Installation of SPM in user images fails

[ylep]

The SPM Standalone installation in /i2bm/local now stores the MATLAB Compiler Runtime in a new location (/i2bm/local/matlab/MATLAB_Runtime/v97), so the default parameters (install_thirdparty=default) result in an exception during user image creation:

+ /casa/install/templates/brainvisa/spm.py
Traceback (most recent call last):
  File "/casa/install/templates/brainvisa/spm.py", line 17, in <module>
    neuroConfig.app.configuration.SPM.spm12_standalone_mcr_path =         glob.glob('/usr/local/spm12-standalone/mcr/v*')[0]
IndexError: list index out of range

We should maybe fix the default to search for the MCR in the new location, or maybe disable the incorporation of SPM Standalone by default... ?

[denisri]

Yes, I admit I have done a local copy of SPM standalone + MCR in order to have it work. The problem is that I don't know a way to guess which MCR is used by a given spm-standalone, so when the MCR is not inside the SPM insall directory, I don't know how to find it.

[ylep]

Yeah, even run_spm12.sh does not know how to find the MCR and you have to provide the path to it manually, which is really not user-friendly...

If a custom install is needed anyway, maybe we should just disable the default behaviour of copying SPM from /i2bm/local? Just so that the default actually works...

[denisri]

I vaguely remember I had disabled the option by default, maybe I have just done it in a dream... I'll check that.

[denisri]

The default value for install_thirdparty is none, so it should actually not try to copy SPM if no option is given. I have not tried right now.

[ylep]

Right, it does not happen by default with create_user_image but it is the default with bbi_daily, is it on purpose?

https://github.com/brainvisa/casa-distro/blob/66e2c106ed12d5277c38376304cd1617d898f5d8/python/casa_distro/admin_commands.py#L1005

I guess the more fundamental question behind that is: do we want to include SPM in our brainvisa and/or cea releases?

[denisri]

Yes it's enabled in bbi_daily, or more precisely in crontabs that run nightly. They are activated in order to test that SPM can actually be shipped and setup in distributions, and we have more or less agreed to ship it in brainvisa releases (Jeff's suggestion). For cea releases the question remains open. The other advantage to ship it is that brainvisa is also automatically setup because its path is known then, so it works out of the box, without any user setup.

[denisri]

Oh you're right the default in casa_distro_admin bbi_daily is still default, not the same as for casa_distro create_user_image. That's a mistake, I'm fixing it.

[ylep]

Okay, then I would propose that we also move the install that you did on your volatile to somewhere under /neurospin/brainvisa, so that all machines that run nightly builds can find an appropriate install, and modify the casa_distro.thirdparty module so that it looks in that new location, what do you think

That way we can stay unaffected by changes that are made to /i2bm/local/spm-standalone

[denisri]

OK. It's too bad we cannot use the "official" install in /i2bm but I could not find a way to detect which MCR was needed. I'm moving it there.

[denisri]

I'm not sure if we should modify the casa_distro.thirdparty module, because it would then contain a non-standard hard-coded path (in /neurospin), which is not very clean even if we test that this directory exists or look in a paths list...?

[denisri]

I have moved it to /neurospin/brainvisa/thirdparty/ there is a file thirdparty.json there which lists the software to be installed (only spm for now). SPM standalone + MCR v97 is 6 GB so the package will grow, and copying SPM from the network will be longer than from /volatile, but at least we have a single place for it now. I have modified crontabs on is234199 (my machine, cea tests) and is234203 (@sapetnioc's, brainvisa tests), @ylep I think you have another one setup ?

[ylep]

@denisri Actually is234203 is mine, so I think everything is covered (I have a nightly for the DISCO tests using MATLAB, but I have disabled installation of thirdparty dependencies there). So from my side we can close the issue. Thanks!