bv_maker failed #43

Mhaalk · 2021-04-29T14:01:47Z

Mhaalk
Apr 29, 2021

Hello,

Je suis sur Ubuntu 18.04, j'essaye d'installer le developer environnement avec des modules privés (le baby pipeline de f. leroy).

j'ai installé le paquet singularity 3.7 distribué sur brainvisa.info
j'ai réussi à lancer singularity sans problème.

une fois arrivé à l'étape de "bv_maker configure" je reçois l'erreur suivante:

Summary of Git repositories in /casa/host/src
=============================================
┌───── * uncommitted working tree changes
│┌──── + uncommitted index changes
││┌─── $ stash present
│││┌── % untracked files
││││ ┌ HEAD
││││ │                 ┌ update status
││││ │                 │ ┌ bv_maker upstream state
││││ │                 │ │  ┌ Git upstream state
││││ │                 │ │  │┌ Directory
     master (88948f70) ✓ U=  aims/aims-free/master
     master (d6e740c)  ✓ U=  aims/aims-gpl/master
     master (fc376ac)  ✓ U=  aims/aims-til/master
     master (bdc5ce40) ✓ U=  anatomist/anatomist-free/master
     master (f467771)  ✓ U=  anatomist/anatomist-gpl/master
     master (d5d55dfd) ✓ U=  axon/master
     master (8a30b54)  ✓ U=  brainvisa-share/master
     master (76676b5)  ✓ U=  capsul/master
     master (966d223)  ✓ U=  development/brainvisa-cmake/master
     master (f85abb4)  ✓ U=  development/brainvisa-release/master
     master (de2a8fd)  ✓ U=  development/casa-distro/master
     master (15899a1)  ✓ U=  highres-cortex/master
     master (750f4ad)  ✓ U=  morphologist/morpho-deepsulci/master
     master (c1cdb6c)  ✓ U=  morphologist/morphologist-ui/master
     master (b92ab3f)  ✓ U=  populse/populse_db/master
     master (cbb2ad7)  ✓ U=  soma/soma-base/master
     master (4b36785)  ✓ U=  soma/soma-io/master
     master (26532b4)  ✓ U=  soma/soma-workflow/master
Traceback (most recent call last):
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 1104, in process
    **meth_kwargs)
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 3736, in configure
    self.process_configuration_lines()
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 3494, in process_configuration_lines
    'components_sources.json')) as f:
IOError: [Errno 2] No such file or directory: u'/brainvisa/source/components_sources.json'
Skipping build of /casa/host/build because it depends on a step that failed.

bv_maker summary:
OK          step sources: /casa/host/src, started: 2021/04/29 15:01, stopped: 2021/04/29 15:01
FAILED      step configure: /casa/host/build, started: 2021/04/29 15:01, stopped: 2021/04/29 15:01
UNMET DEP   step build: /casa/host/build
There were errors.

j'ai essayé grossièrement de contourner le problème en changeant le chemin qui se trouve physiquement à $HOME/casa_distro/brainvisa-opensource-master/src/components_sources.json

mais ça n'a généré que plus d'erreurs... comment puis-je contourner ce problème?

Answered by denisri

Apr 29, 2021

[ build $CASA_BUILD ]
build_type = bug_fix
make_options = -j8
opensource bug_fix /brainvisa/source

OK that's it: the paths you wrote in the config file don't exist in the container. You should use $CASA_SRC instead of /brainvisa/source.

View full answer

sapetnioc · 2021-04-29T14:12:49Z

sapetnioc
Apr 29, 2021
Maintainer

This is weird. Could you please copy the commands you used to setup the environment and launch bv_maker.

2 replies

Mhaalk Apr 29, 2021
Author

I did:

#to install Golang before singularity:
tar -C /usr/local -xzf go1.16.3.linux-amd64.tar.gz 
echo 'export PATH=$PATH:/usr/local/go/bin' >> ~/.bashrc

#to install dependencies required by singularity:
sudo apt-get update && sudo apt-get install -y \
    build-essential \
    uuid-dev \
    libgpgme-dev \
    squashfs-tools \
    libseccomp-dev \
    wget \
    pkg-config \
    git \
    cryptsetup-bin

#then installed this:
https://brainvisa.info/download/singularity-container-3.7.0-ubuntu-18.04.deb


#then:
mkdir -p $HOME/casa_distro/brainvisa-opensource-master

singularity run -B $HOME/casa_distro/brainvisa-opensource-master:/casa/setup $HOME/casa_distro/casa-dev-5.0-1.sif branch=master distro=opensource

echo 'export PATH="$HOME/casa_distro/brainvisa-opensource-master/bin:$PATH""' >> ~/.bashrc

bv bash
bv_maker

denisri Apr 29, 2021
Maintainer

You don't need to install go and its dependencies before singularity: the .deb is ready to install; go is used to compile singularity (and build the .deb, on our side), not to use it.

denisri · 2021-04-29T14:28:17Z

denisri
Apr 29, 2021
Maintainer

Hi,
We reply in english because other people outside of France may read/use the questions and answers and avoid asking again the same...
The path /brainvisa/source/... seems very weird, does not exist, and I don't know how it came here, I don't think it is mentioned anywhere in the code of casa-distro... Did you edit the config file /casa/host/conf/bv_maker.cfg manually and add this path anywhere ?

1 reply

Mhaalk Apr 29, 2021
Author

I did edit bv_maker.cfg manually like this, using the cfg from a previous build:

might it be because of line 3 from the build section?


[ source $CASA_SRC ]
  brainvisa opensource bug_fix
  + perso/fleroy perso/fleroy/bug_fix
  + brainvisa/cortical_surface/cortical_surface-private/branches/bug_fix cortical_surface/cortical_surface-private/bug_fix
  + brainvisa/morphologist/morphologist-private/branches/bug_fix morphologist/morphologist-private/bug_fix
  + baby bug_fix
  - optical_imaging
  - nuclear_imaging
  - fMRI-*
  - web

[ build $CASA_BUILD ]
  build_type = bug_fix
  make_options = -j8
  opensource bug_fix /brainvisa/source
  + /brainvisa/source/cortical_surface/cortical_surface-private/bug_fix
  + /brainvisa/source/morphologist/morphologist-private/bug_fix
  + /brainvisa/source/morphologist/baby/bug_fix  
  + /brainvisa/source/perso/fleroy/bug_fix
  - connectomist-*   
  - brainrat
  - optical_imaging
  - nuclear_imaging
  - snapbase
  - fMRI-*
  - axon_web

denisri · 2021-04-29T14:34:46Z

denisri
Apr 29, 2021
Maintainer

[ build $CASA_BUILD ]
build_type = bug_fix
make_options = -j8
opensource bug_fix /brainvisa/source

OK that's it: the paths you wrote in the config file don't exist in the container. You should use $CASA_SRC instead of /brainvisa/source.

1 reply

Mhaalk Apr 29, 2021
Author

oh thanks my bad!
Now I corrected like this:

I did not understand what -j8 ask Make to do and so how to correct my command (as I were again from my previous .cfg)

[ source $CASA_SRC ]
  brainvisa opensource bug_fix
  + perso/fleroy perso/fleroy/bug_fix
  + brainvisa/cortical_surface/cortical_surface-private/branches/bug_fix cortical_surface/cortical_surface-private/bug_fix
  + brainvisa/morphologist/morphologist-private/branches/bug_fix morphologist/morphologist-private/bug_fix
  + baby bug_fix
  - optical_imaging
  - nuclear_imaging
  - fMRI-*
  - web

[ build $CASA_BUILD ]
  build_type = bug_fix
  make_options = -j8
  opensource bug_fix $CASA_SRC
  + $CASA_SRC/cortical_surface/cortical_surface-private/bug_fix
  + $CASA_SRC/morphologist/morphologist-private/bug_fix
  + $CASA_SRC/morphologist/baby/bug_fix  
  + $CASA_SRC/perso/fleroy/bug_fix
  - connectomist-*   
  - brainrat
  - optical_imaging
  - nuclear_imaging
  - snapbase
  - fMRI-*
  - axon_web

but then bv_maker throw me this:

Building directory: /casa/host/build
$ make -j8
make: *** No targets specified and no makefile found.  Stop.
Traceback (most recent call last):
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 1104, in process
    **meth_kwargs)
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 4023, in build
    timeout=timeout)
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 428, in system
    six.reraise(*error)
  File "/casa/host/bootstrap/brainvisa-cmake/bin/bv_maker", line 417, in system
    raise OSError()
OSError: Command failed: u'make' '-j8'
From directory: /casa/host/build

bv_maker summary:
FAILED      step build: /casa/host/build, started: 2021/04/29 16:40, stopped: 2021/04/29 16:40
There were errors.

denisri · 2021-04-29T15:21:54Z

denisri
Apr 29, 2021
Maintainer

-j8 tells make to run up to 8 compile jobs in parallel because you seem to have 8 CPU cores on your machine. It should be OK.
Here you ran bv_maker build, but did the configure step run without error before that (after you fixed your configuration) ? If this hasn't been done, no wonder the build does not work ;)

1 reply

Mhaalk Apr 29, 2021
Author

Indeed I forgot to relaunch the configure first... now I did and build went all good, thanks!

now, but still I receive warnings at Brainvisa start now:
would that impact any function ?

maxime@dell:~$ bv
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-maxime'
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-maxime'
Loading toolbox baby
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
soma-workflow starting in light mode
Workflow controller initialised
The log file for this session is '/casa/home/.brainvisa/brainvisa.log'

Database /casa/host/build/share/brainvisa-share-5.1 must be updated because
there is no database file.

/usr/local/lib/python2.7/dist-packages/matplotlib/__init__.py:910: MatplotlibDeprecationWarning: The backend.qt5 rcParam was deprecated in version 2.2.  In order to force the use of a specific Qt binding, either import that binding first, or set the QT_API environment variable.
  mplDeprecation)


ERROR: **

    
    
    ImportError: /casa/host/build/brainvisa/toolboxes/cortical_surface/processes/anatomy/tools/ParcelsTextureFromCoordinates.py: No module named sigraph

**

* * *

`**ImportError**`

    
    
    Traceback (most recent call last):
      File "/casa/host/build/python/brainvisa/processes.py", line 6363, in addDir
        toolbox=toolbox)  # two arguments : process fullpath and category (directories separated by /)
      File "/casa/host/build/python/brainvisa/processes.py", line 5948, in readProcess
        sys.exc_info()[2])
      File "/casa/host/build/python/brainvisa/processes.py", line 5933, in readProcess
        moduleName, fileIn, fileName, moduleDescription)
      File "/casa/host/build/brainvisa/toolboxes/cortical_surface/processes/anatomy/tools/ParcelsTextureFromCoordinates.py", line 32, in <module>
        import sigraph
    ImportError: /casa/host/build/brainvisa/toolboxes/cortical_surface/processes/anatomy/tools/ParcelsTextureFromCoordinates.py: No module named sigraph
    



ERROR: **

denisri · 2021-04-30T13:23:02Z

denisri
Apr 30, 2021
Maintainer

Considering your bv_maker.cfg, you have added some non-opensource projects, but not all of them and there are missing dependencies. You'd rather consider using the "bvdev" distro or project group instead of "opensource", or add at least the sulci_private component.

1 reply

Mhaalk May 21, 2021
Author

Hello,
thanks to your guidance I can run BV from GUI perfectly now, but I still receive this:

`(base) maxime@dell:~$ bv
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-maxime'
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-maxime'
Loading toolbox baby
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox spm
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
Loading toolbox My processes
soma-workflow starting in light mode
Workflow controller initialised
The log file for this session is '/casa/home/.brainvisa/brainvisa.log'

/usr/local/lib/python2.7/dist-packages/matplotlib/init.py:910: MatplotlibDeprecationWarning: The backend.qt5 rcParam was deprecated in version 2.2. In order to force the use of a specific Qt binding, either import that binding first, or set the QT_API environment variable.
mplDeprecation)
exec: /casa/host/build/brainvisa/toolboxes/morphologist/startup.py
connect to computing resource: dell
libpng warning: iCCP: known incorrect sRGB profile
libpng warning: iCCP: known incorrect sRGB profile
`

my guess is these are minor error that won't really bother me, do you agree or should I correct it all?

also, (but maybe this shoud be a distinct thread)

I'm now trying to run python scripts that require to import anatomist and soma, I sourced bv_env.sh (both by an export in .bashrc, and by a source ... command, but IPython throw me:

`---> 12 from soma import aims

~/casa_distro/brainvisa-opensource-master/build/python/soma/aims/init.py in
131
132 try:
--> 133 from soma.aims import aimssip
134 except ImportError as exc:
135 if exc.args[0] == ('dynamic module does not define init function '

ImportError: libpython2.7.so.1.0: cannot open shared object file: No such file or directory
`

denisri · 2021-05-21T13:23:37Z

denisri
May 21, 2021
Maintainer

For brainvisa, yes these are minor warnings that are not harmful, it's OK.

For the error while loading soma.aims, I suspect you are trying to load the module from the host system, without getting into the container (which seems to indicate the path "~/casa_distro/brainvisa-opensource-master/build/python/soma/aims/init.py" which is a host path, not a container path). The programs are built inside a container, using a python installed inside the container, thus everything has to run inside the container also. Normally i's just a matter of running bv ipython instead of ipython. brainvisa does it automatically, because it's not installed elsewhere on the system, so we provide a run scripts which does the equivalent of bv brainvisa under the hood (same for all commands anatomist, AimsSomething etc. But we can't do that for python, which exists and is needed on the host system: we can't overload it otherwise we would break the host system.

Denis

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bv_maker failed #43

Mhaalk Apr 29, 2021

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