size_t memory_consumption() const
  {
return 1;
  }
};

struct RightVector {
  typedef double value_type;
  value_type value;

  RightVector =(value_type new_value)
  {
value = new_value;
return *this;
  }
  RightVector *=(value_type scale)
  {
value *= scale;
return *this;
  }
  RightVector /=(value_type scale)
  {
value /= scale;
return *this;
  }
  RightVector +=(const RightVector )
  {
value += u.value;
return *this;
  }
  int size() const
  {
return 1;
  }
  std::size_t memory_consumption() const
  {
return 1;
  }
};

int main()
{
  LinearOperator multiply2;

  multiply2.vmult = [](LeftVector , const RightVector ) {
v.value = 2 * u.value;
  };
  multiply2.vmult_add = [](LeftVector , const RightVector ) {
v.value += 2 * u.value;
  };
  multiply2.Tvmult = [](RightVector , const LeftVector ) {
v.value = 2 * u.value;
  };
  multiply2.Tvmult_add = [](RightVector , const LeftVector ) {
v.value += 2 * u.value;
  };
  multiply2.reinit_range_vector = [](LeftVector &, bool omit_zeroing_values) {
// do nothing
  };
  multiply2.reinit_domain_vector = [](RightVector &, bool omit_zeroing_values) {
// do nothing
  };

  // Small test:

  RightVector u = {4.};
  LeftVector v = {0.};

  multiply2.vmult(v, u);
  std::cout << "2 * " << u.value << " = " << v.value << std::endl;

  multiply2.vmult_add(v, u);
  std::cout << "... + 2 * " << u.value << " = " << v.value << std::endl;

  return 0;
}

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[deal.II] Publications based on deal.II

[Matthias Maier]

All,

as you may know, we try to list all publications based on deal.II at
 http://dealii.org/publications.html
We use this list to justify the effort we spend on writing this software, both
to our universities as well as the funding agencies that support its
development.

In anticipation of the next release, we would like to update this page. If you
have (or know of) a publication that uses deal.II for numerical results and
that isn't already listed, please let us know so we can put it on there. For
this purpose, publications also include MSc, Diploma or PhD theses, or
anything else that may seem appropriate.

We've made the process of submitting entries much simpler than in the
past. Here are a number of ways you can let us know:

* Open a new issue via
  https://github.com/dealii/publication-list/issues/new and just
  copy-paste either a bibtex entry, or just the reference information

* If you want to save us a bit of work, follow the process here:
  https://github.com/dealii/publication-list/blob/master/README.md

* Or email the information directly to me or one of the other principal
  developers.

Thanks
Matthias and Martin (on behalf of the whole deal.II developer team)

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Re: [deal.II] Periodic boundary conditions and the AffineConstraints class

[Matthias Maier]

On Sun, May  5, 2019, at 22:47 CDT, Bruno Blais  wrote:

> I am trying to implement periodic boundary conditions in my CFD solver.
> When looking at the documentation for the make_periodicity_constraints I 
> see that the contraints have to be of type ConstraintsMatrix instead of 
> type AffineConstraints (or another type)

> Is this a current issue or it is better to stick with ConstraintsMatrix for 
> the time being?

You have probably looked at different release versions for both
classes. We have renamed ConstraintMatrix to AffineConstraints (and made
ConstraintMatrix a type alias for AffineConstraints).

The function make_periodicity_constraints will thus of course work with
AffineConstraints.

Best,
Matthias

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Re: [deal.II] Re: dealii compilation on Cray machine

[Matthias Maier]

Cross compilation should work - I have briefly tested it back in
2011 and have written a very minimalistic paragraph about what you have
to do:

  https://www.dealii.org/9.0.0/developers/porting.html

It would be great if someone could verify that it still works :-D

Best,
Matthias



On Fri, Apr  5, 2019, at 14:45 CDT, Bruno Turcksin  
wrote:

> Le ven. 5 avr. 2019 à 14:48, Phani Motamarri  a écrit :
>>
>> No login node is intel-broadwell and compute node is
>> intel-skylake. Problem is that the supercomputer I am compiling on
>> has no way to access compute node (interactive job) directly for
>> compiling. I am not sure if dealii allows for cross compilation.
>
> I've never tried that. Maybe Martin has experience with that?
>
> Bruno

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[deal.II] deal.II at SIAM CSE (Spokane, WA)

[Matthias Maier]

Dear all,

I had a quick chat with Wolfgang today and we were wondering who else is
attending the SIAM CSE conference in Spokane next week?

Also (in very German tradition) we decided that we absolutely have to
get an informal get-together of users and developers going!

Therefore, let's meet on Tuesday evening at 7pm at the "Onion Bar &
Grill" [1].

Please respond (either to the list or via private message) so that I can
get an estimate how many we will be.

Best,
Matthias

[1] No host - have a look at http://theonion.biz/ for menu and pricing

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Re: [deal.II] Warning messages about text-based stub files not syncing with library files when compiling on Mac.

[Matthias Maier]

Dear all,

Just for documenting this publicly:

An alternative workaround is to simply set

  -DDEAL_II_LINKER_FLAGS="-w"

on the command line. This also suppresses the warning (without disabling
lapack and subsequently umfpack).

It would still be nice if we could actually identify the main cause of
this problem. :-D

Best,
Matthias



On Thu, Jan 31, 2019, at 14:42 CST, Jean-Paul Pelteret  
wrote:

> Dear Zachary,
>
> Here’s the relevant part of the detailed.log file:
>
>> #DEAL_II_WITH_LAPACK set up with external dependencies
>> #LAPACK_WITH_64BIT_BLAS_INDICES = OFF
>> #LAPACK_LINKER_FLAGS = 
>> #LAPACK_LIBRARIES = 
>> /System/Library/Frameworks/Accelerate.framework;m
>
>
> So I reckon that if you force deal.II to ignore LAPACK then the
> warning should go away. As I said previously, you should be able to do
> this by cleaning the build directory (at least removing
> CMakeCache.txt), and configuring deal.II with the following settings
>
> cmake -DLAPACK_FOUND=false -DBLAS_FOUND=false  …
>
> and then you’d need to rebuild and reinstall the library. Before you rebuild, 
> may first want to verify that “DEAL_II_WITH_LAPACK = OFF” in the detailed.log.
>
> I hope that this solves the issue.
>
> Best,
> Jean-Paul
>
>> On 31 Jan 2019, at 20:56, Zachary Hardy  wrote:
>> 
>> Attached are the requested files. 
>> 
>> Please let me know what you believe the best remedy would be!
>> 
>> Zachary Hardy '18
>> –––
>> Texas A University
>> B.S. Nuclear Engineering
>> –––
>> –––
>> Cell:(682) 667-3646
>> School Email: zach.ha...@tamu.edu  
>> Personal Email:  zhardy1...@gmail.com  
>> 
>> --
>> 
>> 
>> On Thu, Jan 31, 2019 at 12:26 PM Jean-Paul Pelteret > > wrote:
>> Hi Zachary,
>> 
>> So it looks like maybe the “-framework Accelerate” is what’s being
>> complained about, but I’m not sure. I also don’t have the latest
>> MacOS, so I can’t inspect this myself. But what you could try to do
>> is build deal.II without BLAS and LAPACK support, and this might
>> prevent this from appearing on the link line. To do this I believe
>> that you should pass the following flags to CMake:
>> 
>>   cmake -DLAPACK_FOUND=false -DBLAS_FOUND=false  ...
>> 
>> The two log are files are located in the directory in which you
>> originally built deal.II. It would be great to see those, because
>> then we can inspect which features have been auto detected during
>> the initial configuration.
>> 
>> Best,
>> Jean-Paul
>> 
>> 
>>> On 31 Jan 2019, at 18:58, Zachary Hardy >> > wrote:
>>> 
>>> Hi Jean-Paul,
>>> 
>>> Thanks for the response!
>>> 
>>> I am running on MacOS 10.14.2, with Xcode 10.1. 
>>> 
>>> The verbose output is as follows:
>>> /usr/local/Cellar/cmake/3.13.3/bin/cmake -E cmake_link_script 
>>> CMakeFiles/step-1.dir/link.txt --verbose=1
>>> /Library/Developer/CommandLineTools/usr/bin/c++
>>> -Wl,-search_paths_first -Wl,-headerpad_max_install_names -g -ggdb
>>> CMakeFiles/step-1.dir/step-1.cc.o -o step-1
>>> /Users/ZachHardy/codes/dealii-9.0.1-installed/lib/libdeal_II.g.9.0.1.dylib
>>> -framework Accelerate -lm -lc /usr/lib/libz.dylib
>>> 
>>> Where are the deal.II configuration logs you mentioned located? I am a bit 
>>> new, so I am unsure. 
>>> 
>>> Zachary Hardy '18
>>> –––
>>> Texas A University
>>> B.S. Nuclear Engineering
>>> –––
>>> –––
>>> Cell:(682) 667-3646
>>> School Email: zach.ha...@tamu.edu  
>>> Personal Email:  zhardy1...@gmail.com  
>>> 
>>> --
>>> 
>>> 
>>> On Wed, Jan 30, 2019 at 11:57 PM Jean-Paul Pelteret >> > wrote:
>>> Dear Zachary,
>>> 
>>> I googled this problem and it seems that, dependent on what version
>>> of Xcode and MacOS you’re running, there might be one of two
>>> solutions. Here’s a similar post on the Apple forums that outlines
>>> the two possibilities
>>> .
>>>  The
>>> first possible solution (which may only work for older versions of
>>> Xcode) to remove and reinstall the command line tools. The second
>>> would be that the link line generated by CMake is causing the
>>> issue.
>>> 
>>> This is the selected solution from the Apple forum post
>>> 

Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[Matthias Maier]

On Wed, Oct 24, 2018, at 18:18 CDT, Wolfgang Bangerth  
wrote:

> Chucui,
>
>> My command lines are
>>
>> $cmake /vol7/home/zhaoyucan1016/dealii-9.0.1/dealii-9.0.1  
>> [...]
>> -DCMAKE_INSTALL_PREFIX=/vol7/home/zhaoyucan1016/dealii-9.0.1/build 

This looks odd. You are configuring in-source and installing into the
build directory.

Would you mind to (in addition to Wolfgang's suggestions)

 * download dealii-9.0.1.tar.gz again (verify that the archive is
   complete and not corrupted).

 * unpack the sources to a *new* source directory, say
   /vol7/home/zhaoyucan1016/dealii-9.0.1/sources

 * delete the build directory and simply configure with

   $ mkdir -p /vol7/home/zhaoyucan1016/dealii-9.0.1/build
   $ cd /vol7/home/zhaoyucan1016/dealii-9.0.1/build
   $ cmake ../sources
   $ make ...
   $ make test

 * if above step succeeds, reconfigure by enabling all external packages
   you want.

Best,
Matthias

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Re: [deal.II] Re: After "make install", there are some Errors when install Deal.II-9.0.1

[Matthias Maier]

On Thu, Oct 18, 2018, at 17:48 CDT, David Wells  wrote:

> Hi Chucui,
>
> StraightBoundary was removed in deal.II 9.0; it should not show up in any 
> object files so these errors don't make any sense. Did you use a clean 
> build directory?

Not quite. It got completely removed in the current development version.

In version 9.0.1 it is present in the library. What is surprising though
is the fact that we completely instantiate the class:

grid/tria_boundary.inst.in (on branch dealii-9.0
 18 for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension :  
SPACE_DIMENSIONS)
 19 {   
 
 20 #if deal_II_dimension <= deal_II_space_dimension
 
 21 template class Boundary;
 
 22 template class StraightBoundary; 
 23 #endif  
 
 24 } 

yet, Chucui observes an undefined reference to the constructor. Which is
a bit puzzling.

Chucui, can you please post your full `detailed.log` please? Further,
can you please try to recompile again by (a) unpacking dealii-9.0.1 to a
new directory, and configure and compile in a new build directory?

Best,
Matthias

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Re: [deal.II] Is "-- Configuring incomplete, errors occurred!" OK?

[Matthias Maier]

You have a faulty trilinos installation, in particular the project
configuration file

  /usr/lib/x86_64-linux-gnu/cmake/Trilinos/TrilinosConfig.cmake

is broken (See lines 355 - 2432 of your output file). You can either

 * disable Trilinos for the time being by configuring with
   -DWITH_TRILINOS=OFF,

 * or compile and install a Trilinos version that has a sane
   configuration file and configure with
   -DWITH_TRILINOS=ONF -DTRILINOS_DIR="...",
   (where you replace "..." with a path to your trilinos installation.

Best,
Matthias
   


On Fri, Oct 12, 2018, at 17:36 CDT, Yuxiang Wang  
wrote:

> Thank you Prof. Bangerth for the response!
>
> Actually I kept that window open so I still have the original message. I
> looked into it and saw quite a few optional packages not found, but I
> thought that would be fine. Other than that, I wasn't able to pin-point
> where the problem is. I have attached the entire message sent from cmake as
> attached. I'd really appreciate any feedback!
>
> Best,
> Shawn
>
> On Fri, Oct 12, 2018 at 3:19 PM Wolfgang Bangerth 
> wrote:
>
>> On 10/10/2018 03:33 PM, Yuxiang Wang wrote:
>> >
>> > -- Configuring incomplete, errors occurred!
>> > See also
>> "/mnt/e/dealii/abq1d/dealii/build/CMakeFiles/CMakeOutput.log".
>> >
>> >
>> >
>> > Is this OK and just indicating that there are external dependencies not
>> > met (which is OK for me)? My intent is not to build deal.ii with all
>> > dependencies (I have candi for that), but just to build a minimal build.
>> > I have also attached the CMakeOutput.log and CMakeError.log, just in
>> case.
>>
>> No, these errors are not good.
>>
>> I can't see from the files that you attached what the error really is.
>> But if you run the cmake command again and carefully scroll through the
>> output produced before the "Configuring incomplete" message, you should
>> be able to find which place produced the error message, and that should
>> help figure out why that happened.
>>
>> Best
>>   W.
>>
>>
>> --
>> 
>> Wolfgang Bangerth  email: bange...@colostate.edu
>> www: http://www.math.colostate.edu/~bangerth/
>>
>> --
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>>
>
>
> -- 
> Yuxiang "Shawn" Wang, PhD
> yw...@virginia.edu
> +1 (434) 284-0836

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Re: [deal.II] Compilation problems on RHEL7

[Matthias Maier]

> I believe that you can *force* the cmake script to use the bundled 
> version of TBB over the one on your system. I forgot the flag, but you 
> may be able to find it in the doc/readme.html file.

Correct, -DDEAL_II_FORCE_BUNDLED_THREADS=TRUE does the trick.

Best,
Matthias

  
[1] https://dealii.org/9.0.0/users/cmake.html

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Re: [deal.II] Re: Error during configuration since 9.0.0

[Matthias Maier]

On Wed, May 16, 2018, at 06:11 CDT, Pascal Kraft  wrote:

> Configuration now works if I explicitely switch scalapack off 
> (-DDEAL_II_WITH_SCALAPACK=OFF)... I will try to find out why.

My guess is that scalapack was compiled against a different MPI version.

Best,
Matthias

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[deal.II] Thank you!

[Matthias Maier]

I would like to follow up on the announcement of this release by publicly
saying again how much we appreciate the many contributions from those who
have sent it code, bug reports, fixed grammar and typos, or have helped in
any other way. Many thanks!

The ChangeLog lists at least the following people to whom thanks are due
(though I am certain that I am forgetting someone):

Giovanni Alzetta
Julian Andrej
Rajat Arora
Vishal Boddu
Benjamin Brands
Lucas Campos
Praveen Chandrashekar
Jie Cheng
Emma Cinatl
Conrad Clevenger
Ester Comellas
Sambit Das
Giovanni Di Ilio
Nivesh Dommaraju
Marc Fehling
Niklas Fehn
Menno Fraters
Anian Fuchs
Daniel Garcia-Sanchez
Rene Gassmoeller
Nicola Giuliani
Anne Glerum
Christoph Goering
Alexander Grayver
Samuel Imfeld
Daniel Jodlbauer
Vishal Kenchan
Andreas Kergassner
Eldar Khattatov
Ingo Kligge
Uwe Köcher
Joachim Kopp
Katharina Kormann
Ross Kynch
Konstantin Ladutenko
Tulio Ligneul
Karl Ljungkvist
Santiago Ospina
Alexey Ozeritsky
Dirk Peschka
Simon Puchert
E. G. Puckett
Lei Qiao
Ce Qin
Jonathan Robey
Alberto Sartori
Daniel Shapero
Ben Shields
Simon Sticko
Oliver Sutton
Zhuoran Wang
Xiaoyu Wei
Michał Wichrowski
Julius Witte
Feimi Yu
Weixiong Zheng


Matthias,
on behalf of the whole deal.II developer team:
Daniel Arndt, Wolfgang Bangerth, Denis Davydov, Timo Heister,
Luca Heltai, Guido Kanschat, Martin Kronbichler, Matthias Maier,
Jean-Paul Pelteret, Bruno Turcksin, and David Wells

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signature.asc
Description: PGP signature

[deal.II] deal.II version 9.0 released

[Matthias Maier]

Version 9.0.0 of deal.II, the object-oriented finite element library awarded the
J. H. Wilkinson Prize for Numerical Software, has been released. It is
available for free under an Open Source license from the deal.II homepage at

   https://www.dealii.org/

The major changes of this release are:

- deal.II now requires C++11.

- Support for curved geometries has been improved. Manifold descriptions
  are now exclusively handled via manifold_ids and all compatibility code
  that used boundary indicators has been removed. In addition, every
  function in the GridGenerator namespace now attaches a default manifold
  to the curved parts of the domain described by the generated mesh.

- deal.II now has a dedicated particles module. The module provides a base
  class Particle that represents a particle with position, an ID number and
  a variable number of properties. They are jointly represented by a
  ParticleHandler class that manages the storage and handling of all
  particles.

- deal.II gained dedicated, first-class support for automatic
  differentiation libraries and various capabilities (taped and tapeless
  ADOL-C, Sacado with dynamic forward, reverse, nested dynamic forward, and
  nested reverse support for first and second derivatives).

- Interfaces to a number of additional external libraries has been added.
  deal.II can now be configured with optional support for Assimp,  Gmsh,
  nanoflann, ROL, ScaLAPACK and Sundials.

- This release adds support for computations on GPUs, both, for matrix-based
  and for matrix-free applications. For matrix-based applications, cuSPARSE
  and cuSOLVER are used. Support for matrix-free computation on GPUs is
  preliminary. For now, the evaluation of the operator is limited to meshes
  without hanging-nodes.

- The matrix-free infrastructure in deal.II was significantly overhauled for
  the current release. The major new contribution is the support of face
  integrals through a new class FEFaceEvaluation.

- deal.II has made extensive use of both the Clang-Tidy and Coverity Scan
  static analysis tools for detecting bugs and other issues in the code.
  For example, around 260 issues were detected and fixed using the latter
  tool.

- LinearOperator, a flexible template class that implements the action of a
  linear operator, now supports computations with Trilinos, Schur
  complements, and linear constraints. This class is, as of this release,
  the official replacement for about half a dozen similar (but less
  general) classes, such as FilteredMatrix, IterativeInverse, and
  PointerMatrix.

- A number of non-standard, special-purpose quadrature rules have been
  implemented. Among these are ones for truncating standard formulas to
  simplical domains (QSimplex), singular transformations of the unit cell
  to the unit simplex (QDuffy), composition of simplical quadrature rules
  to a combined rule on the unit cell (QSplit), and transformation of the
  unit square to polar coordinates (QTrianglePolar).

- Support for complex-valued vectors at the same level as real-valued
  vectors.

- A new python tutorial program tutorial-1; as well as updates to step-37.
  In addition, the separate code gallery of deal.II has gained a number of
  new entries.

- Improved support for user-defined run-time parameters: a new
  ParameterAcceptor class has been added to the library. The class is
  intended to be used as a base for any class that wants to handle
  parameters using the ParameterHandler class.

- New caching mechanism for expensive grid computations: we introduced a
  new class GridTools::Cache that caches computationally intensive
  information about a Triangulation. This class allows the user to query
  some of the data structures constructed using functions in the GridTools
  namespace.

- More than 330 other features and bugfixes.

For more information see
- the preprint at https://www.dealii.org/deal90-preprint.pdf
- the list of changes at
  
https://www.dealii.org/developer/doxygen/deal.II/changes_between_8_5_0_and_9_0_0.html

The main features of deal.II are:
- Extensive documentation and 57 fully-functional example programs
- Support for dimension-independent programming
- Locally refined adaptive meshes
- Multigrid support
- A zoo of different finite elements
- Fast linear algebra
- Built-in support for shared memory and distributed parallel computing,
  scaling from laptops to clusters with 100,000+ processor cores
- Interfaces to Trilinos, PETSc, METIS, UMFPACK and other external software
- Output for a wide variety of visualization platforms.


Matthias, on behalf of the deal.II developer team and many contributors.

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Re: [deal.II] Re: Nedelec Elements for unstructured adaptively refined meshes

[Matthias Maier]

On Thu, May 10, 2018, at 15:41 CDT, Bruno Turcksin  
wrote:

> Many people have reported problems see this thread for example
> https://groups.google.com/forum/#!searchin/dealii/nedelec%7Csort:date/dealii/ao-bi_Nh7gc/jHq1qMJlAgAJ
> If I remember correctly, J-P couldn't make Nedelec work for his problem a
> few months ago.

The problem in the thread you cited is for 3D. I am happy to update our
disclaimer for the class.

I am just saying that our statement:

  "For the moment, it is safe to use the element on globally refined
  meshes with consistent orientation of faces."

with the addition "in 2D" and for "lowest and second order" is true :-)

Best,
Matthias

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Re: [deal.II] Release testing (pre-release 9.0.0-rc3)

[Matthias Maier]

Dear all,

Over the weekend we made some progress rooting out quite a number of
bugs. The current release candidate is now v9.0.0-rc3.

It would be great if you could test it on your machine with your typical
configuration. For this update your git repository and switch to the
release branch:

git remote update   
   
git checkout dealii-9.0 
   

Alternatively, download the tagged pre-release at

https://github.com/dealii/dealii/releases/tag/v9.0.0-rc3

If no further regressions show up we plan to do the final release around
Friday, May 11.

Best,
Matthias (on behalf of the whole developer team)


Ps. For the extra paranoid. All release files are signed with one of the
following three PGP keys:

Luca Heltai:C9E1 752D ED3E 32A3 9C6A  66EA C46F 9318 12DB 6E24
Timo Heister:   79CC 65DC BDCE EF67 A483  45B5 55E8 30A3 B1B9 1754
Matthias Maier: 1EE9 7BF6 6221 FC30 69B5  CF90 B5A4 E06F BD3A 97A3


Pps: Timo, your key expired...

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[deal.II] Release preparations

[Matthias Maier]

All,
 

we would like to start the release process for deal.II 9.0 soon. Please let us 
know if you have any last minute things that need to be addressed (bugs,
 
documentation issues, configuration problems, etc.).
 

If you are running the current development version, please update your local
 
working copy and test if everything compiles, especially if you are running a   
 
less common configuration (mac, old compilers, etc.).   
 

Thanks!

Matthias (on behalf of the whole developer team)

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

Status update:

 - We missed the opportunity to do a rebuild for 17.10 [1]
 - In the upcoming 18.04 release everything should be fine again
   (release should be at the end of this month).

Best,
Matthias

[1] https://bugs.launchpad.net/ubuntu/+source/deal.ii/+bug/1729454

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

On Thu, Apr 12, 2018, at 14:48 CDT, Stephen DeWitt  wrote:

> Hi Matthias,
> Ok, that makes sense. 
>
> I think I have both libdeal.ii and libdeal.ii-dev, at least that's what 
> apt-get tells me if I try to install libdeal.ii-dev seperately, although I 
> haven't figured out how to use the dev version rather than the 
> auto-detected release version.

Only the 8.4.1 release is currently packaged for Debian and Ubuntu.

Given the fact that you already installed all dependencies, you can
simply fetch and build the development version via something like:

  $ git clone https://github.com/dealii/dealii
  $ mkdir dealii/build
  $ cd dealii/build
  $ cmake -DWITH_MPI=ON ..
  $ make -j  (where  is the number of parallel builds.)


I will try to fix the binary version installed in Ubuntu.

Thanks for reporting!
Matthias

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Re: [deal.II] Installation error using Ubuntu 17.10 package (missing libsmumps.so)

[Matthias Maier]

Hi there,

The problem is that deal.II's CMake system records the full link
interface of all shared libraries - if a library changes location the
package has to be rebuild (in Ubuntu). If this is indeed the case I will
ask for this to happen.

Did you install just the library libdeal.ii, or also the development
package libdeal.ii-dev?

Best,
Matthias



On Thu, Apr 12, 2018, at 13:19 CDT, Stephen DeWitt  wrote:

> Hello all,
> A PRISMS-PF user recently posted to our forum 
>  that 
> he was having an issue with the deal.ii package he got through apt-get on 
> Ubuntu 17.10. The issue seems to be related to a missing shared object file 
> for MUMPS. I booted up a Ubuntu virtual machine on VirtualBox and saw the 
> same error.
>
> What I did:
>
>1. Installed Ubuntu 17.10 on the VM
>2. Updated apt
>3. Retrieved the deal.ii package ($ sudo apt-get install libdeal.ii)
>4. Found the deal.ii example directory to test the installation and 
>copied it into my home directory
>5. Ran CMake for step-1
>6. Attempted to compile step-1 (both "make release" and "make debug" had 
>the same outcome)
>
> The result:
>
> 
>
> I checked the '/usr/lib/' directory and found a number of MUMPS shared 
> objects (libesmumps-5.1.so, libesmumps.a, libesmumps.so, 
> libptesmumps-5.1.so, libptesmumps.a, and libptesmumps.so), but not 
> "libsmumps.so". I thought that maybe there was a file naming error and 
> renamed a copy of "libesmumps.so" to "libsmumps.so", but then I got a 
> similar error with a different MUMPS shared object. After a few rounds of 
> that, I gave up.
>
> Does anyone know what the issue is and how to solve it? 
>
> Thanks,
> Steve

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Re: [deal.II] TBB error inside FESystem constructor when using development version dealii (dealii-8.5.1 works fine) in debug mode

[Matthias Maier]

On Thu, Mar 22, 2018, at 02:50 CDT, Sambit Das  wrote:

> Hi Matthias,
>
> I reinstalled dealii to use external tbb library and that resolved my issue 
> :) 
> I used the following additional flags:
>
> -DDEAL_II_WITH_THREADS=ON 
> -DTBB_INCLUDE_DIRS="/sw/arcts/centos7/intel/18.1/compilers_and_libraries_2018.1.163/linux/tbb/include/tbb"
>  
> -DTBB_USER_INCLUDE_DIRS="/sw/arcts/centos7/intel/18.1/compilers_and_libraries_2018.1.163/linux/tbb/include/tbb"
>  
> -DTBB_LIBRARIES="/sw/arcts/centos7/intel/18.1/compilers_and_libraries_2018.1.163/linux/tbb/lib/intel64_lin/gcc4.4/libtbb.so"
>
> Thanks a lot for your suggestion.

Very nice!

That's an awkwardly scattered library :-/ - if everything would be in
one place, you could have simply used -DTBB_DIR=... instead.

Best,
Matthias

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Re: [deal.II] TBB error inside FESystem constructor when using development version dealii (dealii-8.5.1 works fine) in debug mode

[Matthias Maier]

Hi,

On Wed, Mar 21, 2018, at 12:56 CDT, Sambit Das  wrote:

> I suspect that when main.cc is compiled standalone it links to the
> dealii's bundled tbb, but when it is compiled with other .cc files it
> links to intel's tbb  as seen from the stacktrace. I have checked my
> dealii installation and it uses bundled tbb. I am using intel/18.0.1,
> openmpi/3.0.0/intel/18.0.1 and cmake/3.5.2 for dealii installation,
> with petsc, slepc and p4est as external libraries.

This is exactly the problem! You cannot mix two TBB libraries (internal
and external in your case, but that doesn't matter) in the link
interface.

Out of curiosity, can you please attach the detailed.log file so that we
can have a look at the full link interface? :-) I am curious where tbb
comes in.

You have to recompile deal.II to use the external TBB library
instead. [1]

Best,
Matthias

[1] I checked - on my systems you minimal example does not show a
problem - nice minimal test case by the way!

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[deal.II] Useless and biased performance check

[Matthias Maier]

Hi all,

I discussed the preconditioned CG method today in class (with SSOR and
optimal relaxation parameter applied to the beloved Laplace problem.)

I was quite surprised that I was able to solve the problem for 1 million
degrees of freedom in about 9 seconds and 80 CG iterations with Julia
(that I use in class). Granted the tolerance for the convergence check
wasn't set very high...

julia> run_test()
8.372644 seconds (1.97 k allocations: 7.065 GiB, 40.45% gc time)
Number of iterations: 80
Error L2: 0.009811802487601433

But bottom line is, I checked how fast I can solve the very same problem
with deal.II's builtin linear algebra:

$ time ./step
DEAL::Number of degrees of freedom: 1048576
DEAL:cg::Starting value 1024.00
DEAL:cg::Convergence step 81 value 0.00899413
./step  8.15s user 0.14s system 210% cpu 3.936 total

(Startup and initalization and assembly - without the solve - takes
roughly 0.9s - So we are more at 3.0s for the solve step. I was simply
too lazy to include a timer.)

That's about as optimal as it gets I'd say.

Code is attached if someone feels the urge to improve above results (or
maybe quickly benchmark the other two linear algebra interfaces we have
:-))

Best,
Matthias

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step.jl
Description: Binary data
#include 
#include 
#include 
#include 
#include 

using namespace dealii;

int main()
{
  constexpr unsigned int m = 1024;
  constexpr unsigned int n = m * m;

  deallog.depth_console(2);
  deallog << "Number of degrees of freedom: " << n << std::endl;


  DynamicSparsityPattern dsp(n);
  for (unsigned int i = 0; i < n; ++i) {
dsp.add(i, i);
if (i < n - 1) {
  dsp.add(i, i + 1);
  dsp.add(i + 1, i);
}
if (i < n - m - 1) {
  dsp.add(i, i + m);
  dsp.add(i + m, i);
}
  }
  SparsityPattern sparsity_pattern;
  sparsity_pattern.copy_from(dsp);

  SparseMatrix system_matrix(sparsity_pattern);
  for (unsigned int i = 0; i < n; ++i) {
system_matrix.set(i, i, 4.);
if (i < n - 1) {
  system_matrix.set(i, i + 1, -1.);
  system_matrix.set(i + 1, i, -1.);
}
if (i < n - m - 1) {
  system_matrix.set(i, i + m, -1.);
  system_matrix.set(i + m, i, -1.);
}
  }

  Vector system_rhs(n);
  for (auto  : system_rhs)
it = 1.0;

  Vector solution(n);

  SolverControl solver_control(1, 1e-2);
  SolverCG<> solver(solver_control);

  constexpr double optimal_omega = 1.993033081086;
  PreconditionSSOR<> preconditioner;
  preconditioner.initialize(system_matrix, optimal_omega);

  solver.solve(system_matrix, solution, system_rhs, preconditioner);
}

Re: [deal.II] LinearOperator -- inverse_operator : Payload for LinearAlgebra::distributed::Vector

[Matthias Maier]

Hi Michał,

It would be helpful if you could sent us a small, minimal example that
shows the problem (in particular, what type is "LevelVectorType" and
"SCPreconditoinMGs", "solver").
The example should be as short as possible and doesn't need to be
functional / or do anything at all - we essentially only need to be able
to figure out the types you try to wrap into the linear_operator object.

Best,
Matthias


On Tue, Feb 13, 2018, at 12:47 CST, Michał Wichrowski  
wrote:

> Dear all, 
> I'm trying to use iterative inverse with distributed deal.II vector. From 
> following lines 
>
> const auto S= linear_operator (mg_sc_matrices[level]);
> const auto Shat = 
> inverse_operator(S,solver,SCPreconditionMGs[level]);
>
>  I get compilation errors:
>
>
> /home/mwichro/lib/deal.II/include/deal.II/lac/linear_operator.h:678:1: 
> note: candidate: template Preconditioner, class Range, class Domain> dealii::LinearOperator Range, Payload> dealii::inverse_operator(const 
> dealii::LinearOperator&, Solver&, const 
> Preconditioner&)
>  inverse_operator(const LinearOperator ,
>  ^
> /home/mwichro/lib/deal.II/include/deal.II/lac/linear_operator.h:678:1: 
> note:   template argument deduction/substitution failed:
> /home/mwichro/deal-ii-projects/StokeMatrixFree/StokesMatrixFree.cc:1051:55: 
> note:   mismatched types 
> ‘dealii::LinearAlgebra::distributed::Vector’ and 
> ‘dealii::internal::LinearOperator::EmptyPayload’
> const auto Shat = 
> inverse_operator(S,solver,SCPreconditionMGs[level]);
>^
> /home/mwichro/deal-ii-projects/StokeMatrixFree/StokesMatrixFree.cc:1051:55: 
> note:   ‘const 
> dealii::LinearOperator dealii::LinearAlgebra::distributed::Vector, 
> dealii::internal::LinearOperator::EmptyPayload>’ is not derived from ‘const 
> dealii::LinearOperator dealii::LinearAlgebra::distributed::Vector >’
> CMakeFiles/StokesMatrixFree.dir/build.make:62: recipe for target 
> 'CMakeFiles/StokesMatrixFree.dir/StokesMatrixFree.cc.o' failed
> make[2]: *** [CMakeFiles/StokesMatrixFree.dir/StokesMatrixFree.cc.o] Error 1
>
>
> I think that proper Payload is needed, but I didn't found right one.
>
> Michał 

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Re: [deal.II] SOURCE_DIR for input data reading in user project unit testing

[Matthias Maier]

On Mon, Feb  5, 2018, at 22:15 CST, Weixiong Zheng  wrote:

> Hello All,
>
> I am trying to get unit test work for my project. It works until reaching 
> the point of reading input data. I tried to specify the directory using 
> getcwd() though it didn't work with ctest. I noticed there was another user 
> having the same issue and the resolution was to use SOURCE_DIR directly in 
> *.cc file. It turns out it was not recognized. Any quick idea how to fix it 
> would be appreciated. Thanks!

SOURCE_DIR is defined when compiling the *.cc file of a test [1]. For
example, if you have the test layout

  my_test.cc
  my_test.output

and you call DEAL_II_PICKUP_TESTS() in that subdirectory. In that case
the my_test.cc file will be compiled with a compiler flag similar to

 -DSOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}

It is not available in any other compilation unit (i.e. *.cc file). Or
for the second class of tests where you specify a *.prm file [2].

Best,
Matthias

[1] The SOURCE_DIR preprocessor definition is set up in line 266 of the
macro cmake/macros/macro_deal_ii_add_test.cmake.

[2] In this case a test gets the full path to the parameter file as
first argument. So simply stripping of the filename should be enough to
get the source directory of the tests.

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Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

[Matthias Maier]

Hi,

is this really the CMakeError.log for the failing configuration (when
MPI is enabled)?

You should have a failing test right at the end with

  Performing C++ SOURCE FILE Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG failed with 
the following output:

  [...]

  Source file was:
  int main(){ return 0; }

Best,
Matthias

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Re: [deal.II] Re: cmake fails when -DDEAL_II_WITH_MPI=ON

[Matthias Maier]

Hi,

On Wed, Jan 24, 2018, at 11:17 CST, Eldar Khattatov  
wrote:

> I forgot to mention, I tried both the development and 8.5.1versions of 
> deal.II and the errors are the same.

The test in question tries to compile a very minimalistic

  int main () { return 0; }

with the given compiler, link interface and linker options.

Have a look at /CMakeFiles/CMakeErrors.log the detailed
compiler output of what exactly fails should be at the very bottom.

I am curious what is going wrong.

Best,
Matthias

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Re: [deal.II] Re: Creation of own CMakeLists.txt

[Matthias Maier]

On Thu, Jan 11, 2018, at 08:52 CST, "'Maxi Miller' via deal.II User Group" 
 wrote:

> An initial investigation shows that DEAL_II_INVOKE_AUTOPILOT calls 
> add_executable, thus I placed the additional libraries after the macro. Is 
> that the correct way to solve it?

The best way would be to simply not use the DEAL_II_INVOKE_AUTOPILOT
macro :-)

A simple skeleton would be [1]:

  CMAKE_MINIMUM_REQUIRED(VERSION 3.0.0)
  FIND_PACKAGE(deal.II 8.5.0 REQUIRED
HINTS ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
)
  DEAL_II_INITIALIZE_CACHED_VARIABLES()

  PROJECT(myproject)

  # other FIND_PACKAGE calls

  # other libraries, etc.

  ADD_EXECUTABLE(main main.cc)
  DEAL_II_SETUP_TARGET(main)
  TARGET_LINK_LIBRARIES(main ...)


You lose the automatic "debug", "release" and "run" targets - if you
want to get those back, simply add the following statements [2], [3].

Best,
Matthias

[1] https://www.dealii.org/8.5.0/users/cmakelists.html
[2] https://www.dealii.org/8.5.0/users/cmakelists.html#cmakesimple.build_type
[3] https://www.dealii.org/8.5.0/users/cmakelists.html#cmakesimple.run

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Re: [deal.II] New deal.II 8.5.1 is 20% slower than deal.II 8.0.0

[Matthias Maier]

Would you mind sending us the "detailed.log" files?

Best,
Matthias


On Tue, Dec 26, 2017, at 12:35 CST, drgulev...@gmail.com wrote:

> Thanks. This is strange as I still get 15-20% consistently better results 
> in favor of older versions
>  on three different machines already. Two more studies on other systems 
> attached below.
>
> TEST: Step-23 (integration time modified from 5 to 150, output suppressed)
> CMAKE_BUILD_TYPE: "Release".
>
> MACHINE 1: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
> $ cat /etc/redhat-release
> CentOS Linux release 7.4.1708 (Core)
> $ gcc --version
> gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
>
> deal v8.1.0 (built and installed from source):
>
> $ time ./step-23
> real1m23.768s
> user5m46.080s
> sys0m4.079s
>
> deal v8.5.1 (built and installed from source):
>
> $ time ./step-23
> real1m42.416s
> user5m37.018s
> sys0m4.340s
>
> MACHINE 2: Intel(R) Xeon(R) CPU X5690  @ 3.47GHz
> $ lsb_release -a
> Description:Ubuntu 14.04.5 LTS
> $ gcc --version
> gcc (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4
>
> deal v8.1.0 (built and installed from source):
>
> $ time ./step-23
> real2m49.114s
> user11m41.429s
> sys0m48.882s
>
> deal v8.5.1 (built and installed from source):
> $ time ./step-23
> real3m20.583s
> user10m54.850s
> sys2m18.989s
>
>
> On Tuesday, December 26, 2017 at 6:08:17 PM UTC+3, Matthias Maier wrote:
>>
>> Hi, 
>>
>> I get relatively comparable results for both versions: 
>>
>> dev: ./step-23  55.55s user 1.64s system 131% cpu 43.637 total 
>> 8.0: ./step-23  55.85s user 1.48s system 129% cpu 44.130 total 
>>
>> Is this the unmodified step-23 tutorial program? 
>>
>> For measuring performance regressions a total runtime of less than 5 
>> seconds doesn't say that much. Never versions allocate and precompute 
>> quite a bunch of stuff upfront which might result in a small (problem 
>> independent) fixed runtime overhead (of a second or less). 
>>
>> Best, 
>> Matthias 
>>
>>
>>
>> On Tue, Dec 26, 2017, at 05:52 CST, drgul...@gmail.com  
>> wrote: 
>>
>> > Deal.II 8.5.1 seems to be 20% slower than 8.0.0. This is the timing I 
>> get 
>> > when running the Step-23 tutorial (output to screen and vtk is 
>> suppressed): 
>> > 
>> > deal.II version 8.0.0: 
>> > 
>> > $ time ./step-23 
>> > Number of active cells: 16384 
>> > Number of degrees of freedom: 16641 
>> > 
>> > real0m3.432s 
>> > user0m6.320s 
>> > sys0m0.612s 
>> > 
>> > deal.II version 8.5.1: 
>> > 
>> > $ time ./step-23 
>> > Number of active cells: 16384 
>> > Number of degrees of freedom: 16641 
>> > 
>> > real0m4.430s 
>> > user0m7.080s 
>> > sys0m0.492s 
>> > 
>> > In general, I get about 20% slow down for my own code when upgrading 
>> from 
>> > 8.0.0 to 8.5.1. What is the reason of such a slow down? Does the deal.II 
>> > follow the right direction given new versions become gradually slower?! 
>>

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