upgrade Gadgetron and ISMRMRD

[KrisThielemans]

New Gadgetron needs gcc 6.0 and newer ISMRMRD. See previous discussion at #145.

Ubuntu 16.04 has 5.4. On the VM it could be possible to install gcc version 6 following this link

@paskino sees a few options:

1. Build a new VM with Ubuntu 18.04 which ships GCC 7.3.0
2. Add the new unofficial repository to get GCC 6 onto the current VM (Ubuntu 16.04)
3. Use conda
4. Keep outdated Gadgetron in the short term.

Although option 3 is still in a work-in-progress phase @paskino strongly believes that we should pursue that direction.

Originally posted by @paskino in #145 (comment)

[KrisThielemans]

Build a new VM with Ubuntu 18.04 which ships GCC 7.3.0

I see no reason not to do this. we'll have to move on soon anyway.

Add the new unofficial repository to get GCC 6 onto the current VM (Ubuntu 16.04)

A pain. I'd like to avoid it.

Use conda

I don't see how conda is going to help avoiding having to use gcc 6 for gadgetron.

Keep outdated Gadgetron in the short term.

As we're moving to SIRF 2.0, it's a good time to upgrade Gadgetron. So I wouldn't choose this option

[KrisThielemans]

@dchansen, @xueh2 what would a good Gadgteron, and ISMRMRD commit be?

[KrisThielemans]

will need to change travis to use g++-6

[paskino]

conda can help by being able to install specific compilers?

[dchansen]

For gadgetron we're currently using both 1 and 2.
We're moving to Ubuntu 18.04 as soon as everything (non-Gadgetron) works on the scanner side, and in the meantime we've upgraded our docker images with GCC 6.

[KrisThielemans]

@dchansen, sorry, not sure what you mean with

For gadgetron we're currently using both 1 and 2.

[KrisThielemans]

conda can help by being able to install specific compilers?

yeah, but who's going to do that, aside from you?

[casperdcl]

I agree you probably don't want to conda install a compiler if you can avoid it - people will get the new compiler overriding their system one in that environment without necessarily realising.

[paskino]

@KrisThielemans it's not so trivial to install a different compiler with conda. Though conda provides new compilers (only for Mac and Linux), conda-forge is not currently using those.

[paskino]

@casperdcl the compiler is requested only for the build (possibly)

[KrisThielemans]

let's not rely on conda for getting the correct compiler for the build. Also, major upgardes between compilers can mean ABIs are not compatible etc. I'm not saying we shouldn't pursue conda, but I think hoping that it will solve our problems for this particular issue is asking for too much.

[bathomas]

I agree with @KrisThielemans, I think using conda in this way is asking for trouble.

[paskino]

OK, I'll proceed with option 1.

[KrisThielemans]

Depends on #162

[KrisThielemans]

@rijobro you're working on this. It's quite tricky though. Please refer to this issue with your updates and comment.

[rijobro]

external fix required (PR on gadgetron: gadgetron/gadgetron#726).

Once this is done, should be ok to update.

[KrisThielemans]

Done in #205