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uDALES / u-dales

uDALES: large-eddy-simulation software for urban flow, dispersion and microclimate modelling
https://udales.github.io/u-dales
GNU General Public License v3.0
54 stars 18 forks source link

Update example simulations after changing floor facet block indices. #89

Closed samoliverowens closed 3 years ago

samoliverowens commented 3 years ago

I have re-run the preprocessing routines after solving issue #56 through commit 065eb8a9018b13f1465495e02a9a546fc6d1b2f0, and put the affected files in this branch.

bss116 commented 3 years ago

@samoliverowens Did you do a test run with any of the example simulations?

samoliverowens commented 3 years ago

@samoliverowens Did you do a test run with any of the example simulations?

Not yet, I'll try now.

samoliverowens commented 3 years ago

@samoliverowens Did you do a test run with any of the example simulations?

Not yet, I'll try now.

I'm having trouble building on my mac - @dmey I feel you might be able to help. Running cmake -LA ../.. gives the following error:

CMake Error in /Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeTmp/CMakeLists.txt:
  Imported target "MPI::MPI_Fortran" includes non-existent path

    "/usr/local/Cellar/open-mpi/4.0.1_2/lib"

This path indeed doesn't exist, it should be /usr/local/Cellar/open-mpi/4.0.5/lib. How do I get it to look for this instead?

samoliverowens commented 3 years ago

(I usually run everything on my linux machine or the HPC but I thought I'd just run the example simulations on my laptop)

dmey commented 3 years ago

@samoliverowens great to try on macOS! I don't have one at hand but it looks like you may have different versions of openMP installed with brew -- can you do a search brew search open-mpi

samoliverowens commented 3 years ago

@samoliverowens great to try on macOS! I don't have one at hand but it looks like you may have different versions of openMP installed with brew -- can you do a search brew search open-mpi

I just get open-mpi. I have had this before and it was to do with the fortran compiler I think...

dmey commented 3 years ago

I just checked on the CI (https://travis-ci.com/github/uDALES/u-dales/jobs/432399341#L153) and it looks like brew is using version 4.0.3 on macOS 10.14.6. I would suggest trying to do brew cleanup and maybe remove and reinstall open-mpi/gfortran/gcc -- We can otherwise specify this in CMake but given that this is due to brew it may make more sense to solve this at the source.

samoliverowens commented 3 years ago

I just checked on the CI (https://travis-ci.com/github/uDALES/u-dales/jobs/432399341#L153) and it looks like brew is using version 4.0.3 on macOS 10.14.6. I would suggest trying to do brew cleanup and maybe remove and reinstall open-mpi/gfortran/gcc -- We can otherwise specify this in CMake but given that this is due to brew it may make more sense to solve this at the source.

I've already done that - it's weird because it finds the correct version for MPI_Fortran_COMPILER_INCLUDE_DIRS. I'll post the whole error message in case that's helpful.


-- The Fortran compiler identification is GNU 10.2.0
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran - skipped
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 - yes
CMake Error in /Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeTmp/CMakeLists.txt:
  Imported target "MPI::MPI_Fortran" includes non-existent path

    "/usr/local/Cellar/open-mpi/4.0.1_2/lib"

  in its INTERFACE_INCLUDE_DIRECTORIES.  Possible reasons include:

  * The path was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and references files it does not
  provide.

CMake Error in /Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeTmp/CMakeLists.txt:
  Imported target "MPI::MPI_Fortran" includes non-existent path

    "/usr/local/Cellar/open-mpi/4.0.1_2/lib"

  in its INTERFACE_INCLUDE_DIRECTORIES.  Possible reasons include:

  * The path was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and references files it does not
  provide.

CMake Error in /Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeTmp/CMakeLists.txt:
  Imported target "MPI::MPI_Fortran" includes non-existent path

    "/usr/local/Cellar/open-mpi/4.0.1_2/lib"

  in its INTERFACE_INCLUDE_DIRECTORIES.  Possible reasons include:

  * The path was deleted, renamed, or moved to another location.

  * An install or uninstall procedure did not complete successfully.

  * The installation package was faulty and references files it does not
  provide.

CMake Error at /usr/local/Cellar/cmake/3.18.4/share/cmake/Modules/FindMPI.cmake:1213 (try_compile):
  Failed to generate test project build system.
Call Stack (most recent call first):
  /usr/local/Cellar/cmake/3.18.4/share/cmake/Modules/FindMPI.cmake:1239 (_MPI_try_staged_settings)
  /usr/local/Cellar/cmake/3.18.4/share/cmake/Modules/FindMPI.cmake:1529 (_MPI_check_lang_works)
  CMakeLists.txt:33 (find_package)

-- Configuring incomplete, errors occurred!
See also "/Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeOutput.log".
See also "/Users/samowens/u-dales-testing/u-dales/build/release/CMakeFiles/CMakeError.log".
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bss116 commented 3 years ago

Have you tried removing the build/release folder to make sure it creates everything from scratch? This fixed some issues for me in the past..

samoliverowens commented 3 years ago

Have you tried removing the build/release folder to make sure it creates everything from scratch? This fixed some issues for me in the past..

Ahh that worked! Now I can build, but I get this error:

make[2]: *** No rule to make target `external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build/src/libfishpack_static.a', needed by `u-dales'.  Stop.
dmey commented 3 years ago

Does it download and build fishpack-cmake? if you use make -j1 it may be easier to read the logs as things don't get interleaved. you should get something like:

Scanning dependencies of target fishpack-cmake-project
[  1%] Creating directories for 'fishpack-cmake-project'
[  3%] Performing download step (git clone) for 'fishpack-cmake-project'
Cloning into 'fishpack-cmake-project'...
Branch 'dmey/cray-support' set up to track remote branch 'dmey/cray-support' from 'origin'.
Switched to a new branch 'dmey/cray-support'
[  5%] No patch step for 'fishpack-cmake-project'
[  7%] Performing update step for 'fishpack-cmake-project'
Current branch dmey/cray-support is up to date.
[  9%] Performing configure step for 'fishpack-cmake-project'
-- The Fortran compiler identification is GNU 7.5.0
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/u-dales/build/release/external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build
[ 11%] Performing build step for 'fishpack-cmake-project'
Scanning dependencies of target objlib
[  4%] Building Fortran object src/CMakeFiles/objlib.dir/blktri.f.o

If not please send me the full log and I can have a look

samoliverowens commented 3 years ago

Does it download and build fishpack-cmake? if you use make -j1 it may be easier to read the logs as things don't get interleaved. you should get something like:

Scanning dependencies of target fishpack-cmake-project
[  1%] Creating directories for 'fishpack-cmake-project'
[  3%] Performing download step (git clone) for 'fishpack-cmake-project'
Cloning into 'fishpack-cmake-project'...
Branch 'dmey/cray-support' set up to track remote branch 'dmey/cray-support' from 'origin'.
Switched to a new branch 'dmey/cray-support'
[  5%] No patch step for 'fishpack-cmake-project'
[  7%] Performing update step for 'fishpack-cmake-project'
Current branch dmey/cray-support is up to date.
[  9%] Performing configure step for 'fishpack-cmake-project'
-- The Fortran compiler identification is GNU 7.5.0
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/u-dales/build/release/external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build
[ 11%] Performing build step for 'fishpack-cmake-project'
Scanning dependencies of target objlib
[  4%] Building Fortran object src/CMakeFiles/objlib.dir/blktri.f.o

If not please send me the full log and I can have a look

Yes my initial log is very similar:

[  1%] Creating directories for 'fishpack-cmake-project'
[  3%] Performing download step (git clone) for 'fishpack-cmake-project'
Cloning into 'fishpack-cmake-project'...
Branch 'dmey/cray-support' set up to track remote branch 'dmey/cray-support' from 'origin'.
Switched to a new branch 'dmey/cray-support'
[  5%] Performing update step for 'fishpack-cmake-project'
[  7%] No patch step for 'fishpack-cmake-project'
[  9%] Performing configure step for 'fishpack-cmake-project'
-- The Fortran compiler identification is GNU 10.2.0
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/local/bin/gfortran - skipped
-- Checking whether /usr/local/bin/gfortran supports Fortran 90
-- Checking whether /usr/local/bin/gfortran supports Fortran 90 - yes
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/samowens/u-dales-testing/u-dales/build/release/external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build
[ 11%] Performing build step for 'fishpack-cmake-project'
Scanning dependencies of target objlib
[  4%] Building Fortran object src/CMakeFiles/objlib.dir/blktri.f.o

Everything appears to work fine until 

...
[ 90%] Building Fortran object CMakeFiles/u-dales.dir/src/scalsource.f90.o
[ 92%] Building Fortran object CMakeFiles/u-dales.dir/src/tstep.f90.o
[ 94%] Building Fortran object CMakeFiles/u-dales.dir/src/wf_gr.f90.o
[ 96%] Building Fortran object CMakeFiles/u-dales.dir/src/wf_uno.f90.o
[ 98%] Building Fortran object CMakeFiles/u-dales.dir/src/wfmneutral.f90.o
make[2]: *** No rule to make target `external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build/src/libfishpack_static.a', needed by `u-dales'.  Stop.
[100%] Built target u-dales
dmey commented 3 years ago

Does external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-build/src/libfishpack_static.a exist? Can you also delete the folder and do 

cmake -LA ../.. > config.log
VERBOSE=1 make > build.log
cd external && tree . > tree.log

and send me those files -- drag and drop in here/email...

samoliverowens commented 3 years ago

Here are the files produced by those commands:

config.log build.log tree.log

Also, here's the result of VERBOSE=1 make -i > build.log:

build.log tree.log

build.log doesn't actually contain all that was output to the terminal - is that alright?

dmey commented 3 years ago

@samoliverowens sorry my bad, forgot to include stderror... Use &> instead of just > i.e. --

cmake -LA ../.. &> config.log
VERBOSE=1 make &> build.log
cd external && tree . &> tree.log

just remove folder and rerun again and no need to run the other make without VEBOSE=1...

samoliverowens commented 3 years ago

@samoliverowens sorry my bad, forgot to include stderror... Use &> instead of just > i.e. --

cmake -LA ../.. &> config.log
VERBOSE=1 make &> build.log
cd external && tree . &> tree.log

just remove folder and rerun again and no need to run the other make without VEBOSE=1...

Ok here are the new files: config.log build.log tree.log

dmey commented 3 years ago

@samoliverowens the error is to with the fishpack library --

Error: Type mismatch in argument 'cbp' at (1); passed REAL(8) to COMPLEX(8)
make[5]: *** [src/CMakeFiles/objlib.dir/blktri.f.o] Error 1
make[4]: *** [src/CMakeFiles/objlib.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-stamp/fishpack-cmake-project-build] Error 2
make[1]: *** [external/CMakeFiles/fishpack-cmake-project.dir/all] Error 2
make: *** [all] Error 2

Given that this is a legacy library, I would be more inclined to limit the supported version of uDALES to GCC versions< 10 as it may take some time to get at the bottom of this... I am going to submit a PR for that, in the meantime can you please install GFortran 9 with brew install gcc@9 and either unlink GFortran 10 or specify GFortran 9 at configure with the FC flag. e.g. FC=gfortran-9 cmake ..

samoliverowens commented 3 years ago

@samoliverowens the error is to with the fishpack library --

Error: Type mismatch in argument 'cbp' at (1); passed REAL(8) to COMPLEX(8)
make[5]: *** [src/CMakeFiles/objlib.dir/blktri.f.o] Error 1
make[4]: *** [src/CMakeFiles/objlib.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [external/fishpack-cmake-project-prefix/src/fishpack-cmake-project-stamp/fishpack-cmake-project-build] Error 2
make[1]: *** [external/CMakeFiles/fishpack-cmake-project.dir/all] Error 2
make: *** [all] Error 2

Given that this is a legacy library, I would be more inclined to limit the supported version of uDALES to GCC versions< 10 as it may take some time to get at the bottom of this... I am going to submit a PR for that, in the meantime can you please install GFortran 9 with brew install gcc@9 and either unlink GFortran 10 or specify GFortran 9 at configure with the FC flag. e.g. FC=gfortran-9 cmake ..

Ok that's got it, thanks! Will now try to run the example sims.