Mrtrix3 for NITRC HCP Computing Environment

1

Dear experts,

I’m working with HCP data in the The NITRC Human Connectome Project Computing Environment with AWS.
mrtrix3 is already there but there are a lot of problem running the script (e.g. 5ttgen etc.). Moreover a lot of programs are not include in the installation such as tckgen etc.)

So I decided to install mrtrix3 again following the Standalone installation on Linux at the following link:

https://mrtrix.readthedocs.io/en/latest/installation/linux_install.html#linux-standalone

So I’ve run the command

./build clean
git pull
./configure -static [-nogui]
./build

but the processing is kind of stuck at this step:

(179/505) [CC] tmp/src/registration/transform/initialiser_helpers.o

Do you have any suggestions

thanks a lot

Davide

2

Have you checked whether your system has run out of RAM and is using swap? Compiling the registration code is quite memory thirsty.

3

Dear Max,

I’ve run

NUMBER_OF_PROCESSORS=1 ./build

but the things didn’t change

Do you have any tips?

Thanks

D

4

Static build isn’t something I do often, so I’m not sure where the problem is. On top of that, I don’t expect many developers in general to be using static builds, it’s quite a rare requirement. There’s a good chance this might be a compiler bug…

What system are you running this on? It might be that the simplest is just to try on a different system running a different version or distribution of Linux – maybe in a VM or container…

5

I can not reproduce this with the latest master using clang 3.8.0 (ubuntu 16.04).

My -static -nogui build completes in 372 steps. I only get 505 steps if I configure without these flags.

6

That’s purely down to the -nogui flag, which skips compilation of any GUI-related source file. Davide seemed to suggest that his static build hangs on that file whether -nogui was specified or not, but presumably we were looking at the output of the ./configure -static run…