[deal.II] MPI libraries

``` -- Could not find a sufficient PETSC installation: PETSC is compiled against a different MPI library than the one deal.II picked up. -- DEAL_II_WITH_PETSC has unmet external dependencies. CMake Error at cmake/configure/configure_3_petsc.cmake:141 (MESSAGE): Could not find the petsc library

[deal.II] More than one instance of _axpy

``` [ 43%] Building CXX object CMakeFiles/aspect.dir/source/particle/interpolator/bilinear_least_squares.cc.o In file included from /opt/apps/intel18/cray_mpich_7_7/dealii/9.2.0/include/deal.II/lac/full_matrix.templates.h(33), from /work/00434/eijkhout/lonestar/aspect/aspect-2.2

Re: [deal.II] Wolfgang's mailbox is full

Oh, I see, my mail program has you at TAMU. Let me change its mind about that. Sorry for the noise. Victor. > On , 2020May19, at 13:10, Wolfgang Bangerth wrote: > > On 5/19/20 11:31 AM, Victor Eijkhout wrote: >> - The following addresses had permanent fatal errors -

[deal.II] Wolfgang's mailbox is full

- The following addresses had permanent fatal errors - (reason: 554 5.4.0 Error: too many hops) -- 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

Re: [deal.II] Dealii & trilinos

On , 2020May1, at 18:39, Matthias Maier mailto:tam...@43-1.org>> wrote: This implies that the CMake configuration that gets installed by Trilinos is broken. Well well well. The file /home1/apps/intel19/impi19_0/trilinos/12.18.1/lib/cmake/ShyLU/ShyLUConfig.cmake contains an include on line

Re: [deal.II] Re: "libpthreads"?

On , 2020Apr28, at 10:21, Wolfgang Bangerth mailto:bange...@colostate.edu>> wrote: Since you already verified that that patch works for you, would it help if we just moved that one patch to the 9.1 release branch and you work with that? No need. I’m simply pretending that this is part of 9.1.

Re: [deal.II] Re: "libpthreads"?

On , 2020Apr24, at 18:03, Marc Fehling mailto:m.fehl...@fz-juelich.de>> wrote: Just compile from the master branch and you're good! I’m allergic to the word “just”. Considering how laborious our installation process is, I try to install only versions that have official numbers on them. Cons

Re: [deal.II] "libpthreads"?

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. Victor. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/

Re: [deal.II] "libpthreads"?

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 re

Re: [deal.II] "libpthreads"?

On , 2020Apr22, at 14:54, Wolfgang Bangerth mailto:bange...@colostate.edu>> wrote: FIND_PACKAGE(Threads) calls a cmake-builtin module that on my system lives in /usr/share/cmake/Modules/FindThreads.cmake. It contains this piece of code: if(CMAKE_HAVE_PTHREAD_H) # # We have pthread.h # L

Re: [deal.II] "libpthreads"?

> In your log file, the error comes from using -lpthreads (not the 's' at the > end). And by “not” you mean “note”? > You don't say what the exact error message is, Is the last error in the CMakeError.log the relevant one? Configuration error: Cannot compile a test program with the fina

Re: [deal.II] installation fails with intel/19.0.5

On Oct 5, 2019, at 4:13 PM, Timo Heister mailto:timo.heis...@gmail.com>> wrote: -D DEAL_II_WITH_MPI=ON \ -D DEAL_II_CXX_FLAGS="-march=native" \ -D DEAL_II_WITH_CXX17=OFF \ -D DEAL_II_WITH_64BIT_INDICES=ON \ -D DEAL_II_COMPONENT_EXAMPLES=OFF \ -D CMAKE_INSTALL_PREFIX=`pwd

Re: [deal.II] installation fails with intel/19.0.5

On Oct 5, 2019, at 9:27 AM, Timo Heister mailto:heis...@clemson.edu>> wrote: Otherwise I have no problem running with 19.0.5 on Frontera. Dictate me you cmake line? Victor. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google

Re: [deal.II] installation fails with intel/19.0.5

On Sep 30, 2019, at 5:29 PM, Marc Fehling mailto:m.fehl...@fz-juelich.de>> wrote: DDEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0 Hm. Turns out I had an explicit c++14 in my compiler specification. At least now I don’t get that fallthrough message anymore. But I’m still not finishing the cmake.

[deal.II] installation fails with intel/19.0.5

CMakeError.log attached. -- 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

Re: [deal.II] Compilation problem: obj_numerics_release/data_out.cc

It looks like gcc is getting hold of an old TBB, not the one in the Intel compiler tree. An extra include dir fixes it. Thanks. Victor. -- 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 receiv

[deal.II] Compilation problem: obj_numerics_release/data_out.cc

For a change, this problem only appears with gcc 7.1, not Intel 17. [ 35%] Building CXX object source/numerics/CMakeFiles/obj_numerics_release.dir/data_out.cc.o cd /tmp/dealii-build/source/numerics && /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx -I/tmp/dealii-b

Re: [deal.II] Re: CMake extra libraries?

Thanks for the hint. My cmake was indeed shifting under me. After completely removing the install it all went fine. Of course "make test" bombs on something trilinos related Victor. On Thursday, July 13, 2017 at 3:58:43 PM UTC-5, Bruno Turcksin wrote: > > Victor, > > I have never seen any

Re: [deal.II] Re: CMake extra libraries?

PS where it actually crashes is this: Dependee "/opt/apps/intel17/boost/1.64/include/boost/visit_each.hpp" does not exist for depender "source/numerics/CMakeFiles/obj_numerics_release.dir/vector_tools_rhs.cc.o". Dependee "/opt/apps/intel17/boost/1.64/include/boost/weak_ptr.hpp" does not

Re: [deal.II] Re: CMake extra libraries?

Our boost was broken. Having repaired it, I get the following: [ 36%] Built target obj_numerics_inst make -f source/numerics/CMakeFiles/obj_numerics_release.dir/build.make source/numerics/CMakeFiles/obj_numerics_release.dir/depend make[2]: Entering directory `/tmp/dealii-build' cd /tmp/dealii-

Re: [deal.II] Re: CMake extra libraries?

Ok, this was my error. I thought you guys picked u the compiler flags from Trilinos, but turns out I specify them. If I add the AVX instructions to the debug flags (which I don't like!) it compiles fine. Until here: make -f examples/CMakeFiles/step-53.release.dir/build.make examples/ CMa

Re: [deal.II] Re: CMake extra libraries?

On Friday, July 7, 2017 at 7:22:14 AM UTC-5, Bruno Turcksin wrote: > > This is very strange. Do you set the AVX flags yourself? > Yes. The CMakeOutput.log starts with: The system is: Linux - 3.10.0-514.21.2.el7.x86_64 - x86_64 Compiling the C compiler identification source file "CMakeCCompile

[deal.II] Re: CMake extra libraries?

Hm. That second compile line should be: [ 63%] Building CXX object source/numerics/CMakeFiles/obj_numerics_debug.dir /vector_tools_boundary.cc.o cd /tmp/dealii-build/source/numerics && /opt/intel/ compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx -DDEBUG - DTBB_DO_ASSERT=1

[deal.II] Re: CMake extra libraries?

Yay! Finally compiling. Mind if I just continue in this ticket even though the question is moving on? I think I'm correctly specifying a bunch of AVX flags to trilinos. In the deal build they show up in compile lines such as: [ 63%] Building CXX object source/physics/CMakeFiles/obj_physics_rel

[deal.II] Re: CMake extra libraries?

Denis: I can not remove pytrilinos because I actually need it in trilinos. Bruno: > add the flag that you need in SET(Trilinos_CXX_COMPILER_FLAGS) build@build-BLDCHROOT:12.10.1> find . -name \*.cmake -exec grep COMPILER_FLAGS {} \; -print

Re: [deal.II] "file name too long" for download

On Jun 19, 2017, at 4:25 PM, Bruno Turcksin mailto:bruno.turck...@gmail.com>> wrote: wget https://github.com/dealii/dealii/releases/download/v8.5.0/dealii-8.5.0.tar.gz -O dealii-8.5.0.tar.gz Yes, the explicit out

[deal.II] "file name too long" for download

wget https://github.com/dealii/dealii/releases/download/v8.5.0/dealii-8.5.0.tar.gz --2017-06-19 15:59:53-- https://github.com/dealii/dealii/releases/download/v8.5.0/dealii-8.5.0.tar.gz Resolving github.com... 192.30.253.113, 192.30.253.112 Connecting to github.com|192.30.253.113|:443... connecte

[deal.II] Re: CMake extra libraries?

On Thursday, June 15, 2017 at 3:40:35 PM UTC-5, Bruno Turcksin wrote: > > >> > I am not sure that you and Denis are talking about the same problem. Do > you get this problem when you compile deal.II or when you compile your own > project on top of deal.II? > > > Ha. Good point. I'm trying t

Re: [deal.II] Re: CMake extra libraries?

On Thursday, June 15, 2017 at 12:56:14 PM UTC-5, Denis Davydov wrote: > > > Nope. You add things to **your** CMakeList.txt > You mean that I should edit **your** CMakeLists.txt, right? Not make an extra one of my own? (Speaking of your: it has a line #See doc/readme.html and doc/developm

[deal.II] Re: CMake extra libraries?

That reply is way too cryptic for me. You seem to be saying that I need to add something to a file that is generated by cmake. But my cmake crashes to begin with. And even then, it seems to be about a file deal.IIFeatureConfig.cmake which I can't find anywhere. Victor PS so there is no simple

[deal.II] CMake extra libraries?

Is there a cmake flag for specifying some extra libraries? Trilinos seems to have been built with a python interface, but deal is somehow not linking the libpython, so the cmake fails. It would probably be easiest if I can explicitly give cmake a couple of extra libraries to link. What’s the fl

Re: [deal.II] Examples makefile

> On Jan 15, 2017, at 9:24 PM, Wolfgang Bangerth wrote: > > After calling 'cmake' in the example program, compile everything using > make VERBOSE=ON > and it should tell you the command lines being used. Thanks. That was useful. Apparently a file cmake_link_script is being executed. After add

Re: [deal.II] Examples makefile

On Jan 14, 2017, at 4:54 PM, Jean-Paul Pelteret mailto:jppelte...@gmail.com>> wrote: you could instead just not build Trilinos with PyTrilinos. No, I need that for another reason, and for as far as I can tell the build is correct. How can I see the link line that deal.II is using for its exam

Re: [deal.II] Examples makefile

On Jan 14, 2017, at 5:48 AM, 'Seyed Ali Mohseni' via deal.II User Group mailto:dealii@googlegroups.com>> wrote: I would check first of all, if you compiled Trilinos with the correct settings, I believe so. It’s just a case of a missing python library. Can you explain how I can add an extra li

[deal.II] Examples makefile

I'm trying to compile an example, and get these errors: [ 50%] Linking CXX executable step-1 icpc: command line warning #10006: ignoring unknown option '-fuse-ld=gold' /home1/apps/intel15/mvapich2_2_1/dealii/8.4.1/include/deal.II/numerics/derivative_a

Re: [deal.II] DWARF version?

> On Nov 4, 2016, at 8:53 AM, Wolfgang Bangerth wrote: > > On 11/04/2016 07:50 AM, Victor Eijkhout wrote: >> You guys don’t run into problems with trilinos? > > No, I install it all the time. It may be that we don't because we don't > usually use STK… I ha

Re: [deal.II] DWARF version?

> On Nov 4, 2016, at 8:23 AM, Bruno Turcksin wrote: > > The problem is again from Trilinos. Your install of Trilinos looks > broken. I would try to reinstall it from scratch instead of changing > the config file by hand. I always install from scratch. You guys don’t run into problems with tril

Re: [deal.II] DWARF version?

> > /work/00434/eijkhout/trilinos/installation-12.2.1/lib/cmake/STK/STKConfig.cmake > says that this file needs tot exist > /work/00434/eijkhout/trilinos/installation-12.2.1/lib/cmake/STK/../STKDoc_tests/STKDoc_testsConfig.cmake > Can you check if it is there? Ok, I fixed this one by editing o

Re: [deal.II] DWARF version?

> On Oct 14, 2016, at 3:12 PM, Timo Heister wrote: > >> The cmake aborts somewhere and I was trying to figure out where. I’m >> attaching the log and the output. > > What is the output to the terminal before it aborts? ### # # deal.II configuration: #CMAKE_BUILD_TYPE: DebugRele

[deal.II] Re: DWARF version?

PS this is only a problem with Intel 15; it's solved in 16. Unfortunately our software stack is complete for 15 and updating to 16 or 17 is slow Victor. -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii

[deal.II] DWARF version?

The 8.4.1 cmake throws an error because of the "-gdwarf-2" flag on the Intel compiler. Is that flag needed? If no, how can I disable it? This is what I found in the CmakeError: Run Build Command:"/usr/bin/gmake" "cmTryCompileExec3077733329/fast" gmake[1]: Entering directory `/work/00434/eijkho