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vais-ral / CCPi-VirtualMachine

Set of scripts and configuration to prepare VM based on Scientific Linux 7 from scratch with CCPi from binaries or source codes.
MIT License
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installing ccppetmr fails in SL7 #7

Closed TomasKulhanek closed 5 years ago

TomasKulhanek commented 5 years ago

Launching ./UPDATE.sh from https://github.com/CCPPETMR/CCPPETMR_VM.git fails in SL7 on following:

paskino commented 5 years ago

FFTW3 should be found with FindFFTW3.cmake. It seems that passing FFTW3_ROOT_DIR variable to cmake could help.

What is strange is that in Ubuntu you find the file in the exact same location /usr/include/fftw3.h

TomasKulhanek commented 5 years ago

Attached vagrant.log with fftw3.h and Dunno about this gcc errors.

paskino commented 5 years ago

It seems to have found the proper FFTW3 library. 

2483: default: FFTW3 UNIX libraries: /usr/lib64/libfftw3.so
2484: default: -- Found FFTW3: /usr/lib64/libfftw3.so  
2485: default: -- USING the system FFTW3, found FFTW3_INCLUDE_DIR=/usr/include,

and at 

16774 default: -- FFTW3 UNIX libraries: /usr/lib64/libfftw3f.so
16775 default: -- Found FFTW3: /usr/lib64/libfftw3f.so  
16776 default: FFTW3 and Boost Found... building utilities

however, it doesn't work.

Could you please run UPDATE.sh with one thread? Now the output of the log is interleaving 2 progresses (both of which fail) and it's not easy to understand what went wrong.

This can be achieved by calling UPDATE.sh -j 1 at this line.

TomasKulhanek commented 5 years ago

moved UPDATE.sh into this git repo, added -DUSE_SYSTEM_ACE=Off \ 

    default: -- Configuring incomplete, errors occurred!
    default: See also "/root/devel/buildVM/builds/Gadgetron/build/CMakeFiles/CMakeOutput.log".
    default: CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    default: Please set them or make sure they are set and tested correctly in the CMake files:
    default: ACE_INCLUDE_DIR

attached vagrant.log vagrant.log

paskino commented 5 years ago

The log says:

default: usage: conda [-h] [-V] command ...
    default: conda: error: unrecognized arguments: conda-forge paskino
    default: Solving environment: ...working... 
    default: failed
    default: 
    default: PackagesNotFoundError: The following packages are not available from current channels:
    default: 
    default:   - ccpi-segmentation
    default:   - ccpi-quantification
    default:   - ccpi-regulariser
    default:   - ccpi-preprocessing
    default:   - ace
    default:   - ccpi-reconstruction
    default: 
    default: Current channels:
    default: 
    default:   - https://repo.anaconda.com/pkgs/main/linux-64
    default:   - https://repo.anaconda.com/pkgs/main/noarch
    default:   - https://repo.anaconda.com/pkgs/free/linux-64
    default:   - https://repo.anaconda.com/pkgs/free/noarch
    default:   - https://repo.anaconda.com/pkgs/r/linux-64
    default:   - https://repo.anaconda.com/pkgs/r/noarch
    default:   - https://repo.anaconda.com/pkgs/pro/linux-64
    default:   - https://repo.anaconda.com/pkgs/pro/noarch
    default:

Apparently the command that was issued is not correct? Maybe it does not accept a list of channels. Try one command each.

ACE must be installed from my conda channel paskino before build. Or alternatively set the USE_SYSTEM_ACE to OFF.

TomasKulhanek commented 5 years ago

It's irrelevant whether ACE was installed or not. It fails. vagrant.log

paskino commented 5 years ago

Well, it does complain that ACE is not found. 

default: CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    default: Please set them or make sure they are set and tested correctly in the CMake files:
    default: ACE_INCLUDE_DIR
    default: ACE_LIBRARY

I'm afraid the version of the Superbuild you're trying to build does just rely on finding system ACE. Try setting the environment variable ACE_ROOT to the location of the conda_installation/bin

paskino commented 5 years ago

Try to use a more recent SuperBuild tag than v.1.1.1 (like master)