[Mrtrix-discussion] Error when ./configure mrtrix3

[J-Donald Tournier]

Hi Sharon,

It looks like your system ran out of RAM. Or you've made a lot of CPU cores
available to the VM...? If the latter, you can try to restrict how many
cores 'build' will use while compiling using the NUMBER_OF_PROCESSORS
environment variable, like this:

$ NUMBER_OF_PROCESSORS=1 ./build


If that's not sufficient, you'll need to increase the amount of RAM your VM
is set to use. Unfortunately, some of the code is very demanding on the
compiler, and it ends up using gigabytes of RAM in the process. Thankfully,
you should only need the extra RAM during the 'build' cycle - although the
chances are if it's struggling to build now, it'll probably struggle with
large datasets like the HCP...

On a different note: this mailing list is really for the old version of
MRtrix (0.2.X), and will eventually be phased out. The appropriate forum
for MRrix3 is here: http://community.mrtrix.org/

Cheers,
Donald.


On 2 June 2016 at 12:00, Geva, Sharon <s.geva at ucl.ac.uk> wrote:

> Hi,
>
> I am trying to install mrtrix3 on a neurodebian machine (Oracle VM virtual
> box). I have all requirements and I successfully installed dependencies and
> did Git setup. I then try to build mrtrix, but after typing ./configure it
> runs up to 51/432 and then stops, giving me the following error message:
>
>
> ERROR: ( 51/432) [CC] release/cmd/mrregister.o
> ERROR: ( 51/432) [CC] release/cmd/mrregister.o
> g++ -c -std=c++11 -pthread -fPIC -march=native -DMRTRIX_WORD64 -isystem
> /usr/include/eigen3 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -isystem
> /usr/include/eigen3 cmd/mrregister.cpp -o release/cmd/mrregister.o
> failed with output
> virtual memory exhausted: Cannot allocate memory
>
> I am not sure how to solve the issue…
>
> Thanks,
>
> Sharon
>
>
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-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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