Installation error on Linux


#1

Hi everyone,

I am going to install MRtrix on Linux. But, this does not compile on my systems due to following error which is related to memory error:
I am grateful if you could give me any suggestion in order to solve this problem and install it successfully.

Best,
Behnam

_        Looking for compiler [g++]: g++ (Debian 4.9.2-10) 4.9.2_
_        Checking for C++11 compliance: ok_
_        Checking shared library generation: ok_
_        Detecting pointer size: 64 bit_
_        Detecting byte order: little-endian_
_        Checking for variable-length array support: ok_
_        Checking for non-POD variable-length array support: ok_
_        Checking for ::max_align_t: 16 bytes_
_        Checking for std::max_align_t: 16 bytes_
_        Checking for Eigen3 library: 3.2.2_
_        Checking for zlib compression library: 1.2.8_
_        Checking for "JSON for Modern C++" requirements: ok_
_        Checking for TIFF library: LIBTIFF, Version 4.0.3_
_        Checking for FFTW library: fftw-3.3.4-sse2-avx_
_        Checking for Qt moc: moc (version 4.8.6)_
_        Checking for Qt qmake: qmake (version 4.8.6)_
_        Checking for Qt rcc: rcc (version 4.8.6)_
_        Checking for Qt: 4.8.6_

_        writing configuration to file './config': ok_

_        # ./build_
_        (  1/498) [CC] tmp/cmd/labelconvert.o_
_        (  3/498) [MOC] tmp/src/gui/opengl/lighting_moc.cpp_
_        (  4/498) [CC] tmp/cmd/mrcalc.o_
_        (  6/498) [CC] tmp/src/gui/projection.o_
_        (  7/498) [CC] tmp/cmd/mrdump.o_
_        (  5/498) [CC] tmp/core/version.o_
_        (  8/498) [CC] tmp/core/file/dicom/tree.o_
_        (  2/498) [CC] tmp/src/dwi/directions/file.o_
_        (  9/498) [CC] tmp/src/registration/transform/rigid.o_
_        ( 10/498) [MOC] tmp/src/gui/shview/render_window_moc.cpp_
_        ( 11/498) [CC] tmp/src/dwi/tractography/resampling/upsampler.o_
_        ( 12/498) [CC] tmp/cmd/dirstat.o_
_        ( 13/498) [CC] tmp/src/gui/shapes/cylinder.o_
_        ( 14/498) [CC] tmp/cmd/mrconvert.o_
_        ERROR: (  9/498) [CC] tmp/src/registration/transform/rigid.o_
_        g++ -c -std=c++11 -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/x86_64-linux-gnu -DEIGEN_FFTW_DEFAULT -Wall -O3 -DNDEBUG -Isrc -I./core -Icmd -isystem /usr/include/eigen3 -DEIGEN_DONT_PARALLELIZE src/registration/transform/rigid.cpp -o tmp/src/registration/transform/rigid.o_
_        failed with output_
_        cc1plus: out of memory allocating 4064 bytes after a total of 35667968 bytes_
_        ( 15/498) [CC] tmp/src/dwi/tractography/mapping/mapper.o_
_        ERROR: (  7/498) [CC] tmp/cmd/mrdump.o_
_        g++ -c -std=c++11 -pthread -fPIC -DMRTRIX_WORD64 -DMRTRIX_TIFF_SUPPORT -isystem /usr/include/x86_64-linux-gnu -DEIGEN_FFTW_DEFAULT -Wall -O3 -DNDEBUG -Isrc -I./core -Icmd -isystem /usr/include/eigen3 -DEIGEN_DONT_PARALLELIZE cmd/mrdump.cpp -o tmp/cmd/mrdump.o_
_        failed with output_
_        virtual memory exhausted: Cannot allocate memory_

#2

Hi Benham,

Yep, that looks like a typical out-of-memory issue, as described in the documentation here. Give the fix suggested in that page a try, and let us know if it works.

Rob


#3

Hi Rob,

Thank you for your suggestion. Now it works successfully.

Best
Behnam