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OpenCMISS / setup

Helpful CMake based solution to creating an OpenCMISS libraries installation
Apache License 2.0
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Installation in Ubuntu #19

Open brycause opened 4 years ago

brycause commented 4 years ago

There says that we shoul reach the directory /OPENCMISS_ROOT/manage/build but in the archive here in the project there is no carpet called /build

sgenie68 commented 4 years ago

It looks like a typo, the correct path is OPENCMISS_ROOT/build/manage - I will take a look at the document

brycause commented 4 years ago

thank you for the answer. I'm actually right now trying to install it and there is no directory called build in the root carpet. The only carpet available is /manage

sgenie68 commented 4 years ago

Hi, I already replied to you in the email but I didn't realise it wouldn't be added to the github replies - just for completeness I will copy my email to you here, so ignore it:

he best way to install OpenCMISS is the following sequence:

git clone https://github.com/OpenCMISS/setup.git mkdir opencmiss mkdir setup-build cd setup-build

export CC=gcc export CXX=g++ export FC=gfortran cmake -DOPENCMISS_ROOT=../opencmiss -DOPENCMISS_LIBRARIES=iron ../setup make

This way all the service directories are created during the setup phase and you can compile parts of the system easily later on

Cheers, Gene

brycause commented 4 years ago

thank you very much Gene :^) I've tried again with this way, but again I get an error with it let me get you a shot of it captura

thanks for the help again

sgenie68 commented 4 years ago

Can you send me the content of the OC_IRON_CONFIGURE_err.log, please?

sgenie68 commented 4 years ago

Sorry, I mean this file:

/home/bryanaleman/OPENCMISS_ROOT/opencmiss/build/iron/release/extproj/stamp/OC_IRON-configure-err.log

brycause commented 4 years ago

Yup, my mistake, let me copy that for you haha Traceback (most recent call last): File "/home/bryanaleman/OPENCMISS_ROOT/opencmiss/src/iron/utils/numpy_include.py", line 1, in <module> import numpy ModuleNotFoundError: No module named 'numpy' CMake Error at bindings/CMakeLists.txt:96 (message): Could not detect NumPy includes. Unable to generate Python bindings for Iron.

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sgenie68 commented 4 years ago

Yeap - it cannot find numpy module - do you have it installed? What version of Python do you use?

brycause commented 4 years ago

I've got 2.7.17 Let me go ahead and install a 3 version

brycause commented 4 years ago

Thank you. I've already updated python and numpy package, but I've still got the same error

captura_1

Actually, all the times the problem is within the same directory

sgenie68 commented 4 years ago

Can you check if you have virtualenv directory created in opencmiss/install directory?

hsorby commented 4 years ago

The contents of the file: /home/bryanaleman/OPENCMISS_ROOT/opencmiss/build/iron/release/extproj/stamp/OC_IRON-configure-err.log

and also the file: /home/bryanaleman/OPENCMISS_ROOT/opencmiss/build/iron/release/extproj/stamp/OC_IRON-configure-out.log

would be really helpful in seeing what is going wrong.

brycause commented 4 years ago

@sgenie68 Thank you so much. I've already tried creating a new virtual enviroment in the install directory, but it didn't work either. @hsorby Let me get here what I got in those files

OC_IRON-configure-out.log Not searching for unused variables given on the command line. -- Iron::Instrumentation: -- Checking method: F77_HEADER -- Checking method: F08_MODULE -- Checking method: F90_MODULE -- FindLLVM wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindZLIB wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindLibXml2 wrapper: System search enabled -- FindLibXml2 wrapper: Trying to find version 2.7.6 on system in MODULE mode -- FindLibXml2 wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindClang wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindCSim wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Building with CELLML () -- Building with FIELDML (/home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake) -- Looking for SCALAPACK.. -- FindLAPACK wrapper: System search enabled -- FindLAPACK wrapper: Trying to find version 3.5.0 on system in MODULE mode -- A library with BLAS API found. -- FindLAPACK wrapper: Found: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so;gfortran -- FindBLAS wrapper: System search enabled -- FindBLAS wrapper: Trying to find version on system in MODULE mode -- FindBLAS wrapper: Found: /usr/lib/x86_64-linux-gnu/libblas.so -- FindSCALAPACK wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Looking for SCALAPACK.. found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake -- Looking for MUMPS.. -- FindPARMETIS wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindMUMPS wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Looking for MUMPS.. found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake -- Looking for HYPRE.. -- FindSUPERLU wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindHYPRE wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Looking for HYPRE.. found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake -- Looking for SUNDIALS.. -- FindSUNDIALS wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Looking for SUNDIALS.. found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake -- Looking for PETSC.. -- FindBZip2 wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindPASTIX wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindSUITESPARSE wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindSUPERLU_DIST wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- FindPETSC wrapper: Found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake in CONFIG mode -- Looking for PETSC.. found at /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/cmake -- Creating C bindings -- Creating Python bindings -- Configuring incomplete, errors occurred! See also "/home/bryanaleman/OPENCMISS_ROOT/opencmiss/build/iron/release/CMakeFiles/CMakeOutput.log". See also "/home/bryanaleman/OPENCMISS_ROOT/opencmiss/build/iron/release/CMakeFiles/CMakeError.log".

OC_IRON-configure-err.log

Traceback (most recent call last): File "/home/bryanaleman/OPENCMISS_ROOT/opencmiss/src/iron/utils/numpy_include.py", line 1, in <module> import numpy ModuleNotFoundError: No module named 'numpy' CMake Error at bindings/CMakeLists.txt:96 (message): Could not detect NumPy includes. Unable to generate Python bindings for Iron.

I don't know why it still says that I don't have pynumpy installed, I already prepared those when I installed all the requisites

sgenie68 commented 4 years ago

Can you try, this, please? In opencmiss/install/virtual_environments there is another directory oclibs_venv_XXXX something - make sure it is created. Then do this:

source /home/bryanaleman/OPENCMISS_ROOT/opencmiss/install/virtual_environments/oclibs_venv_XXXX/bin/activate pip install numpy deactivate

and then try running make again

If pip command fails with "missing interpreter" error, try using this:

python -m pip install numpy

Cheers, Gene

sgenie68 commented 4 years ago

Hi,

It just occurred to me that there might be a problem with the way virtual environment is being generated. Could you give me full path to the bin directory in the virtual_environment structure that OpenCMISS make generated?

Gene

sgenie68 commented 4 years ago

I have made a small change in one of the cmake files to avoid the problem you are seeing - can you try updating your code and running the build again?