[deal.II] Re: Installation error, unable to configure with p4est
Okay, I found the error. Some time back, I noted changing include/deal.II/base/config.h.in to include/deal.II/base/config.h (removed the .in). I don't remember exactly, but the reason I did this was because some error popped up while compiling one of the initial tutorials. This was my mistake. The complete error message of cmake (on the terminal) mentions that config.h.in file is missing. So now, I made a copy and, the configuration and installation went fine. However, make test for p4est failed with the following message There are not enough slots available in the system to satisfy the 10 slots that were requested by the application: ./p4est.debug Either request fewer slots for your application, or make more slots available for use. It is true that my PC has only 4 slots (8 with hyper threading). So can I ignore this error? -- 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. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/418ae277-bf9d-4b83-b987-a03a3d48a4be%40googlegroups.com.
[deal.II] Large Memory Consumption making BlockDynamicSparsityPattern
Hello, I'm currently working on the upgrading of my code, adding PETSc as an alternative to Trilinos for the Linear Algebra package. I'm implementing this option following Tutorial 55. However, I'm dealing with some issues when I try to run massive parallel simulations. Especially large memory consumption occurs in the system setup phase. After some debugging, I was able to figure out that the part of the code responsible for this is the generation of the sparsity pattern, i.e., the following rows: BlockDynamicSparsityPattern dsp(local_partitioning); DoFTools::make_sparsity_pattern(dof_handler, scratch_coupling, dsp, constraints, false, this_mpi_process); I wanted to point out that this behavior doesn't depend on PETSc, but it is related only with the procedure wherewith we make the Block Sparsity Pattern (BSP). Indeed I ran into the same issue with Trilinos if the above strategy is selected. In the previous version of the code, I used these rows to generate the BSP: TrilinosWrappers::BlockSparsityPattern sp(local_partitioning,MPI_COMM_WORLD); DoFTools::make_sparsity_pattern(dof_handler, matrix_coupling, sp, constraints, false, this_mpi_process); sp.compress(); In this last case, the amount of memory required to generate the BSP is much less respect with the first case. Any ideas what is going on? Am I doing wrong something? Thank you very much for your support. Matteo -- 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. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/42a40c37-eb6b-4f0c-994d-4e74e57c3764%40googlegroups.com.
[deal.II] Crowdsourcing some deal.II-related tasks
All, as you know, we try to keep a list of publications using deal.II at https://dealii.org/publications.html but given how many entries we now have to add to it every year, it has become an impossible task to keep it up to date. So we need help: * Timo has used a script to generate a list of candidate entries at https://docs.google.com/document/d/1agTpMQWok0JxrbmMCpF0tnJY7RtCy2DfhT2xetMvojk/edit?usp=sharing * We need *your* help identifying which of these are actually *using* deal.II. Instructions on how to do that are in the google document. For many of the articles, you will have to have access to journal websites (generally through your university) to download PDF files. If you have ten or twenty or thirty minutes, we would be extremely grateful if you could go over there and help us out with a few entries. My experience is that it takes 3-5 minutes per entry; there are ~160 entries, so if only 20 of you were willing to help, we'd be done within a day or two! Thanks you in advance! Wolfgang -- 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 --- 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. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6fba3653-d94d-d07c-d7e0-33a46b4a2fb9%40colostate.edu.
[deal.II] Error during refinement of a parallel distibuted quarter hyperball
Dear all,
during the refinement of a quarter hyper ball in 3D in debug mode, I
receive the following error when running on a single core (mpirun -np 1):
*An error occurred in line <2764> of file
in functionvoid
dealii::parallel::distributed::Triangulation::copy_local_forest_to_triangulation() [with int dim = 3; int
spacedim = 3]The violated condition was: static_cast(parallel_forest->local_num_quadrants) == total_local_cells*
When running on multiple cores I hit another error message (probably
because there are no ghosts when using only one core):
*An error occurred in line <2670> of file
in functionvoid
dealii::parallel::distributed::Triangulation::copy_local_forest_to_triangulation() [with int dim = 3; int
spacedim = 3]The violated condition was: num_ghosts ==
parallel_ghost->ghosts.elem_cou*nt
Currently I am using deal.II 9.0.1.
This is the relevant part of the code (a full MWE is attached):
const unsigned int dim = 3;
parallel::distributed::Triangulation tria (
mpi_communicator,
typename
Triangulation::MeshSmoothing(Triangulation::smoothing_on_refinement),
parallel::distributed::Triangulation::default_setting);
GridGenerator::quarter_hyper_ball(tria);
for (unsigned int i_refinement = 0; i_refinement < 6;
++i_refinement)
{
auto cell = tria.begin_active();
auto endc = tria.end();
for (; cell!=endc; ++cell)
if(cell->is_locally_owned() && cell->at_boundary())
cell->set_refine_flag ();
tria.prepare_coarsening_and_refinement ();
tria.execute_coarsening_and_refinement ();
}
Is there something wrong with my code? Or maybe with my installation (can
anyone confirm the error)?
The code works in 2D but crashes in 3D. When the number of refinement
cycles is reduced to 4 instead of 6, it also works.
Out of curiosity, I've tried using GridGenerator::hyper_cube instead of the
hyper_ball, there the code works just fine in 2D and 3D.
I would really appreciate if anyone can help me with this.
Kind regards,
Stefan
--
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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"deal.II User Group" group.
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#include
#include
#include
int main (int argc, char *argv[]) {
try {
using namespace dealii;
Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
const unsigned int dim = 3;
MPI_Comm mpi_communicator = MPI_COMM_WORLD;
parallel::distributed::Triangulation tria (
mpi_communicator,
typename Triangulation::MeshSmoothing(Triangulation::smoothing_on_refinement),
parallel::distributed::Triangulation::default_setting);
GridGenerator::quarter_hyper_ball(tria);
for (unsigned int i_refinement = 0; i_refinement < 6; ++i_refinement)
{
auto cell = tria.begin_active();
auto endc = tria.end();
for (; cell!=endc; ++cell)
if(cell->is_locally_owned() && cell->at_boundary())
cell->set_refine_flag ();
tria.prepare_coarsening_and_refinement ();
tria.execute_coarsening_and_refinement ();
}
}
catch (std::exception &exec)
{
std::cout << std::flush;
std::cerr << "\n\n\n"
<< "Exception thrown :\n" << exec.what() << std::endl
<< "Aborting!\n"
<< "" << std::endl;
return 1;
}
catch (...)
{
std::cout << std::flush;
std::cerr << "\n\n\n"
<< "Unknown exception!\n"
<< "Aborting!\n"
<< "" << std::endl;
return 1;
}
return 0;
}
[deal.II] Re: Installation error, unable to configure with p4est
Sorry for incomplete information, cmake exits with the following message. ### # # deal.II configuration: #CMAKE_BUILD_TYPE: DebugRelease #BUILD_SHARED_LIBS: ON #CMAKE_INSTALL_PREFIX: /home/vachan/bin/dealii #CMAKE_SOURCE_DIR: /home/vachan/dealii-9.1.1 #(version 9.1.1) #CMAKE_BINARY_DIR: /home/vachan/build/dealii #CMAKE_CXX_COMPILER: GNU 7.4.0 on platform Linux x86_64 #/usr/local/bin/mpicxx # # Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON): # ( DEAL_II_WITH_64BIT_INDICES = OFF ) # ( DEAL_II_WITH_ADOLC = OFF ) # ( DEAL_II_WITH_ARPACK = OFF ) # ( DEAL_II_WITH_ASSIMP = OFF ) #DEAL_II_WITH_BOOST set up with bundled packages # ( DEAL_II_WITH_COMPLEX_VALUES = OFF ) # ( DEAL_II_WITH_CUDA = OFF ) #DEAL_II_WITH_CXX14 = ON #DEAL_II_WITH_CXX17 = ON # ( DEAL_II_WITH_GINKGO = OFF ) # ( DEAL_II_WITH_GMSH = OFF ) # ( DEAL_II_WITH_GSL = OFF ) # ( DEAL_II_WITH_HDF5 = OFF ) # ( DEAL_II_WITH_LAPACK = OFF ) # ( DEAL_II_WITH_METIS = OFF ) #DEAL_II_WITH_MPI set up with external dependencies #DEAL_II_WITH_MUPARSER set up with bundled packages # ( DEAL_II_WITH_NANOFLANN = OFF ) # ( DEAL_II_WITH_NETCDF = OFF ) # ( DEAL_II_WITH_OPENCASCADE = OFF ) #DEAL_II_WITH_P4EST set up with external dependencies #DEAL_II_WITH_PETSC set up with external dependencies # ( DEAL_II_WITH_SCALAPACK = OFF ) # ( DEAL_II_WITH_SLEPC = OFF ) # ( DEAL_II_WITH_SUNDIALS = OFF ) # ( DEAL_II_WITH_SYMENGINE = OFF ) #DEAL_II_WITH_THREADS set up with bundled packages # ( DEAL_II_WITH_TRILINOS = OFF ) # ( DEAL_II_WITH_UMFPACK = OFF ) #DEAL_II_WITH_ZLIB set up with external dependencies # # Component configuration: # ( DEAL_II_COMPONENT_DOCUMENTATION = OFF ) #DEAL_II_COMPONENT_EXAMPLES # ( DEAL_II_COMPONENT_PACKAGE = OFF ) # ( DEAL_II_COMPONENT_PYTHON_BINDINGS = OFF ) # # Detailed information (compiler flags, feature configuration) can be found in detailed.log # # Run $ make info to print a help message with a list of top level targets # ### -- Configuring incomplete, errors occurred! See also "/home/vachan/build/dealii/CMakeFiles/CMakeOutput.log". See also "/home/vachan/build/dealii/CMakeFiles/CMakeError.log". -- 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. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/74b5c4d1-7098-417c-bca2-260b4ca48a10%40googlegroups.com.
[deal.II] Re: error during installation with spack on CentOS7
Hi Alberto,
Try reporting issue on Spack Github and ping @balay .
Denis.
On Friday, October 4, 2019 at 12:50:24 PM UTC+2, Alberto Salvadori wrote:
>
> Dear community
>
> I apologize for this too long bothering on installing deal.ii on a linux
> machine equipped with CentOS7. I am having quite a large amount of issues,
> perhaps related to the gcc compiler(?).
> The very last, which I was unable to solve up to now, relates to slepc . I
> wonder if any of you had a similar problem and in case could address its
> solution.
>
> Here is the outcome of installation via spack:
>
> *==>* *Installing* *slepc*
>
> *==>* Searching for binary cache of slepc
>
> *==>* Warning: No Spack mirrors are currently configured
>
> *==>* No binary for slepc found: installing from source
>
> *==>* Fetching http://slepc.upv.es/download/distrib/slepc-3.12.0.tar.gz
>
>
> 100.0%
>
> *==>* Staging archive:
> /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/slepc-3.12.0.tar.gz
>
> *==>* Created stage in
> /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
>
> *==>* No patches needed for slepc
>
> *==>* Building slepc [Package]
>
> *==>* Executing phase: 'install'
>
> *==>* Error: ProcessError: Command exited with status 1:
>
> './configure'
> '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr'
>
> '--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib'
>
> '--with-arpack-flags=-lparpack,-larpack'
>
> See build log for details:
>
>
> /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-build-out.txt
>
>
> and the log (s):
>
> ==> Executing phase: 'install'
>
> ==> [2019-10-03-20:48:03.194513] './configure'
> '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr'
>
> '--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib'
>
> '--with-arpack-flags=-lparpack,-larpack'
>
> Checking environment... done
>
> Checking PETSc installation...
>
> ERROR: Unable to link with PETSc
>
> ERROR: See "installed-arch-linux2-c-opt/lib/slepc/conf/configure.log" file
> for details
>
>
>
>
>
> Starting Configure Run at Thu Oct 3 20:48:03 2019
>
> Configure Options:
> --prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
>
> --with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib
>
> --with-arpack-flags=-lparpack,-larpack
>
> Working directory:
> /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src
>
> Python version:
>
> 2.7.16 (default, Oct 3 2019, 20:40:41)
>
> [GCC 9.2.0]
>
> make: /usr/bin/gmake
>
> PETSc source directory:
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s
>
> PETSc install directory:
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s
>
> PETSc version: 3.12.0
>
> SLEPc source directory:
> /tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src
>
> SLEPc install directory:
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
>
> SLEPc version: 3.12.0
>
>
>
>
> Checking PETSc installation...
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
> Running command:
>
> cd /tmp/slepc-7TxU8j;/usr/bin/gmake checklink TESTFLAGS=""
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>
> #include "petscsnes.h"
>
> int main() {
>
> Vec v; Mat m; KSP k;
>
> PetscInitializeNoArguments();
>
> VecCreate(PETSC_COMM_WORLD,&v);
>
> MatCreate(PETSC_COMM_WORLD,&m);
>
> KSPCreate(PETSC_COMM_WORLD,&k);
>
> return 0;
>
> }
>
> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpicc
>
> -o checklink.o -c -fPIC
> -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/include
>
> -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hypre-2.18.0-dbexk2cnwvnsjd5fm6ltw7o7q66ik3hy/include
>
> -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/superlu-dist-6.1.1-stsykz4xojdqtlnjavms2opkppopzush/include
>
> -I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/include
>
> -I/home/deal.ii/spack/opt/spack/linu
[deal.II] Re: error during installation with spack on CentOS7
Dear community
I apologize for this too long bothering on installing deal.ii on a linux
machine equipped with CentOS7. I am having quite a large amount of issues,
perhaps related to the gcc compiler(?).
The very last, which I was unable to solve up to now, relates to slepc . I
wonder if any of you had a similar problem and in case could address its
solution.
Here is the outcome of installation via spack:
*==>* *Installing* *slepc*
*==>* Searching for binary cache of slepc
*==>* Warning: No Spack mirrors are currently configured
*==>* No binary for slepc found: installing from source
*==>* Fetching http://slepc.upv.es/download/distrib/slepc-3.12.0.tar.gz
100.0%
*==>* Staging archive:
/tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/slepc-3.12.0.tar.gz
*==>* Created stage in
/tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
*==>* No patches needed for slepc
*==>* Building slepc [Package]
*==>* Executing phase: 'install'
*==>* Error: ProcessError: Command exited with status 1:
'./configure'
'--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr'
'--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib'
'--with-arpack-flags=-lparpack,-larpack'
See build log for details:
/tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-build-out.txt
and the log (s):
==> Executing phase: 'install'
==> [2019-10-03-20:48:03.194513] './configure'
'--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr'
'--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib'
'--with-arpack-flags=-lparpack,-larpack'
Checking environment... done
Checking PETSc installation...
ERROR: Unable to link with PETSc
ERROR: See "installed-arch-linux2-c-opt/lib/slepc/conf/configure.log" file
for details
Starting Configure Run at Thu Oct 3 20:48:03 2019
Configure Options:
--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
--with-arpack-dir=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/arpack-ng-3.7.0-i5fx7mowpxx7acbasidsfc4r3owcd2vx/lib
--with-arpack-flags=-lparpack,-larpack
Working directory:
/tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src
Python version:
2.7.16 (default, Oct 3 2019, 20:40:41)
[GCC 9.2.0]
make: /usr/bin/gmake
PETSc source directory:
/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s
PETSc install directory:
/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s
PETSc version: 3.12.0
SLEPc source directory:
/tmp/deal.ii/spack-stage/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr/spack-src
SLEPc install directory:
/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/slepc-3.12.0-5md6u45rynyaqtcta4e5dmecqhkp2jkr
SLEPc version: 3.12.0
Checking PETSc installation...
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Running command:
cd /tmp/slepc-7TxU8j;/usr/bin/gmake checklink TESTFLAGS=""
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#include "petscsnes.h"
int main() {
Vec v; Mat m; KSP k;
PetscInitializeNoArguments();
VecCreate(PETSC_COMM_WORLD,&v);
MatCreate(PETSC_COMM_WORLD,&m);
KSPCreate(PETSC_COMM_WORLD,&k);
return 0;
}
/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openmpi-3.1.4-4lzhe2gtz3nzhffn6efu2fzgochphcix/bin/mpicc
-o checklink.o -c -fPIC
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/petsc-3.12.0-7b3mdm63ap32riorneym2mtcmwjlb63s/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hypre-2.18.0-dbexk2cnwvnsjd5fm6ltw7o7q66ik3hy/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/superlu-dist-6.1.1-stsykz4xojdqtlnjavms2opkppopzush/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/hdf5-1.10.5-lt5jyi3ix6dbrbblku7ygutgek7wg5w2/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/parmetis-4.0.3-p3vaameiqho6enhkpjhcupk5lam6jvc6/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/metis-5.1.0-zepovp3vvqzcirbxoqyb33fg5mm26spe/include
-I/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj/include
`pwd`/checklink.c
/home/deal.ii/spack/opt/spack/linux-centos7-ivybridg
Re: [deal.II] Re: error during installation with spack on CentOS7
Great, happy to hear you sorted this out by tweaking compilers.yaml
settings.
On Friday, October 4, 2019 at 12:38:20 PM UTC+2, Alberto Salvadori wrote:
>
> Hi Denis
>
> thanks for your note. I figured out that by adding the path in the
> compilers.yaml file, in this way
>
> - compiler:
>
> environment:
>
> append-path:
>
> LD_LIBRARY_PATH: /usr/local/lib64
>
> extra_rpaths: []
>
> flags: {}
>
> modules: []
>
> operating_system: centos7
>
> paths:
>
> cc: /usr/local/bin/gcc
>
> cxx: /usr/local/bin/g++
>
> f77: /usr/local/bin/gfortran
>
> fc: /usr/local/bin/gfortran
>
> spec: gcc@9.2.0
>
> target: x86_64
>
> sorts out the issue.
>
>
> Il giorno mercoledì 2 ottobre 2019 19:26:06 UTC+2, Denis Davydov ha
> scritto:
>>
>> Hi Alberto,
>>
>> Looks like the issue is known to Spack community:
>> https://github.com/spack/spack/issues/11224 where there is also a
>> possible source of the problem you can try as a fix (un-do on-line PR).
>>
>> Regards,
>> Denis.
>>
>> On Wednesday, October 2, 2019 at 3:14:46 PM UTC+2, Bruno Turcksin wrote:
>>>
>>> Alberto,
>>>
>>> So what happens is that spack is using gcc 9.2 like you want but it
>>> usess the libstdc++ from gcc 4.8.5 I usually spack to install a new
>>> compiler and my compilers.yaml looks like your *but* I have the path
>>> to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module.
>>> So I guess you need to add that path somewhere in your compilers.yaml
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori
>>> a écrit :
>>> >
>>> > Thank you, Bruno. In fact, my aim was to use my system compiler.
>>> > Here is my .spack/linux/packages.yaml:
>>> >
>>> > packages:
>>> >
>>> > all:
>>> >
>>> > compiler: [gcc]
>>> >
>>> > providers:
>>> >
>>> > mpi: [openmpi]
>>> >
>>> > openmpi:
>>> >
>>> > version: [3.1.4]
>>> >
>>> > paths:
>>> >
>>> > openmpi@3.1.4%gcc@9.2.0: /usr/local/
>>> >
>>> > buildable: False
>>> >
>>> > perl:
>>> >
>>> > paths:
>>> >
>>> > perl@5.16.3%gcc@9.2.0: /usr
>>> >
>>> > cmake:
>>> >
>>> > version: [3.15.3]
>>> >
>>> > paths:
>>> >
>>> > cmake@3.15.3%gcc@9.2.0: /usr/local/
>>> >
>>> > hdf5:
>>> >
>>> > version: [1.8.12]
>>> >
>>> > paths:
>>> >
>>> > hdf5@1.8.12%gcc@9.2.0: /usr
>>> >
>>> > variants: +hl+fortran
>>> >
>>> > netcdf:
>>> >
>>> > version: [7.2.0]
>>> >
>>> > paths:
>>> >
>>> > netcdf@7.2.0%gcc@9.2.0: /usr
>>> >
>>> > netcdf-cxx:
>>> >
>>> > version: [4.2.8]
>>> >
>>> > paths:
>>> >
>>> > netcdf-cxx@4.2.8%gcc@9.2.0: /usr
>>> >
>>> > dealii:
>>> >
>>> > variants: +optflags~python
>>> >
>>> >
>>> > Shall I perhaps add something to the compiler flag (paths or so)?
>>> > Here is also my .spack/linux/compilers.yaml
>>> >
>>> > compilers:
>>> >
>>> > - compiler:
>>> >
>>> > environment: {}
>>> >
>>> > extra_rpaths: []
>>> >
>>> > flags: {}
>>> >
>>> > modules: []
>>> >
>>> > operating_system: centos7
>>> >
>>> > paths:
>>> >
>>> > cc: /usr/bin/gcc
>>> >
>>> > cxx: /usr/bin/g++
>>> >
>>> > f77: /usr/bin/gfortran
>>> >
>>> > fc: /usr/bin/gfortran
>>> >
>>> > spec: gcc@4.8.5
>>> >
>>> > target: x86_64
>>> >
>>> > - compiler:
>>> >
>>> > environment: {}
>>> >
>>> > extra_rpaths: []
>>> >
>>> > flags: {}
>>> >
>>> > modules: []
>>> >
>>> > operating_system: centos7
>>> >
>>> > paths:
>>> >
>>> > cc: /usr/local/bin/gcc
>>> >
>>> > cxx: /usr/local/bin/g++
>>> >
>>> > f77: /usr/local/bin/gfortran
>>> >
>>> > fc: /usr/local/bin/gfortran
>>> >
>>> > spec: gcc@9.2.0
>>> >
>>> > target: x86_64
>>> >
>>> >
>>> >
>>> > Alberto
>>> >
>>> >
>>> > Alberto Salvadori
>>> > Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
>>> > Universita` di Brescia, via Branze 43, 25123 Brescia
>>> > Italy
>>> > tel 030 3711239
>>> > fax 030 3711312
>>> >
>>> > e-mail:
>>> > alberto@unibs.it
>>> > web-page:
>>> > http://m4lab.unibs.it/faculty.html
>>> >
>>> >
>>> >
>>> > On Wed, Oct 2, 2019 at 2:41 PM Bruno Turcksin
>>> wrote:
>>> >>
>>> >> Alberto,
>>> >>
>>> >> On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori
>>> wrote:
>>> >>>
>>> >>>
>>> >>> Thank you so much W and D,
>>> >>> As you pointed out there seems to be a mistake in the most recent
>>> version of perl during installation.
>>> >>> I will propagate this to the proper communities.
>>> >>>
>>> >>> As Denis proposed, I went on simply tell Spack to use Perl from
>>> system:
>>> >>>
>>> >>> perl:
>>> >>> paths:
>>> >>> perl@5.26.2%gcc@9.2.0: /usr
>>> >>>
>>> >>> but I bumped into another issue:
>>> >>>
>>> >>> [deal.ii@localhost spack]$ spack
Re: [deal.II] Re: error during installation with spack on CentOS7
Hi Denis
thanks for your note. I figured out that by adding the path in the
compilers.yaml file, in this way
- compiler:
environment:
append-path:
LD_LIBRARY_PATH: /usr/local/lib64
extra_rpaths: []
flags: {}
modules: []
operating_system: centos7
paths:
cc: /usr/local/bin/gcc
cxx: /usr/local/bin/g++
f77: /usr/local/bin/gfortran
fc: /usr/local/bin/gfortran
spec: gcc@9.2.0
target: x86_64
sorts out the issue.
Il giorno mercoledì 2 ottobre 2019 19:26:06 UTC+2, Denis Davydov ha scritto:
>
> Hi Alberto,
>
> Looks like the issue is known to Spack community:
> https://github.com/spack/spack/issues/11224 where there is also a
> possible source of the problem you can try as a fix (un-do on-line PR).
>
> Regards,
> Denis.
>
> On Wednesday, October 2, 2019 at 3:14:46 PM UTC+2, Bruno Turcksin wrote:
>>
>> Alberto,
>>
>> So what happens is that spack is using gcc 9.2 like you want but it
>> usess the libstdc++ from gcc 4.8.5 I usually spack to install a new
>> compiler and my compilers.yaml looks like your *but* I have the path
>> to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module.
>> So I guess you need to add that path somewhere in your compilers.yaml
>>
>> Best,
>>
>> Bruno
>>
>> Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori
>> a écrit :
>> >
>> > Thank you, Bruno. In fact, my aim was to use my system compiler.
>> > Here is my .spack/linux/packages.yaml:
>> >
>> > packages:
>> >
>> > all:
>> >
>> > compiler: [gcc]
>> >
>> > providers:
>> >
>> > mpi: [openmpi]
>> >
>> > openmpi:
>> >
>> > version: [3.1.4]
>> >
>> > paths:
>> >
>> > openmpi@3.1.4%gcc@9.2.0: /usr/local/
>> >
>> > buildable: False
>> >
>> > perl:
>> >
>> > paths:
>> >
>> > perl@5.16.3%gcc@9.2.0: /usr
>> >
>> > cmake:
>> >
>> > version: [3.15.3]
>> >
>> > paths:
>> >
>> > cmake@3.15.3%gcc@9.2.0: /usr/local/
>> >
>> > hdf5:
>> >
>> > version: [1.8.12]
>> >
>> > paths:
>> >
>> > hdf5@1.8.12%gcc@9.2.0: /usr
>> >
>> > variants: +hl+fortran
>> >
>> > netcdf:
>> >
>> > version: [7.2.0]
>> >
>> > paths:
>> >
>> > netcdf@7.2.0%gcc@9.2.0: /usr
>> >
>> > netcdf-cxx:
>> >
>> > version: [4.2.8]
>> >
>> > paths:
>> >
>> > netcdf-cxx@4.2.8%gcc@9.2.0: /usr
>> >
>> > dealii:
>> >
>> > variants: +optflags~python
>> >
>> >
>> > Shall I perhaps add something to the compiler flag (paths or so)?
>> > Here is also my .spack/linux/compilers.yaml
>> >
>> > compilers:
>> >
>> > - compiler:
>> >
>> > environment: {}
>> >
>> > extra_rpaths: []
>> >
>> > flags: {}
>> >
>> > modules: []
>> >
>> > operating_system: centos7
>> >
>> > paths:
>> >
>> > cc: /usr/bin/gcc
>> >
>> > cxx: /usr/bin/g++
>> >
>> > f77: /usr/bin/gfortran
>> >
>> > fc: /usr/bin/gfortran
>> >
>> > spec: gcc@4.8.5
>> >
>> > target: x86_64
>> >
>> > - compiler:
>> >
>> > environment: {}
>> >
>> > extra_rpaths: []
>> >
>> > flags: {}
>> >
>> > modules: []
>> >
>> > operating_system: centos7
>> >
>> > paths:
>> >
>> > cc: /usr/local/bin/gcc
>> >
>> > cxx: /usr/local/bin/g++
>> >
>> > f77: /usr/local/bin/gfortran
>> >
>> > fc: /usr/local/bin/gfortran
>> >
>> > spec: gcc@9.2.0
>> >
>> > target: x86_64
>> >
>> >
>> >
>> > Alberto
>> >
>> >
>> > Alberto Salvadori
>> > Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
>> > Universita` di Brescia, via Branze 43, 25123 Brescia
>> > Italy
>> > tel 030 3711239
>> > fax 030 3711312
>> >
>> > e-mail:
>> > alberto@unibs.it
>> > web-page:
>> > http://m4lab.unibs.it/faculty.html
>> >
>> >
>> >
>> > On Wed, Oct 2, 2019 at 2:41 PM Bruno Turcksin
>> wrote:
>> >>
>> >> Alberto,
>> >>
>> >> On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori
>> wrote:
>> >>>
>> >>>
>> >>> Thank you so much W and D,
>> >>> As you pointed out there seems to be a mistake in the most recent
>> version of perl during installation.
>> >>> I will propagate this to the proper communities.
>> >>>
>> >>> As Denis proposed, I went on simply tell Spack to use Perl from
>> system:
>> >>>
>> >>> perl:
>> >>> paths:
>> >>> perl@5.26.2%gcc@9.2.0: /usr
>> >>>
>> >>> but I bumped into another issue:
>> >>>
>> >>> [deal.ii@localhost spack]$ spack install dealii^cmake@3.9.4
>> >>>
>> >>> ==> libsigsegv is already installed in
>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463
>>
>>
>> >>>
>> >>> ==> m4 is already installed in
>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt
>>
>>
>> >>>
>> >>> ==> perl@5.16.3 : externa
