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populse / populse_mia

Multiparametric Image Analysis
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[work on virtualisation] Current issues with virtualisation in macos #216

Closed servoz closed 2 years ago

servoz commented 3 years ago

Following the last update of the virtualisation documentation it appears that anatomist is not available in mia. I open this ticket to help solve this.

montigno commented 3 years ago

Here is the error message:

from soma import aims
ImportError: cannot import name 'aims' from 'soma' (/home/brainvisa/Apps/MIA/soma-base/python/soma/__init__.py)

When we type the 'anatomist' command in the terminal, it works

servoz commented 3 years ago

I think we should check two things first:

Please, can you give:

denisri commented 3 years ago

Hm, I guess the problem stands from a double installation of soma-base. The python aims module is installed as a sub-package of the main package soma (soma.aims), but here you seem to have reinstalled soma-base, which provides the main package soma. However soma.aims is not reinstalled in soma-base (soma-base is python-only, whereas aims is a C++/python binding). When you are working with a developer VM installation, you should rather install source code using bv_maker, which already manages sources, compilation and installs in a consistent location.

montigno commented 3 years ago

I had installed soma-base in the same root repertory as populse_mia (by git clone).

I have remove it, and when I launch populse_mia, I have this new error message :

ImportError: version mismatch: you are running Python 3.7.11 but the soma.aims module was likely compiled for Python 2.

Mia is launched with this command : 'python3 populse_mia/python/populse_mia/main.py' The bv_maker command does'nt work. The bv_maker.cfg is located at /casa/install/share/casa-distro-3.0/distro/brainvisa/conf/bv_maker.cfg

servoz commented 3 years ago

Thanks. So the first point is now fixed (double installation of soma-base) and i guess we have still to fix the second point (compilation with Python 3). Can you past the /casa/install/share/casa-distro-3.0/distro/brainvisa/conf/bv_maker.cfg, please ? You need access to bv_maker ! @denisri i feel a path definition issue. What do you think about it ? @montigno, do you have bv_maker on your distrib ? (maybe in /casa/install/share/casa-distro-3.0/distro/brainvisa/bin ?) for me:

$ which bv_maker
~/casa_distro/brainvisa-opensource-master/bin/bv_maker
servoz commented 3 years ago

First thing to do, get access to bv_maker. Can you search where it is located on your distribution (locate ,find, etc.). I suspect a wong $PATH.

denisri commented 3 years ago

The docs in https://github.com/populse/populse_mia/blob/master/developer_doc/UsingVirtualisation.md seem OK to me, the explanation about switching to python3 is correct:

"add cmake_options += -DPYTHON_EXECUTABLE=/usr/bin/python3 in the [ build $CASA_BUILD ] section of the $HOME/casa_distro/brainvisa-opensource-master/conf/bv_maker.cfg file (host) to make python3 as default"

montigno commented 3 years ago

I have several bv_maker.cfg files: 

/casa/install/share/casa-distro-3.0/distro/brainvisa/conf/bv_maker.cfg
/casa/install/share/casa-distro-3.0/distro/bvdev/conf/bv_maker.cfg
/casa/install/share/casa-distro-3.0/distro/cati_platform/conf/bv_maker.cfg
/casa/install/share/casa-distro-3.0/distro/cea/conf/bv_maker.cfg
/casa/install/share/casa-distro-3.0/distro/opensource/conf/bv_maker.cfg
/casa/install/share/casa-distro-3.0/distro/web/conf/bv_maker.cfg

I think the first is the good.

I added the line cmake_options in [ build $CASA_BUILD ] section, and I restarted the virtual machine : the problem is not solved.

To answer @servoz, I have not /casa/install/share/casa-distro-3.0/distro/brainvisa/bin .

montigno commented 3 years ago

I am on leave this evening and I will be back next Tueasday. In the docs https://github.com/populse/populse_mia/blob/master/developer_doc/UsingVirtualisation.md, I added the installation procedure with SingularityCE Vagrant Box, you will see the error message when we run the 'bv' command.

Thanks.

denisri commented 3 years ago

No, none of them is the right one. These are template conf files, but one additional one should be found in $HOME/casa_distro/brainvisa-opensource-master/conf/ as explained in @servoz's doc. Isn't it here ? (moreover you don't need to restart the VM)

denisri commented 3 years ago

Uh oh I think I understand. I had not fully read the doc on https://github.com/populse/populse_mia/blob/master/developer_doc/UsingVirtualisation.md, and it's wrong for the MacOS / VM case, the doc asks to install the image file "Brainvisa 5.0.2", which is a user image, already compiled for python2. Here you should install a developer image, as explained in: https://brainvisa.info/web/download.html#installing-a-virtualbox-developer-environment The dev image allows to get the svn/git sources and rebuild everything, using either python2 or python3. The user image is not meant to develop and rebuild.

servoz commented 3 years ago

oh yes, that makes sense!!! I think you have discovered the issue, @denisri! @montigno will tell us, next week when he comes back from vacations.

montigno commented 3 years ago

Sorry for this lost time !

So, I imported and configured the developer image 'casa-dev-5.0-1.ova' in VirtualBox (like the user image).

Brainvisa and Anatomist don't seem to be installed, bv_maker doesn't work. The searching of these items indicates that they exist in the folder /casa/bootstrap/brainvisa-cmake-5.0/cmake

The folders /casa/conf/svn.secret and /casa/conf/bv_maker.cfg (as explained in https://brainvisa.info/web/download.html#installing-a-virtualbox-developer-environment) don't exist.

What procedures should you follow now ? As if we were under Linux and follow the procedure https://github.com/populse/populse_mia/blob/master/developer_doc/UsingVirtualisation.md ?

Thanks for your help !

servoz commented 3 years ago

Brainvisa and Anatomist don't seem to be installed => I think this is normally before the first run of bv_maker bv_maker doesn't work. => I think this is what we need to fix first.

You don't have bv_maker in /casa/bootstrap ? For me: $ pwd /casa/bootstrap $ find . -name bv_maker ./brainvisa-cmake/bin/bv_maker

I think @denisri could give us some advice (he knows much better than I do about BV image architecture)

servoz commented 3 years ago

I think it can be useful. That too. And in a more general way.

montigno commented 3 years ago

yes I have bv_maker in /casa/bootstrap/brainvisa-cmake/bin, when I launch it I have this message : 

Configuration file: None

bv_maker summary:
All went good.

I will look at the @servoz's link (How to compile BrainVISA projects)

servoz commented 3 years ago

I think it does not find a configuration file (bv_maker.cfg) ... This is the next step to fix

denisri commented 3 years ago

I took the time to try the vbox developer image, and it's outdated. I have opened a ticket: brainvisa/casa-distro#272 It's possible to fix things manually using the current image, but we'd better build a new one (and fix things if needed)

servoz commented 3 years ago

Oh thanks @denisri for your message. That explains why @montigno had problems with this part!

Our goal, for the moment, is to evaluate how mia works (fluidity, heaviness) before proposing also the virtualisation for populse (and mia). If the correction of the image is fast, we might as well wait. If the manual corrections are fast enough, maybe we can already do them to continue our test phase?

The next step will be to modify the images to provide mia turnkey as it is the case for BV and Anatomist. For this last part we will have to consult each other a bit I think (Do you agree that we should propose an image with BV, anatomist and mia? Why not include all populse, also mia_processes and populse_mia, in the bv_maker? etc. and etc. Anyway, I think we'll have to talk at some point about the global roadmap of our project).

But this last step will come when we will have finished the installation and operation tests.

montigno commented 3 years ago

thanks @denisri for this information.

So I wait for the next virtual image and in the meantime I continue to test the method singularity-vagrant.

servoz commented 2 years ago

I guess the issues for this this ticket are now fixed, right? Please, @urlub , if that's the case, can you close that ticket?