Question - cmake runs examples fine but not after I copy them to ~/shared

[yw5aj]

Short summary: cmake runs examples fine when I run it in the pre-installed src example folder, but not after I copied it to ~/shared. Could you please help see why?

Full story: first, when I run it in the pre-installed src example folder, it works:

E:\dealii>docker pull dealii/dealii:v8.5.1-gcc-mpi-fulldepscandi-debugrelease
v8.5.1-gcc-mpi-fulldepscandi-debugrelease: Pulling from dealii/dealii
Digest: sha256:5c6ed25801292f715136bdad411e7dcda1d8f647f60c31be10533aa2697582ac
Status: Image is up to date for dealii/dealii:v8.5.1-gcc-mpi-fulldepscandi-debugrelease

E:\dealii>docker run -i -t -v E:\dealii:/home/dealii/shared dealii/dealii:v8.5.1-gcc-mpi-fulldepscandi-debugrelease
dealii@d0e24c0315a5:~$ cd dealii-v8.5.1-src/examples/step-1
dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ cmake CMakeLists.txt
-- The C compiler identification is GNU 6.2.0
-- The CXX compiler identification is GNU 6.2.0
-- Check for working C compiler: /usr/bin/mpicc
-- Check for working C compiler: /usr/bin/mpicc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx
-- Check for working CXX compiler: /usr/bin/mpicxx -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Autopilot invoked
###
#
#  Project  step-1  set up with  deal.II-8.5.1  found at
#      /home/dealii/dealii-v8.5.1
#
#  CMAKE_BUILD_TYPE:          Debug
#
#  You can now run
#       $ make                - to compile and link the program
#       $ make run            - to (compile, link and) run the program
#
#       $ make debug          - to switch the build type to 'Debug'
#       $ make release        - to switch the build type to 'Release'
#
#       $ make edit_cache     - to change (cached) configuration variables
#                               and rerun the configure and generate phases of CMake
#
#       $ make strip_comments - to strip the source files in this
#                               directory off the documentation comments
#       $ make clean          - to remove the generated executable as well as
#                               all intermediate compilation files
#       $ make runclean       - to remove all output generated by the program
#       $ make distclean      - to clean the directory from _all_ generated
#                               files (includes clean, runclean and the removal
#                               of the generated build system)
#       $ make info           - to view this message again
#
#  Have a nice day!
#
###
-- Configuring done
-- Generating done
-- Build files have been written to: /home/dealii/dealii-v8.5.1-src/examples/step-1
dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ make run
Scanning dependencies of target step-1
[ 33%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o
[ 66%] Linking CXX executable step-1
[ 66%] Built target step-1
Scanning dependencies of target run
[100%] Run step-1 with Debug configuration
Grid written to grid-1.eps
Grid written to grid-2.eps
[100%] Built target run

However, if I copy the examples to my local folder, it wouldn't work. (Edit on 3/23 - removed the confusion parts of the code where I forgot to clean the old cmake file first)

(I cleaned the folder and then copied the examples to ~/shared/examples)

dealii@d0e24c0315a5:~/shared/examples/step-1$ ls
CMakeLists.txt  step-1.cc
dealii@d0e24c0315a5:~/shared/examples/step-1$ cmake CMakeLists.txt
-- The C compiler identification is GNU 6.2.0
-- The CXX compiler identification is GNU 6.2.0
-- Check for working C compiler: /usr/bin/mpicc
-- Check for working C compiler: /usr/bin/mpicc -- broken
CMake Error at /usr/share/cmake-3.5/Modules/CMakeTestCCompiler.cmake:61 (message):
  The C compiler "/usr/bin/mpicc" is not able to compile a simple test
  program.

  It fails with the following output:

   Change Dir: /home/dealii/shared/examples/step-1/CMakeFiles/CMakeTmp

  Run Build Command:"/usr/bin/make" "cmTC_f6b04/fast"

  make: *** No rule to make target 'cmTC_f6b04/fast'.  Stop.

  CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:38 (PROJECT)

-- Configuring incomplete, errors occurred!
See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeOutput.log".
See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeError.log".

Could you please help?

Thank you, Shawn

[Rombur]

Remove the CMakeCache.txt file. You have a problem because you first configured the test and then moved the directory. Because of that all the paths are wrong. You need to remove CMakeCache.txt in order to do a clean configure.

[yw5aj]

@Rombur Thank you Rombur for your response! Yes I tried that already and posted it in the first message, but I failed to explain it clearly enough (I did not break them up into sub paragraphs). Apologies for the confusion.

At first I did forget to remove the CMakeCache.txt:

dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ cp -r ~/dealii-v8.5.1-src/examples ~/shared/examples
dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ cd ~/shared/examples/step-1
dealii@d0e24c0315a5:~/shared/examples/step-1$ cmake CMakeLists.txt
CMake Error: The current CMakeCache.txt directory /home/dealii/shared/examples/step-1/CMakeCache.txt is different than the directory /home/dealii/dealii-v8.5.1-src/examples/step-1 where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt
CMake Error: The source "/home/dealii/shared/examples/step-1/CMakeLists.txt" does not match the source "/home/dealii/dealii-v8.5.1-src/examples/step-1/CMakeLists.txt" used to generate cache.  Re-run cmake with a different source directory.

So I removed all those files except for the step-1.cc and the CMakeLists.txt:

dealii@d0e24c0315a5:~/shared/examples/step-1$ ls | grep -v 'CMakeLists.txt\|step-1.cc' | xargs rm -rf
dealii@d0e24c0315a5:~/shared/examples/step-1$ ls
CMakeLists.txt  step-1.cc

And then I re-ran the cmake command, and encountered an issue where mpicc is not working:

dealii@d0e24c0315a5:~/shared/examples/step-1$ cmake CMakeLists.txt
-- The C compiler identification is GNU 6.2.0
-- The CXX compiler identification is GNU 6.2.0
-- Check for working C compiler: /usr/bin/mpicc
-- Check for working C compiler: /usr/bin/mpicc -- broken
CMake Error at /usr/share/cmake-3.5/Modules/CMakeTestCCompiler.cmake:61 (message):
  The C compiler "/usr/bin/mpicc" is not able to compile a simple test
  program.

  It fails with the following output:

   Change Dir: /home/dealii/shared/examples/step-1/CMakeFiles/CMakeTmp

  Run Build Command:"/usr/bin/make" "cmTC_f6b04/fast"

  make: *** No rule to make target 'cmTC_f6b04/fast'.  Stop.

  CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:38 (PROJECT)

-- Configuring incomplete, errors occurred!
See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeOutput.log".
See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeError.log".

[luca-heltai]

remove also the directory CMakeFiles…

L.

On 23 Mar 2018, at 16:14, Yuxiang Wang notifications@github.com wrote:

@Rombur Thank you Rombur for your response! Yes I tried that already and posted it in the first message, but I failed to explain it clearly enough. Apologies for the confusion.

At first I did forget to remove the CMakeCache.txt:

dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ cp -r ~/dealii-v8.5.1-src/examples ~/shared/examples dealii@d0e24c0315a5:~/dealii-v8.5.1-src/examples/step-1$ cd ~/shared/examples/step-1 dealii@d0e24c0315a5:~/shared/examples/step-1$ cmake CMakeLists.txt CMake Error: The current CMakeCache.txt directory /home/dealii/shared/examples/step-1/CMakeCache.txt is different than the directory /home/dealii/dealii-v8.5.1-src/examples/step-1 where CMakeCache.txt was created. This may result in binaries being created in the wrong place. If you are not sure, reedit the CMakeCache.txt CMake Error: The source "/home/dealii/shared/examples/step-1/CMakeLists.txt" does not match the source "/home/dealii/dealii-v8.5.1-src/examples/step-1/CMakeLists.txt" used to generate cache. Re-run cmake with a different source directory.

So I removed all those files except for the step-1.cc and the CMakeLists.txt:

dealii@d0e24c0315a5:~/shared/examples/step-1$ ls | grep -v 'CMakeLists.txt|step-1.cc' | xargs rm -rf dealii@d0e24c0315a5:~/shared/examples/step-1$ ls CMakeLists.txt step-1.cc

And then I re-ran the cmake command, and encountered an issue where mpicc is not working:

dealii@d0e24c0315a5:~/shared/examples/step-1$ cmake CMakeLists.txt -- The C compiler identification is GNU 6.2.0 -- The CXX compiler identification is GNU 6.2.0 -- Check for working C compiler: /usr/bin/mpicc -- Check for working C compiler: /usr/bin/mpicc -- broken CMake Error at /usr/share/cmake-3.5/Modules/CMakeTestCCompiler.cmake:61 (message): The C compiler "/usr/bin/mpicc" is not able to compile a simple test program.

It fails with the following output:

Change Dir: /home/dealii/shared/examples/step-1/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_f6b04/fast"

make: *** No rule to make target 'cmTC_f6b04/fast'. Stop.

CMake will not be able to correctly generate this project. Call Stack (most recent call first): CMakeLists.txt:38 (PROJECT)

-- Configuring incomplete, errors occurred! See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeOutput.log". See also "/home/dealii/shared/examples/step-1/CMakeFiles/CMakeError.log".

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[yw5aj]

@luca-heltai Thanks for you response! Yes I did - I only left step-1.cc and CMakeLists.txt, by running ls | grep -v 'CMakeLists.txt\|step-1.cc' | xargs rm -rf. And the mpicc still failed.

[luca-heltai]

is the directory writeable by you?

[yw5aj]

@luca-heltai Thank you for the quick response.

1) Yes I do - I tried the following:

dealii@4672ffbca33e:~/shared/examples/step-1$ touch test.txt
dealii@4672ffbca33e:~/shared/examples/step-1$ ls
CMakeLists.txt  step-1.cc  test.txt

2) I had the same question yesterday, because in the CMakeError.log I read the following lines:

Determining if the C compiler works failed with the following output:
Change Dir: /home/dealii/shared/examples/step-1/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_a147c/fast"
make: *** No rule to make target 'cmTC_a147c/fast'.  Stop.

[luca-heltai]

Mmmm... it seems like it does not create directories. Can you create directories?

[yw5aj]

@luca-heltai Yes I feel the same way - it seems like it failed to create cmTC_a147c/fast. However, it did create all the other folders like CMakeFiles, CMakeTmp. Also, I tried the following:

dealii@4672ffbca33e:~/shared/examples/step-1$ ls
CMakeLists.txt  step-1.cc
dealii@4672ffbca33e:~/shared/examples/step-1$ mkdir testdir
dealii@4672ffbca33e:~/shared/examples/step-1$ cd testdir
dealii@4672ffbca33e:~/shared/examples/step-1/testdir$ touch test.txt
dealii@4672ffbca33e:~/shared/examples/step-1/testdir$ ls
test.txt
dealii@4672ffbca33e:~/shared/examples/step-1/testdir$ cd ..
dealii@4672ffbca33e:~/shared/examples/step-1$ ls
CMakeLists.txt  step-1.cc  testdir

[satrapes]

Maybe this could help to debug it. https://intellij-support.jetbrains.com/hc/en-us/community/posts/207460115/comments/360002077699