Re: [deal.II] treatment of handing nodes in the heat conduction problem

2021-03-21 Thread Anton Ermakov 
Yes, that part now works. Thank you, Wolfgang.

Anton.

On Wednesday, March 17, 2021 at 3:13:17 PM UTC-7 Wolfgang Bangerth wrote:

> On 3/17/21 10:41 PM, Anton Ermakov wrote:
> > Thanks for the reply. I think I got it. Basically, I had to manually 
> place the 
> > local matrices into the global matrix, without taking into account the 
> hanging 
> > node constraints, which are later taken care of by
> > 
> > /constraints.condense(system_matrix, system_rhs);/
> > 
> > In the case of the mass matrix, I had to use this:
> > 
> > /for (unsigned int i = 0; i < dofs_per_cell; ++i)/
> > 
> > /for (unsigned int j = 0; j < dofs_per_cell; ++j)/
> > 
> > 
> /mass_matrix.add(local_dof_indices[i], local_dof_indices[j], cell_matrix(i, 
> j));/
> > 
> > Instead of
> > 
> > /constraints.distribute_local_to_global(cell_matrix, local_dof_indices, 
> > mass_matrix);/
>
> Ah yes, that makes sense. So do I understand right that whatever you have 
> now 
> actually works?
>
> Best
> W.
>
>
> -- 
> 
> Wolfgang Bangerth email: bang...@colostate.edu
> www: http://www.math.colostate.edu/~bangerth/
>
>

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[deal.II] Installing 9.2.0 with HDF5

2021-03-21 Thread Curro Trigo 
Hello:

I'm trying to install deal II 9.2.0 on Ubuntu 20.04.2 LTS realease. And I 
succeded.

But if I try to install it with HDF5 activated I get errors like those 
shown below in the cmake process (while executing 'cmake 
-DDEAL_II_DIR=/home/curro/dealii-9.2.0/ ../'):

-- Include /home/curro/dealii-9.2.0/cmake/configure/configure_hdf5.cmake
-- HDF5_INCLUDE_DIR not found! Call:
-- FIND_PATH(HDF5_INCLUDE_DIR hdf5.h HINTS PATH_SUFFIXES hdf5 
hdf5/include include/hdf5 include)
-- HDF5_LIBRARY not found! Call:
-- FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5 HINTS PATH_SUFFIXES hdf5/lib 
lib lib64 lib)
-- HDF5_HL_LIBRARY not found! Call:
-- FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl HINTS PATH_SUFFIXES lib 
lib64 lib)
-- HDF5_PUBCONF not found! Call:
-- FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS 
HDF5_INCLUDE_DIR-NOTFOUND PATH_SUFFIXES hdf5 hdf5/include include/hdf5 
include)
--   HDF5_LIBRARIES: *** Required variable "HDF5_HL_LIBRARY" set to 
NOTFOUND ***
--   HDF5_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to 
NOTFOUND ***
--   HDF5_USER_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set 
to NOTFOUND ***
-- Could NOT find HDF5
-- DEAL_II_WITH_HDF5 has unmet external dependencies.

I've downloaded from 'https://www.hdfgroup.org/' the file 
'hdf5-1.12.0-linux-centos7-x86_64-shared-production.tar.gz'. And I have 
expanded it. Also, I've set the environment variable LD_LIBRARY_PATH to the 
folder where I've expanded it. With no success.

Any help will be welcome. Thanks a lot in advance.

Curro Trigo

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Re: [deal.II] Installing 9.2.0 with HDF5

2021-03-21 Thread Wolfgang Bangerth 

On 3/21/21 1:41 PM, Curro Trigo wrote:


I've downloaded from 'https://www.hdfgroup.org/' the file 
'hdf5-1.12.0-linux-centos7-x86_64-shared-production.tar.gz'. And I have 
expanded it. Also, I've set the environment variable LD_LIBRARY_PATH to the 
folder where I've expanded it. With no success.


You also need files such as hdf5.h, i.e., header files and not just the 
libraries.

I would suspect that there is an ubuntu package for hdf5. It would probably be 
easier if you installed that through the regular package manager, than do it 
by hand.


Best
 W.

--

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

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RE: [deal.II] Installing 9.2.0 with HDF5

2021-03-21 Thread Francisco Trigo 
Hello again,

 

The problem is when I type 'apt-cache search hdf5' I get 103 packages (attached 
to this e-mail) in Ubuntu related to hdf5. Which ones do I have to select?

 

I've selected these four packages:

 

  hdf5-helpers  

  libhdf5-103

  libhdf5-cpp-103

  libhdf5-dev

  

with the same result:

  

-- Include /home/curro/dealii-9.2.0/cmake/configure/configure_hdf5.cmake

-- HDF5_INCLUDE_DIR not found! Call:

-- FIND_PATH(HDF5_INCLUDE_DIR hdf5.h HINTS /usr/lib/x86_64-linux-gnu/hdf5 
PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

-- HDF5_LIBRARY not found! Call:

-- FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5 HINTS 
/usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES hdf5/lib lib lib64 lib)

-- HDF5_HL_LIBRARY not found! Call:

-- FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl HINTS 
/usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES lib lib64 lib)

-- HDF5_PUBCONF not found! Call:

-- FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS 
HDF5_INCLUDE_DIR-NOTFOUND /usr/lib/x86_64-linux-gnu/hdf5 PATH_SUFFIXES hdf5 
hdf5/include include/hdf5 include)

--   HDF5_LIBRARIES: *** Required variable "HDF5_HL_LIBRARY" set to NOTFOUND ***

--   HDF5_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to 
NOTFOUND ***

--   HDF5_USER_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to 
NOTFOUND ***

-- Could NOT find HDF5

-- DEAL_II_WITH_HDF5 has unmet external dependencies.

 

Any suggestion?

 

Thank you!

 

De: dealii@googlegroups.com  En nombre de Curro Trigo
Enviado el: domingo, 21 de marzo de 2021 13:42
Para: deal.II User Group 
Asunto: [deal.II] Installing 9.2.0 with HDF5

 

Hello:

 

I'm trying to install deal II 9.2.0 on Ubuntu 20.04.2 LTS realease. And I 
succeded.

 

But if I try to install it with HDF5 activated I get errors like those shown 
below in the cmake process (while executing 'cmake 
-DDEAL_II_DIR=/home/curro/dealii-9.2.0/ ../'):

 

-- Include /home/curro/dealii-9.2.0/cmake/configure/configure_hdf5.cmake

-- HDF5_INCLUDE_DIR not found! Call:

-- FIND_PATH(HDF5_INCLUDE_DIR hdf5.h HINTS PATH_SUFFIXES hdf5 hdf5/include 
include/hdf5 include)

-- HDF5_LIBRARY not found! Call:

-- FIND_LIBRARY(HDF5_LIBRARY NAMES hdf5 HINTS PATH_SUFFIXES hdf5/lib lib 
lib64 lib)

-- HDF5_HL_LIBRARY not found! Call:

-- FIND_LIBRARY(HDF5_HL_LIBRARY NAMES hdf5_hl HINTS PATH_SUFFIXES lib lib64 
lib)

-- HDF5_PUBCONF not found! Call:

-- FIND_FILE(HDF5_PUBCONF NAMES H5pubconf.h H5pubconf-64.h HINTS 
HDF5_INCLUDE_DIR-NOTFOUND PATH_SUFFIXES hdf5 hdf5/include include/hdf5 include)

--   HDF5_LIBRARIES: *** Required variable "HDF5_HL_LIBRARY" set to NOTFOUND ***

--   HDF5_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to 
NOTFOUND ***

--   HDF5_USER_INCLUDE_DIRS: *** Required variable "HDF5_INCLUDE_DIR" set to 
NOTFOUND ***

-- Could NOT find HDF5

-- DEAL_II_WITH_HDF5 has unmet external dependencies.

 

I've downloaded from 'https://www.hdfgroup.org/' the file 
'hdf5-1.12.0-linux-centos7-x86_64-shared-production.tar.gz'. And I have 
expanded it. Also, I've set the environment variable LD_LIBRARY_PATH to the 
folder where I've expanded it. With no success.

 

Any help will be welcome. Thanks a lot in advance.

 

Curro Trigo

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 .
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 .

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bcolz-doc - high performant compressed data container (documentation)
field3d-doc - documentation for Field3D
h5utils - Herramientas de visualización para archivos HDF5
hdf5-helpers - Hierarchical Data Format 5 (HDF5) - Helper tools
hdf5-tools - «Hierarchical Data Format 5» (HDF5), herramientas de ejecución
libfield3d-dev - development files for Field3D
libfield3d1.7 - library for storing voxel data on disk and in memory
libhdf5-103 - Hierarchical Data Format 5 (HDF5) - runtime files - serial version
libhdf5-cpp-103 - Hierarchical Data Forma

[deal.II] Step-7 Extension : How to get the runtime at each cycle to plot it

2021-03-21 Thread pushkar...@gmail.com 
Dear Deal.II Community

I am currently trying to implement the extensions in Step-7 tutorial 
program wherein I have to plot the runtime Vs error in order to get a 
better idea about the convergence characteristic of the solver as suggested 
in the documentation.Any help in this regard will be beneficial.

Regards
Pushkar

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