Deal.ii installation

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Prasad Adhav

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Apr 27, 2020, 5:27:31 AM4/27/20
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Hello,

I am trying to install deal.ii for the first time.
I followed the instructions on the readme page(https://www.dealii.org/current/readme.html)

I use the following for cmake and it worked fine:

prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/
prasad/Downloads/dealii-9.1.1/dealii_install/ ..

Then I tried to do `make`, `make info` and `make install`, I get a similar error as follows:
prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info
make: *** No rule to make target 'info'.  Stop.

prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make install
make: *** No rule to make target 'install'.  Stop.

I apologize if this was already posted, in my search I did not find any questions similar to this.
Can anyone help with this?
Thank you.



CMakeError.log
CMakeOutput.log

Wolfgang Bangerth

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Apr 27, 2020, 8:52:42 AM4/27/20
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On 4/27/20 3:27 AM, Prasad Adhav wrote:
>
> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ cmake
> -DCMAKE_INSTALL_PREFIX=/home/
> prasad/Downloads/dealii-9.1.1/dealii_install/ ..
>
> Then I tried to do `make`, `make info` and `make install`, I get a similar
> error as follows:
> prasad@XDEM-laptop:~/Downloads/dealii-9.1.1/build$ make info
> make: *** No rule to make target 'info'.  Stop.

In your build directory, is there actually a 'Makefile' file? My suspicion is
that cmake did not, in fact, succeed...

Best
W.


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Wilmar Alves Cruvinel Lima

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Apr 27, 2020, 2:18:24 PM4/27/20
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Hi, Prasad,

I am installing Dealii too. I apologise by not have the solution, but I want to ask you if you first installed Cmake and begin using it. You didn't do that?

Thank you.

Wilmar.
 

Prasad Adhav

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Apr 28, 2020, 2:24:05 AM4/28/20
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Hello Wilmar,

I did install cmake for another library I am using. 
The installation worked and I have tested out those installations.

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Marc Fehling

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Apr 28, 2020, 4:47:26 AM4/28/20
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Hi Prasad!

Thank you for providing the logs! It seems like this here is the cause of it:
/usr/bin/ld: cannot find -lpthreads

It seems like this is again related to the `-lpthread` problem. Just out of curiosity: Which version of cmake and which OS are you using? They may have updated CMake in their repository which could be the reason why we see this issue more frequently recently...

This may have been fixed upstream in pull request #9117. This issue only occurs with CMake version >= 3.16. Just compile from the master branch and you should be good!

Best,
Marc

Prasad Adhav

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Apr 28, 2020, 4:54:54 AM4/28/20
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Hello Marc,

Thank you for your reply.
I am using cmake version 3.10.2
My OS is Ubuntu 18.04 LTS.

Do you think the cmake version is an issue?
I will try the fix from the issue you suggested.

Regards,
Prasad

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Marc Fehling

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Apr 28, 2020, 5:07:30 AM4/28/20
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Hi Prasad!


On Tuesday, April 28, 2020 at 10:54:54 AM UTC+2, Prasad Adhav wrote:
I am using cmake version 3.10.2

With version 3.10.2, it is less likely that my suggestion will fix your problem.

Did cmake actually finished the configuration, as Wolfgang pointed out? Going through the error log, you may not have all dependencies of deal.II fulfilled, and I'm not entirely sure which tests are mandatory to pass. What does cmake print in your console when you run `cmake ..`? The end of the console output should give you a hint on what's missing.

Best,
Marc

Prasad Adhav

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Apr 28, 2020, 7:35:36 AM4/28/20
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@Marc I tried doing the whole thing again and I do get some warning at the end which I didn't get before.
-- Configuring incomplete, errors occurred!
See also "/home/prasad/Downloads/dealii/build/CMakeFiles/CMakeOutput.log".
See also "/home/prasad/Downloads/dealii/build/CMakeFiles/CMakeError.log".
I think there are some dependencies missing, but not sure which.

The errors are on line 11 and 14.
I have attached the error log though.

Performing C++ SOURCE FILE Test DEAL_II_HAVE_FLAG_Wclass_memaccess failed with the following output:
Change Dir: /home/prasad/Downloads/dealii/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_a2197/fast"
/usr/bin/make -f CMakeFiles/cmTC_a2197.dir/build.make CMakeFiles/cmTC_a2197.dir/build
make[1]: Entering directory '/home/prasad/Downloads/dealii/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_a2197.dir/src.cxx.o
/usr/bin/c++    -DDEAL_II_HAVE_FLAG_Wclass_memaccess   -Wclass-memaccess -o CMakeFiles/cmTC_a2197.dir/src.cxx.o -c /home/prasad/Downloads/dealii/build/CMakeFiles/CMakeTmp/src.cxx
c++: error: unrecognized command line option '-Wclass-memaccess'
CMakeFiles/cmTC_a2197.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_a2197.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_a2197.dir/src.cxx.o] Error 1
make[1]: Leaving directory '/home/prasad/Downloads/dealii/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_a2197/fast' failed

make: *** [cmTC_a2197/fast] Error 2




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CMakeError.log
CMakeOutput.log

Marc Fehling

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Apr 28, 2020, 10:04:31 AM4/28/20
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Prasad!

If you look closely into your CMakeError.log file, you'll find that there are multiple tests failing. This is not a bad thing: deal.II figures out your system configuration this way and enables/disables certain features. However in your case, it seems that there is a mandatory test failing, and I can not figure out which one by these two log files alone. Could you provide your cmake console output?

Could you redirect your console output into a file e.g. via `cmake .. > console.log` and forward it?

Best,
Marc

Prasad Adhav

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Apr 28, 2020, 10:22:52 AM4/28/20
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Marc,

I hope this helps with figuring out the failing test.
Thank you very much for your help.

Regards,
Prasad

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console.log

Marc Fehling

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Apr 28, 2020, 1:09:29 PM4/28/20
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Hi Prasad!

My guess now is the following: You have PETSc and Trilinos installed on your device, which deal.II finds, but complains that PETSc has been installed with a different MPI configuration as is available for deal.II.

-- Include /home/prasad/Downloads/dealii/cmake/configure/configure_3_petsc.cmake
-- Found PETSC_LIBRARY
-- Found PETSC_INCLUDE_DIR_ARCH
-- Found PETSC_INCLUDE_DIR_COMMON
-- PETSC_PETSCVARIABLES not found! Call:
--     FIND_FILE(PETSC_PETSCVARIABLES NAMES petscvariables HINTS /usr/lib/petscdir/3.6.2//x86_64-linux-gnu-real /usr/lib/petscdir/3.6.2/ PATH_SUFFIXES conf lib/petsc/conf)
--   PETSC_VERSION: 3.7.7.0
--   PETSC_LIBRARIES: /usr/lib/x86_64-linux-gnu/libpetsc.so
--   PETSC_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
--   PETSC_USER_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
-- Found PETSC
-- Could not find a sufficient PETSc installation: PETSc has to be configured with the same MPI configuration as deal.II.
-- DEAL_II_WITH_PETSC has unmet external dependencies.

Later, we find:

-- Include /home/prasad/Downloads/dealii/cmake/configure/configure_p4est.cmake
-- DEAL_II_WITH_P4EST has unmet configuration requirements: DEAL_II_WITH_MPI has to be set to "ON".
--
-- Include /home/prasad/Downloads/dealii/cmake/configure/configure_scalapack.cmake
-- DEAL_II_WITH_SCALAPACK has unmet configuration requirements: DEAL_II_WITH_MPI has to be set to "ON".
--
-- Include /home/prasad/Downloads/dealii/cmake/configure/configure_slepc.cmake
-- DEAL_II_WITH_SLEPC has unmet configuration requirements: DEAL_II_WITH_PETSC has to be set to "ON".

Is your intention to use parallel features of deal.II? Otherwise I'd suggest to explicitly disable all parallel features for now with:
cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF -DDEAL_II_WITH_PETSC=OFF ..

Hope this helps for now!

Best,
Marc

Prasad Adhav

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Jun 3, 2020, 5:21:49 AM6/3/20
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I am sorry to be a bother, but the last time I tried the suggestion without any success. 
cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF -DDEAL_II_WITH_PETSC=OFF ..

I had to shift to a different task.

I have to come back to install deal.ii though. I thought of starting a from new.
I want to run a coupled simulation using the preCICE library, where deal.ii will be used for FEM part.( hence I am trying to install v9.1.0).

I am using Ubuntu 18.04 LTS.
cmake version 3.10.2

I first did
cmake -DCMAKE_INSTALL_PREFIX=/home/prasad/bin/deal.II ../

then I did
cmake -DDEALII_WITH_MPI=OFF -DDEALII_WITH_TRILINOS=OFF -DDEAL_II_WITH_PETSC=OFF ..

The dealii_cmake.log has the output for my terminal.
CMakeError.log and CmakeOutput.log are also attached. 

The immediate issues seen are 
-- Include /home/prasad/bin/dealii-9.1.0/cmake/configure/configure_muparser.cmake
-- MUPARSER_LIBRARY not found! Call:
--     FIND_LIBRARY(MUPARSER_LIBRARY NAMES muparser muparserd HINTS PATH_SUFFIXES lib lib64 lib)
-- MUPARSER_INCLUDE_DIR not found! Call:
--     FIND_PATH(MUPARSER_INCLUDE_DIR muParserDef.h HINTS PATH_SUFFIXES include)
--   MUPARSER_LIBRARIES: *** Required variable "MUPARSER_LIBRARY" set to NOTFOUND ***
--   MUPARSER_INCLUDE_DIRS: *** Required variable "MUPARSER_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find MUPARSER
-- DEAL_II_WITH_MUPARSER has unmet external dependencies.
-- DEAL_II_WITH_MUPARSER successfully set up with bundled packages.


The further output shows, with examples with dependencies not satisfied.
-- Configuring done. Proceed to target definitions now.
-- Setting up bundled features
-- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1
-- Performing Test DEAL_II_HAVE_FLAG_flifetime_dse=1 - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0
-- Performing Test DEAL_II_HAVE_FLAG_Wimplicit_fallthrough=0 - Success
-- Setting up bundled features - Done
-- Setting up library
-- Setting up library - Done
-- Setting up project configuration
-- Setting up project configuration - Done
-- Setting up examples
--   step-17 - dependencies not satisfied
--   step-18 - dependencies not satisfied
--   step-32 - dependencies not satisfied
--   step-36 - dependencies not satisfied
--   step-40 - dependencies not satisfied
--   step-42 - dependencies not satisfied
--   step-45 - dependencies not satisfied
--   step-54 - dependencies not satisfied
--   step-55 - dependencies not satisfied
--   step-62 - dependencies not satisfied
--   step-64 - dependencies not satisfied
-- Setting up examples - Done
-- Setting up quick_tests in DEBUG mode
-- Setting up quick_tests in DEBUG mode - Done
-- Setting up testsuite
-- Setting up testsuite - Done

Thank you in advance for your help and patience.

Regards,
Prasad ADHAV

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dealii_cmake.log
CMakeError.log
CMakeOutput.log

Daniel Arndt

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Jun 3, 2020, 8:39:22 AM6/3/20
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Prasad,

CMake ran successfully and the output looks fine. Some of the example steps require certain dependencies which you just didn't activate.
Note, that you will not be able to use MPI with this configuration.

Best,
Daniel


Prasad Adhav

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Jun 3, 2020, 11:11:00 AM6/3/20
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Dear Daniel,

Thank you for your reply.

1. The thing is after I do the cmake step, and go on to do  make --jobs=4 install , I get the following output in the terminal.
make: *** No rule to make target 'install'.  Stop.
Am I running this command from a wrong directory?

2. For the dependencies, should I install them manually? and add them to cmake command I pass?

Thank you for all the help.
Regards,
Prasad


Prasad Adhav

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Jun 3, 2020, 1:24:29 PM6/3/20
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I was able to solve the issue by installing trilinos-all-dev.

~$ sudo apt-get update -y
~$ sudo apt-get install -y trilinos-all-dev

Download Deal.ii
Moved it to bin

~/bin$ tar -xvf deal.II-9.1.1.tar.gz
~/bin/dealii-9.1.1$ mkdir build
~/bin/dealii-9.1.1$ cd build
~/bin/dealii-9.1.1/buildcmake -DCMAKE_INSTALL_PREFIX=/home/prasad/bin/deal.II ..
~/bin/dealii-9.1.1/buildmake install
~/bin/dealii-9.1.1/buildmake test

prasad@XDEM-laptop:~/bin/dealii-9.1.1/build$ make test
Scanning dependencies of target test
Running quicktests...
Test project /home/prasad/bin/dealii-9.1.1/build/tests/quick_tests
   Start 1: step.debug
   Start 2: step.release
   Start 3: affinity.debug
   Start 4: tbb.debug
   Start 5: lapack.debug
   Start 6: umfpack.debug
   Start 7: boost_zlib.debug
   Start 8: gmsh.debug
1/8 Test #5: lapack.debug .....................   Passed   34.73 sec
2/8 Test #4: tbb.debug ........................   Passed   38.34 sec
3/8 Test #8: gmsh.debug .......................   Passed   44.55 sec
4/8 Test #7: boost_zlib.debug .................   Passed   44.97 sec
5/8 Test #3: affinity.debug ...................   Passed   44.98 sec
6/8 Test #6: umfpack.debug ....................   Passed   48.18 sec
7/8 Test #2: step.release .....................   Passed   52.11 sec
8/8 Test #1: step.debug .......................   Passed   54.85 sec

100% tests passed, 0 tests failed out of 8

Total Test time (real) =  54.85 sec
Built target test

Jean-Paul Pelteret

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Jun 9, 2020, 4:26:33 PM6/9/20
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Dear Prasad,

I’m glad to hear that you solved your problem. I must say, though, that the problem and the solution only seems to me to be tangentially related.  Although neither you, I, nor probably anyone else could have guessed from the cryptic and nondescript error message, you were probably missing some critical core package required to build the library. Many of these dependencies would be installed via

sudo apt-get install build-essential  

but it could be that something else is required. Here, for example, is a list of the packages assumed to be installed when building deal.II using Candi.


Note through that many of these packages would only be required by the dependencies (e.g. Trilinos). The key one there is, again, probably build-essential . But this is just speculation - I currently don’t have an Ubuntu installation with to test my suspicion. But I thought I’d just share my thoughts in case someone else hits the same problem and spots this thread while looking for a solution.

Best,
Jean-Paul

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