Re: [deal.II] Re: intel 19 compilation failure
Hi, I returned to this today and using the installed PETSc module (which links against mkl_blacs_intelmpi_lp64 [not ilp]), setting the paths for the BLAS_DIR and LAPACK_DIR CMake variables in dealii.package, allowed for a complete installation and passing the quick_tests. Thanks Bruno ( and also at FZJ to Lucas and Marc for their advice), Best, Sean On Thursday, February 14, 2019 at 5:04:17 PM UTC+1, Sean McGovern wrote: > > OK. I will look into it. > Thanks, Bruno! > > On Thursday, February 14, 2019 at 4:49:35 PM UTC+1, Bruno Turcksin wrote: >> >> Sean, >> >> It looks like you need to link against blacs (mkl_blacs_intelmpi_ilp64) >> see here >> <https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/698061> >> >> but I don't know where you need to add the flag in CANDI :( >> >> Best, >> >> bruno >> >> Le jeu. 14 févr. 2019 à 10:35, Sean McGovern a écrit : >> >>> Hi Bruno! >>> Attached is the configuration log. >>> >>> I use MKL for petsc and p4est. >>> >>> Thanks, >>> Sean >>> >>> On Thursday, February 14, 2019 at 4:22:39 PM UTC+1, Bruno Turcksin wrote: >>>> >>>> Sean, >>>> >>>> On Thursday, February 14, 2019 at 9:48:56 AM UTC-5, Sean McGovern wrote: >>>>> >>>>> I am trying to install dealii with petsc and p4est on the cluster in >>>>> Juelich with intel 19. It has been running with intel 18. As others have >>>>> suggested, I have turned DEAL_II_WITH_CXX17=OFF, I have used the flag >>>>> "-xhost", but I run into errors relating to vectorization (ALTIVEC). I >>>>> have used the bundled tbb, and using the loaded tbb module, I get the >>>>> errors in the log attached. >>>>> >>>> This error is normal, we check for ALTIVEC which you don't have on your >>>> machine (ALTIVEC is only for IBM machine) and since we can't find >>>> altivec.h, we disable the altivec vectorization. What bothers me more is >>>> that it seems that you have a problem with MKL: >>>> >>>> /gpfs/software/juwels/stages/2018b/software/imkl/2019.0.117-ipsmpi-2018b/mkl/lib/intel64/libmkl_core.a(mkl_get_mpi_wrappers_static.o):mkl_get_mpi_wrappers.c:function >>>> mkl_serv_get_mpi_wrappers: error: undefined reference to >>>> 'MKLMPI_Get_wrappers' >>>> >>>> >>>> What's the configuration you are trying to use? >>>> >>>> Best, >>>> >>>> Bruno >>>> >>> -- >>> 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 >>> --- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "deal.II User Group" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/dealii/plJ81xhINQ0/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> dealii+un...@googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: intel 19 compilation failure
OK. I will look into it. Thanks, Bruno! On Thursday, February 14, 2019 at 4:49:35 PM UTC+1, Bruno Turcksin wrote: > > Sean, > > It looks like you need to link against blacs (mkl_blacs_intelmpi_ilp64) > see here > <https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/698061> > > but I don't know where you need to add the flag in CANDI :( > > Best, > > bruno > > Le jeu. 14 févr. 2019 à 10:35, Sean McGovern > a écrit : > >> Hi Bruno! >> Attached is the configuration log. >> >> I use MKL for petsc and p4est. >> >> Thanks, >> Sean >> >> On Thursday, February 14, 2019 at 4:22:39 PM UTC+1, Bruno Turcksin wrote: >>> >>> Sean, >>> >>> On Thursday, February 14, 2019 at 9:48:56 AM UTC-5, Sean McGovern wrote: >>>> >>>> I am trying to install dealii with petsc and p4est on the cluster in >>>> Juelich with intel 19. It has been running with intel 18. As others have >>>> suggested, I have turned DEAL_II_WITH_CXX17=OFF, I have used the flag >>>> "-xhost", but I run into errors relating to vectorization (ALTIVEC). I >>>> have used the bundled tbb, and using the loaded tbb module, I get the >>>> errors in the log attached. >>>> >>> This error is normal, we check for ALTIVEC which you don't have on your >>> machine (ALTIVEC is only for IBM machine) and since we can't find >>> altivec.h, we disable the altivec vectorization. What bothers me more is >>> that it seems that you have a problem with MKL: >>> >>> /gpfs/software/juwels/stages/2018b/software/imkl/2019.0.117-ipsmpi-2018b/mkl/lib/intel64/libmkl_core.a(mkl_get_mpi_wrappers_static.o):mkl_get_mpi_wrappers.c:function >>> mkl_serv_get_mpi_wrappers: error: undefined reference to >>> 'MKLMPI_Get_wrappers' >>> >>> >>> What's the configuration you are trying to use? >>> >>> Best, >>> >>> Bruno >>> >> -- >> 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 >> --- >> You received this message because you are subscribed to a topic in the >> Google Groups "deal.II User Group" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/plJ81xhINQ0/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> dealii+un...@googlegroups.com . >> For more options, visit https://groups.google.com/d/optout. >> > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: intel 19 compilation failure
Hi Bruno! Attached is the configuration log. I use MKL for petsc and p4est. Thanks, Sean On Thursday, February 14, 2019 at 4:22:39 PM UTC+1, Bruno Turcksin wrote: > > Sean, > > On Thursday, February 14, 2019 at 9:48:56 AM UTC-5, Sean McGovern wrote: >> >> I am trying to install dealii with petsc and p4est on the cluster in >> Juelich with intel 19. It has been running with intel 18. As others have >> suggested, I have turned DEAL_II_WITH_CXX17=OFF, I have used the flag >> "-xhost", but I run into errors relating to vectorization (ALTIVEC). I >> have used the bundled tbb, and using the loaded tbb module, I get the >> errors in the log attached. >> > This error is normal, we check for ALTIVEC which you don't have on your > machine (ALTIVEC is only for IBM machine) and since we can't find > altivec.h, we disable the altivec vectorization. What bothers me more is > that it seems that you have a problem with MKL: > > /gpfs/software/juwels/stages/2018b/software/imkl/2019.0.117-ipsmpi-2018b/mkl/lib/intel64/libmkl_core.a(mkl_get_mpi_wrappers_static.o):mkl_get_mpi_wrappers.c:function > mkl_serv_get_mpi_wrappers: error: undefined reference to > 'MKLMPI_Get_wrappers' > > > What's the configuration you are trying to use? > > Best, > > Bruno > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout. -- This is CMake 3.13.0 -- -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/setup_external_macros.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_add_flags.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_check_compiler_setup.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_check_cxx_compiler_bug.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_check_mpi_interface.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_clear_cmake_required.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_configure_feature.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_add_definitions.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_add_library.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_add_test.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_find_file.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_find_library.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_find_path.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_find_program.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_insource_setup_target.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_invoke_autopilot.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_package_handle.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_pickup_tests.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_query_git_information.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_deal_ii_setup_target.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_decorate_with_stars.cmake -- Include /p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/unpack/deal.II-master/cmake/macros/macro_enable_if_links.cmake -- Include /p/proj
[deal.II] intel 19 compilation failure
Hi all,
I am trying to install dealii with petsc and p4est on the cluster in
Juelich with intel 19. It has been running with intel 18. As others have
suggested, I have turned DEAL_II_WITH_CXX17=OFF, I have used the flag
"-xhost", but I run into errors relating to vectorization (ALTIVEC). I
have used the bundled tbb, and using the loaded tbb module, I get the
errors in the log attached.
Thanks for any advice on where to look next.
Best,
Sean
--
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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Performing C++ SOURCE FILE Test DEAL_II_HAVE_ALTIVEC failed with the following
output:
Change Dir:
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_81f3e/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_81f3e.dir/build.make
CMakeFiles/cmTC_81f3e.dir/build
gmake[1]: Entering directory
`/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_81f3e.dir/src.cxx.o
/gpfs/software/juwels/stages/2018b/software/psmpi/5.2.1-1-iccifort-2019.0.117-GCC-7.3.0/bin/mpicxx
-DDEAL_II_HAVE_ALTIVEC -xhost -o CMakeFiles/cmTC_81f3e.dir/src.cxx.o -c
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx(3):
error: #error directive: "__ALTIVEC__ flag not set, no support for Altivec"
#error "__ALTIVEC__ flag not set, no support for Altivec"
^
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx(5):
catastrophic error: cannot open source file "altivec.h"
#include
^
compilation aborted for
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx
(code 4)
gmake[1]: *** [CMakeFiles/cmTC_81f3e.dir/src.cxx.o] Error 4
gmake[1]: Leaving directory
`/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_81f3e/fast] Error 2
Return value: 1
Source file was:
#ifndef __ALTIVEC__
#error "__ALTIVEC__ flag not set, no support for Altivec"
#endif
#include
#undef vector
#undef pixel
#undef bool
int main()
{
__vector double a, b, data1, data2;
const int n_vectors = sizeof(a)/sizeof(double);
double * ptr = reinterpret_cast(&a);
ptr[0] = static_cast(1.0);
for (int i=1; i(2.25));
data1 = vec_add (a, b);
data2 = vec_mul (b, data1);
ptr = reinterpret_cast(&data2);
int return_value = 0;
if (ptr[0] != 7.3125)
return_value += 1;
for (int i=1; i(-1.0));
data1 = vec_abs(vec_mul (b, data2));
vec_vsx_st(data1, 0, ptr);
b = vec_vsx_ld(0, ptr);
ptr = reinterpret_cast(&b);
if (ptr[0] != 7.3125)
return_value += 4;
for (int i=1; i
int main()
{
std::cyl_bessel_j(1.0, 1.0);
std::cyl_bessel_jf(1.0f, 1.0f);
std::cyl_bessel_jl(1.0, 1.0);
}
Performing C++ SOURCE FILE Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED
failed with the following output:
Change Dir:
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_2812f/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_2812f.dir/build.make
CMakeFiles/cmTC_2812f.dir/build
gmake[1]: Entering directory
`/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_2812f.dir/src.cxx.o
/gpfs/software/juwels/stages/2018b/software/psmpi/5.2.1-1-iccifort-2019.0.117-GCC-7.3.0/bin/mpicxx
-DDEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED -xhost -fpic -ansi -w2
-diag-disable=remark -wd21 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279
-wd327 -wd383 -wd981 -wd1418 -wd1478 -wd1572 -wd2259 -wd2536 -wd2651 -wd3415
-wd15531 -wd111 -wd128 -wd185 -wd186 -wd280 -qopenmp-simd -std=c++14 -Werror
-Wno-unused-command-line-argument -o CMakeFiles/cmTC_2812f.dir/src.cxx.o -c
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx
icpc: command line warning #10148: option '-Wno-unused-command-line-argument'
not supported
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/src.cxx(18):
error: identifier "bar" is undefined
using bar __attribute__((deprecated)) = foo<2>;
^
/p/project/cesmtst/esmtst19/18b_dev_deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CM
Re: [deal.II] cumulative displacement / deformation
Hi Jane, Hi Wolfgang, The case that I was looking at was to solve for a velocity field variable. As Wolfgang nicely describes, the power of the idea is to take a line integral equation and by operating on the equality, to formulate it as a PDE. So, if you are interested in a displacement field as the solution variable then, properly formulated, that should work fine with the technique of moving from integral to differential formulation. A quick remark: This line of your attached code does not, on the face of it, make sense to me dimensionally. cell->vertex(v) += vertex_displacement*timestep_size; For a displacement to add to a vertex coordinate [L], shouldn't we expect a velocity [L/T] on the right hand side to be mulitiplied by dt [T]? Best, Sean On Monday, October 15, 2018 at 4:46:50 PM UTC+2, Wolfgang Bangerth wrote: > > On 10/15/2018 05:27 AM, Jane Lee wrote: > > > > I see what you mean though I am confused how you got to the equation for > > the displacement? Surely there needs to be some time dependence > > somewhere at least for it to make sense dimensionally? > > I may have used the wrong terminology and forgotten a factor of delta t. > But if you start here: > > > > However, I realised that this moves each vertex by the velocity > > at that point, > > > but I need, for example, a vertex on the top boundary to have > > moved as much as > > > the ones below it has moved as well as the velocity at the points > > itself. > > ...then you get to an equation like this: > > > d(x,y,z) = \int_z^0 v(x,y,zeta) dzeta > > ...where d(...) is the *cumulative displacement* by which you want to > move the vertex and v(...) is the individual displacement you get. If > you differentiate the formula by z, then you get > > d/dz d(x,y,z) = -v(x,y,z) > > which is the advection equation I mentioned in my previous post, and for > which it is substantially easier to solve than to compute the integral. > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Old Mac Users wanted.
Hi Luca, I am running OSX 13.3 with XCode 9.2 (9C40b) and clang version 9.0.0 (clang-900.0.39.2). With that package, I was able to successfully run some examples through the app's terminal. Best, Sean On Saturday, May 19, 2018 at 10:10:24 AM UTC+2, Luca Heltai wrote: > > Dear All, > > I just uploaded a version of deal.II 9.1.0pre (master version of > yesterday) here: > > https://github.com/luca-heltai/dealii/releases/tag/v9.1.0-pre-1 > > This was compiled with clang 6.0.0, downloaded from the official llvm > website. The compiler is included in the package, making this a good > candidate for users of older Macs that did not (or do not want to) update > Xcode to get Apple clang 9.1.0. > > This package should work for you too. If there is anyone that has not > updated yet to Apple clang 9.1.0, can you try to see if this package works > for you? > > Thanks! > Luca. > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Compile my first program
Good to hear. The whole suite of step tutorials is very valuable. Best, Sean On Friday, February 2, 2018 at 3:45:23 PM UTC+1, simone cammarasana wrote: > > Hello Sean, > > well it works perfectly in this way, thank you. > > Simone > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: Compile my first program
Hi Simone, Were you able to successfully compile one of the "step" programs? https://www.dealii.org/developer/doxygen/deal.II/step_1.html does a nice job describing the approach using cmake. Modifying the CMakeLists.txt of one of the step tutorials for your own user code is common. Best, Sean On Friday, February 2, 2018 at 2:55:35 PM UTC+1, simone cammarasana wrote: > > Hello everybody, > > I have just started using Deal II (target is to interface it with PETSc) > and I've successfully installed it..also make test went good. > > Here is my configuration: > cmake -DCMAKE_INSTALL_PREFIX=~/dealii-8.5.1/build ~ -DEAL_II_WITH_MPI=ON - > DPETSC_DIR=~~/petsc -DPETSC_ARCH=arch-linux2-c-opt > > > > Now I have a very simple question..how can I compile my first program? > I've tried searching into this database but I have not found an > appropriate answer. > > I've reached, after several trials, a single line compilation like below > (I''ve added second include because of a compiling error in "include > " > > g++ myProg.cc -o myProg.out -I~/build/include -I~~/boost1.60.0-0/include/ > -std=c++11 > > but I still get an error.. > file not present > # include > > Probably I'm completly missing the approach.. > Can anybody give me some suggestion? > > thanks a lot > Simone > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] macOS High Sierra (10.3) and CMake not finding MPI Library
Thanks, Wolfgang. Using CMake 3.9.6 seems to be working fine. Best, Sean On Monday, January 1, 2018 at 1:59:01 PM UTC-5, Wolfgang Bangerth wrote: > > On 01/01/2018 10:16 AM, Sean McGovern wrote: > > > > > > In the past, I've used candi and homebrew successfully on the mac > (Sierra > > 10.2) to install v8.5.1. Now trying to install 9.0.0-pre on 10.3, I've > run > > into a CMake issue. > > I am trying to install deal.II master on High Sierra with XCode (Version > 9.2 > > (9C40b)) and Apple LLVM version 9.0.0 (clang-900.0.39.2). I'm using > CMake 3.10.1. > > Yes, there is a problem with cmake 3.10 that we haven't fixed yet: >https://github.com/dealii/dealii/issues/5510 > > Can you downgrade to an earlier version of cmake? > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] macOS High Sierra (10.3) and CMake not finding MPI Library
Hi all, Happy New Year! In the past, I've used candi and homebrew successfully on the mac (Sierra 10.2) to install v8.5.1. Now trying to install 9.0.0-pre on 10.3, I've run into a CMake issue. I am trying to install deal.II master on High Sierra with XCode (Version 9.2 (9C40b)) and Apple LLVM version 9.0.0 (clang-900.0.39.2). I'm using CMake 3.10.1. The configuration fails on setting up MPI. I have tried with both open-mpi and mpich (--force uninstalling between, so 1 mpi implementation at a time). One form of the relevant error message is below: --- -- Include /Users/dhilbert/dev-deal.ii-candi/tmp/unpack/deal.II-master/cmake/configure/configure_1_mpi.cmake -- Performing Test MPI_HAVE_MPI_SEEK_SET -- Performing Test MPI_HAVE_MPI_SEEK_SET - Success -- Found MPI_MPI_H -- MPI_VERSION: 3.1 -- MPI_LIBRARIES: /usr/local/Cellar/mpich/3.2.1/lib/libmpicxx.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libmpi.dylib;/usr/local/Cellar/mpich/3.2.1/lib/libpmpi.dylib;/usr/local/lib/libmpi.dylib -- MPI_INCLUDE_DIRS: *** Required variable "MPI_CXX_INCLUDE_PATH" empty *** -- MPI_USER_INCLUDE_DIRS: *** Required variable "MPI_CXX_INCLUDE_PATH" empty *** -- MPI_CXX_FLAGS: -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -- MPI_LINKER_FLAGS: -Wl,-flat_namespace -Wl,-commons,use_dylibs -- Could NOT find MPI -- DEAL_II_WITH_MPI has unmet external dependencies. CMake Error at cmake/configure/configure_1_mpi.cmake:77 (MESSAGE): Could not find any suitable mpi library! Please ensure that an mpi library is installed on your computer and set CMAKE_CXX_COMPILER to the appropriate mpi wrappers: $ CXX=".../mpicxx" cmake <...> $ cmake -DCMAKE_CXX_COMPILER=".../mpicxx" <...> Or with additional C and Fortran wrappers (recommended!): $ CC=".../mpicc" CXX=".../mpicxx" F90=".../mpif90" cmake <...> $ cmake -DCMAKE_C_COMPILER=".../mpicc"\ -DCMAKE_CXX_COMPILER=".../mpicxx"\ -DCMAKE_Fortran_COMPILER=".../mpif90"\ <...> Call Stack (most recent call first): /Users/dhilbert/dev-deal.ii-candi/tmp/build/deal.II-master/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1 (FEATURE_MPI_ERROR_MESSAGE) cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE) cmake/macros/macro_configure_feature.cmake:267 (EVALUATE_EXPRESSION) cmake/configure/configure_1_mpi.cmake:94 (CONFIGURE_FEATURE) cmake/macros/macro_verbose_include.cmake:19 (INCLUDE) CMakeLists.txt:124 (VERBOSE_INCLUDE) - It has certainly found the mpicc/cxx/f compiler wrappers. It finds some of the MPI Libraries, though it says the CXX_INCLUDE_PATH is unset. It says this despite my having tried to set the CMakeCache variable explicitly with ~/dev-deal.ii-candi/tmp/build/deal.II-master$ cmake -DMPI_INCLUDE_DIRS="/usr/local/Cellar/mpich/3.2.1/include/" -DMPI_CXX_INCLUDE_PATH="/usr/local/Cellar/mpich/3.2.1/include/" . I've tried changing MPI_CXX_SKIP_MPICXX to On or Off (but I don't really know what that flag means). Could it be a cmake macro issue on the new version of the OS? Or have I missed something? Dependencies with mpi like p4est, petsc, trilinos have installed fine. Thanks for the help! Best, Sean -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] Re: deal.II's birthday
Happy Birthday! (belated) >From my experience, I'd say it's a testament to top-notch technical know-how, as well as the desire and ability to educate and communicate well. I'd like to express my gratitude to Wolfgang and the community. Best, Sean On Saturday, November 25, 2017 at 2:25:23 AM UTC+1, Wolfgang Bangerth wrote: > > > All, > today 20 years ago -- on November 24 1997 -- is the date of the first > commit > to the deal.II repository. If you had asked me at the time whether I > thought > that (i) deal.II would still exist 20 years later, (ii) anyone would > actually > care about the first point, (iii) people would still use C++, or (iv) I > would > still be in academia today, I would not have had an answer. I might have > said > "no" to any of these questions. > > But deal.II is still around, with more users and developers than ever > before: >http://dealii.org/publications.html >http://dealii.org/authors.html >https://github.com/dealii/dealii/graphs/contributors > > What a ride it's been! And what a community we've built -- thanks to all > of > you who have participated, in one way or the other! > > To many more years! >Wolfgang > > -- > > Wolfgang Bangerth email: bang...@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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] integrating a scalar in a vertical column (e.g. finding hydrostatic pressure at a point)
Hi Wolfgang, Thanks for the wonderfully clear answer. For my function f, I can basically treat the line integral like a "normal" volume integral, setting the direction using the delta functions. This would be the right approach for a distributed adaptive setting as well, no? It makes no assumptions about cell layout and is defined at the functional level. If I may ask a follow up with an added wrinkle - it concerns the interplay of material_id (cells) and functions: What if I don't have the form of f? In my case, I have been using the material_id marker at the cell level to indicate different materials, that in the assembly loops, then provide different coefficient values to the local sums. Suppose that the distribution of these cell identities(material_id) is updated based on the results of some FE field calculations. Then given the configuration of the cells at that time step, I would like to do the line integral (essentially compute the weight of the material above the point), and go on to another FE solve. However, I do not have a functional form to put in my line integral. I don't know how to describe the weight function globally, but locally (at the cell level) it is defined. Would it be possible to: 1) somehow turn the distribution of cell->material_id over my mesh into a Function object (via the characteristic function)? or 2) enumerate the material property (i.e., densities) into a vector defined at quadrature points over the whole mesh? Thanks for your help. Best, Sean PS "The material of a cell may be used during matrix generation in order to implement different coefficients in different parts of the domain. It is not used by functions of the grid and dof handling libraries." [1] Generally, I am hoping to better understand the relationship of the mesh( things like looping over cells, querying for the local properties, ...) and the Function object class which returns values based on the spatial position. [1]https://www.dealii.org/developer/doxygen/deal.II/classTriangulation.html On Monday, June 5, 2017 at 10:55:48 PM UTC+2, Wolfgang Bangerth wrote: > > On 06/02/2017 07:37 AM, Sean McGovern wrote: > > > > What's a good way to integrate a quantity in the vertical direction? For > > example, how do I find the weight of water above a point (assuming > variable > > density, so that the integration is necessary)? > > In a structured regular mesh, I would fix the x and y coordinates of the > grid > > and iterate over the z coordinate adding up the different weight > contributions > > per cell. > > What would the way to emulate this in dealii be (in a globally refined > context)? > > What you want to do (a line integral) is, in general, a difficult > operation on > non-uniform meshes. As with all integrals, you will want to approximate it > with some kind of quadrature rule, which would require you to evaluate the > solution at quadrature points that are located *somewhere*, as far as the > mesh > is concerned. You can do this evaluation with VectorTools::point_value(), > and > this will work if you use a relatively small number of quadrature points > located along your vertical line. But the function is expensive if you > need a > lot of quadrature points. > > An alternative is to rewrite the line integral as a volume integral. For > example, your integral > >\int_a^b f(x0,y0,z) dz > > (where 'f' is a function of your finite element solution, and x0,y0 are > the > coordinates of the vertical line you're trying to integrate along) is > equal to > >\int\int\int f(x,y,z) \delta(x-x0) \delta(y-y0) dz dy dz > > If you replace the delta functions by an appropriate approximation (e.g., > a > Gaussian with a width equal to several times the mesh size), then the > integral > is approximated by the volume integral > >\int\int\int f(x,y,z) K(x,y,z) dz dy dz > > with some kernel K(x,y,z). This is now just any other ordinary volume > integral > where K(x,y,z) is explicitly given. It is easy to integrate on a finite > element mesh. > > Best > W. > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] integrating a scalar in a vertical column (e.g. finding hydrostatic pressure at a point)
Hello, What's a good way to integrate a quantity in the vertical direction? For example, how do I find the weight of water above a point (assuming variable density, so that the integration is necessary)? In a structured regular mesh, I would fix the x and y coordinates of the grid and iterate over the z coordinate adding up the different weight contributions per cell. What would the way to emulate this in dealii be (in a globally refined context)? Cheers, Sean -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] nonlinear solvers (e.g., petsc snes)
Hi Wolfgang, Thanks very much for your comments. I realize that nonlinearity manifests itself in various ways, with various possibilities for addressing it. Also, I found revisiting your video lectures 31.x to be valuable. > That said, you can always extract the PETSc objects from the PETScWrappers objects, and pass that to SNES. The same is possible for Trilinos. So you can always use these two packages already, without the need for any wrappers in deal.II. > I did not realize that this is possible. Best, Sean On Sunday, May 7, 2017 at 11:12:31 PM UTC+2, Wolfgang Bangerth wrote: > > > Sean, > > > I am interested in solving a nonlinear problem with Newton's method. I > would > > describe it as a heat equation with a nonlinear diffusion coefficient, > thus > > building on step-15, 25 and 26. > > I've found step-15, step-25 and step-57 very helpful for understanding > how to > > set up the linear system for the residual and solve it at each step of > the > > nonlinear iteration. > > > > 1) Is that the best approach to take in dealii, i.e. compute the > residual > > manually and manually do the nonlinear iteration until convergence is > satisfied? > > If you have a relatively simple nonlinearity, and if you know that you > don't > need things such as line search, then yes that is the way many of us do > things. > > > > In step-25, the scalar time-dependent system admits a straightforward > > expression for F'(u, delta_u) from F(u). > > In step-33, an automatic differentiation package, trilinos::sacado, is > used to > > facilitate the computation of the vector-valued conservation law's > "terrible > > beast" of a Jacobian. > > For computing the residual, automatic differentiation seems like it can > help > > in certain situations. > > Yes. If the nonlinearity is awkward, then it's the more reliable way to > compute its derivatives. > > > > 2) Are there other options to help "automate" the nonlinear treatment? > For > > example, does anyone have any experience with the petsc nonlinear > solvers (snes)? > > For example, might it allow to easily switch between a Picard > (fixed-point) > > loop, if the Newton loop does not converge? > > > > I note that in the PETScWrappers namespace there are no entries related > to the > > snes package. Why/why not? > > I don't think there is a particular reason. Like most open source > projects, > people implement things to "scratch an itch". Nobody so far felt the need > to > use SNES (or the Trilinos equivalent 'nox'), or had the need badly enough > to > write a comprehensive interface. That doesn't mean that that would be a > bad > idea -- in fact, I think that using SNES or nox is a much better idea than > doing things yourself. > > That said, you can always extract the PETSc objects from the PETScWrappers > objects, and pass that to SNES. The same is possible for Trilinos. So you > can > always use these two packages already, without the need for any wrappers > in > deal.II. > > Best > W. > > > -- > > Wolfgang Bangerth email: bang...@colostate.edu > > www: http://www.math.colostate.edu/~bangerth/ > > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] nonlinear solvers (e.g., petsc snes)
Dear dealii community, I am interested in solving a nonlinear problem with Newton's method. I would describe it as a heat equation with a nonlinear diffusion coefficient, thus building on step-15, 25 and 26. I've found step-15, step-25 and step-57 very helpful for understanding how to set up the linear system for the residual and solve it at each step of the nonlinear iteration. 1) Is that the best approach to take in dealii, i.e. compute the residual manually and manually do the nonlinear iteration until convergence is satisfied? In step-25, the scalar time-dependent system admits a straightforward expression for F'(u, delta_u) from F(u). In step-33, an automatic differentiation package, trilinos::sacado, is used to facilitate the computation of the vector-valued conservation law's "terrible beast" of a Jacobian. For computing the residual, automatic differentiation seems like it can help in certain situations. 2) Are there other options to help "automate" the nonlinear treatment? For example, does anyone have any experience with the petsc nonlinear solvers (snes)? For example, might it allow to easily switch between a Picard (fixed-point) loop, if the Newton loop does not converge? I note that in the PETScWrappers namespace there are no entries related to the snes package. Why/why not? With many thanks, Sean -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: fe_enriched and step-47
> Would the general point be that if one can go to higher resolutions with > distributed parallelism that the enhanced accuracy of the enrichment > functions can be compensated for? > > > Sorry, i did not get what you mean. > > Regards, > Denis. > > Hi Denis, Thanks for your prompt answers. I was shooting for a very generic question about the tradeoffs of a high-resolution parallel approach, vs the more subtle XFEM on a coarser grid. So, for example, consider an immiscible two-phase flow where the boundary between the two fluids is defined by a level set function (like in the code gallery's two_phase_flow). One way to represent the interface accurately would be to use very high-resolution so that the location of the material discontinuity, and its effect on, say, pressure, is highly localized. Another might be to essentially smooth out the pressure over the intersected cells (with material discontinuity) through the use of enrichment functions (if I understand XFEM well). I wonder if this is a reasonable way to view the tradeoffs around interface representation (handling internal discontinuities)? Since from an implementation point of view, I currently see a choice point between pursuing XFEM(with hp::DoFHandler) or high-res (p::d::tria). Best, Sean -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
Re: [deal.II] Re: fe_enriched and step-47
Hi, Thanks to you all for the feedback. The ANS paper and the plans for sophisticated quadrature are great. One further point of clarification: I am new to XFEM, but have been interested in level sets for a while, in particular in the distributed parallel context. Do I understand correctly that the FE_Enriched/ ANS paper approach require the use of FE_Nothing and hence hp::DofHandler? So, then this would, at present, not work with p::d::triangulation. Would the general point be that if one can go to higher resolutions with distributed parallelism that the enhanced accuracy of the enrichment functions can be compensated for? Best, Sean On Sunday, April 9, 2017 at 9:18:05 PM UTC+2, Denis Davydov wrote: > > Hi > > On Sunday, April 9, 2017 at 10:20:13 AM UTC+2, Simon Sticko wrote: >> >> Hi. >> Regarding this: >> >> > On Thursday, April 6, 2017 at 1:51:41 PM UTC+2, Denis Davydov wrote: >> > >> > The issue with integrating and quadrature would still remain. >> >> >> I've been implementing an algorithm to generate bulk and surface >> quadrature given a level set function as boundary description. It's mainly >> an implementation of this algorithm: dx.doi.org/10.1137/140966290. >> I'm hoping to finish this within the coming weeks and contribute with >> this to dealii. >> > > that would be very nice! I look forward to your pull request (PR). > > ps. You can also create a work-in-progress (WIP) pull-request so that > others may provide feedback straight-away. > Or one may split it into two or more PRs. For example I don't think there > is any functionality in deal.II to work with level sets. > If you use/implement this as a part of your work, you may also first > create a PR with this part only. > > Regards, > Denis. > -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[deal.II] fe_enriched and step-47
Dear dealii community, I was wondering if anyone could comment on how the introduction of the fe_enriched class functionality in the developer branch would affect a program like step-47. In other words, if one were interested in implementing something like step-47 with the latest dealii version, what are the most important differences that would jump out? With many thanks, Sean McGovern -- 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 --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to dealii+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
