Installation in Ubuntu

[brycause]

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]

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

[brycause]

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]

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]

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

thanks for the help again

[sgenie68]

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

[sgenie68]

Sorry, I mean this file:

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

[brycause]

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.

`

[sgenie68]

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

[brycause]

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

[brycause]

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

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

[sgenie68]

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

[hsorby]

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]

@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]

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]

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]

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?