[Mrtrix-discussion] MRTrix Ubuntu build error

Thu Jan 9 07:36:54 PST 2014

Hi Ralf,

Good to hear the -march=x86-64 trick did the job. As to setting up
multithreading, there's a few issues there. First, the
/etc/ld.so.conf.d/mrtrix.conf file should contain only the line
"/opt/mrtrix/lib" - nothing else. You'll then need to run "sudo ldconfig"
to tell the system to take it into account. That said, it doesn't sound
like this is a problem since if any of the MRtrix commands run at all, that
bit must be working fine.

To set up multi-threading, try typing this command:

echo "NumberOfThreads: 4" > ~/.mrtrix.conf

Things should work after that. Basically, the "NumberOfThreads: 4" line
belongs in the ~/.mrtrix.conf file, not the ld.so one (the latter is
required to tell the system where to find the libmrtrix.so file).

By the way, if you're working in a virtual machine, you'll only get the
benefit of multi-threading if your virtual machine is set up with multiple
cores...

Cheers,

Donald.

On 9 January 2014 15:22, Ralf <computervisualistik at gmail.com> wrote:

> Hi Donald,
>
>
> the $ gcc -march.....  gave me:
> -march=corei7-avx
>
> The workaround with -marchx86-64 (hyphen) worked fine and its now running
> on the Ubuntu 1.04 VMWare.
> Thank you.
>
> I have two other questions:
>
> It takes very long to do the csd. So I tried to use the multithread. I
> found one mrtrix.conf file in "/etc/ld.so.conf.d/".
> The path looks a bit strange, but I filled in the line. It looks like this:
>
> /opt/mrtrix/lib
> NumberOfThreads: 4
>
> But it didn't work. Is there a way to test if mrtrix finds the right file
> or give mrtrix a new one at a new location?
>
> Is there any way to know which lmax during the estimate response is the
> right one? I have 130 directions and could go up to 12, if I look it up in
> the manual.
>
> I thank you for your help,
> now I have a working VMWare with MRTrix and everybody can use it
> everywhere. Maybe a good idea to put it on the net to download.
>
> Thanks again,
>
> Ralf
>
>
> ------------------------------
> *Von:* Donald Tournier [jdtournier at gmail.com]
> *Gesendet:* Mittwoch, 8. Januar 2014 16:54
> *An:* Lützkendorf, Ralf
> *Cc:* mrtrix mailinglist
> *Betreff:* Re: [Mrtrix-discussion] MRTrix Ubuntu build error
>
> Hi Ralf,
>
> I've never seen anything like this - the compiler generating assembly
> instructions that don't exist. The compiler is set to using the native
> architecture, but it would well be that in a virtual machine, the compiler
> gets confused as to what the 'native' CPU actually is. You can query what
> the compiler thinks your CPU is using this command:
>
> $ gcc -march=native -Q --help=target | grep march
>
> Can you run this and report back on the output?
>
> As a potential workaround, you could try editing sysconf/linux.py and
> replace the '-march=native' option with '-march=x86-64', which is pretty
> generic - assuming you're running a 64-bit virtual machine.
>
> Cheers,
> Donald.
>
> PS: could be that you need to put 'x86_64' - I can never remember whether
> it's an underscore or a hyphen...
>
>
>
>
> On 8 January 2014 15:22, Ralf <luetzken at med.ovgu.de<https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=mailto%3aluetzken%40med.ovgu.de>
> > wrote:
>
>> Hello,
>>
>> I tried to compile MRTrix on Ubuntu 12.04.
>> I installed all the compile-time and Run-time dependencies
>> The package manager didn't find nvidia-glx, the other stuff was properly
>> installed.
>> After unpacking and starting building, the following error message popped
>> up:
>>
>> root at ubuntu-virtual-machine:/home/ubuntu/Desktop/mrtrix-0.2.11# ./build
>>
>> [CC] src/dwi/tractography/tracker/sd_prob.o[CC] src/min_max.o
>>
>>
>> ERROR: [CC] src/min_max.o
>>
>> g++ -c -Wall -march=native -fPIC -fno-strict-aliasing
>> -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -O2 -pthread -I/usr/include/glibmm-2.4
>> -I/usr/lib/x86_64-linux-gnu/glibmm-2.4/include -I/usr/include/sigc++-2.0
>> -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include -I/usr/include/glib-2.0
>> -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Ilib -Isrc src/min_max.cpp -o
>> src/min_max.o
>>
>> failed with output:
>>
>> /tmp/cc85kt0Q.s: Assembler messages:
>> /tmp/cc85kt0Q.s:83: Error: no such instruction: `vfmadd312ss
>> 512(%r13),%xmm0,%xmm1'
>> /tmp/cc85kt0Q.s:113: Error: no such instruction: `vfmadd312ss
>> 512(%r13),%xmm0,%xmm1'
>>
>> STOP
>>
>> ERROR: [CC] src/dwi/tractography/tracker/sd_prob.o
>>
>> g++ -c -Wall -march=native -fPIC -fno-strict-aliasing
>> -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -O2 -pthread -I/usr/include/glibmm-2.4
>> -I/usr/lib/x86_64-linux-gnu/glibmm-2.4/include -I/usr/include/sigc++-2.0
>> -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include -I/usr/include/glib-2.0
>> -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Ilib -Isrc
>> src/dwi/tractography/tracker/sd_prob.cpp -o
>> src/dwi/tractography/tracker/sd_prob.o
>>
>> failed with output:
>>
>> /tmp/ccqC5s0Q.s: Assembler messages:
>> /tmp/ccqC5s0Q.s:449: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:465: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:481: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:497: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:513: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:529: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:545: Error: no such instruction: `vfmadd312ss
>> -72(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:2047: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm6'
>> /tmp/ccqC5s0Q.s:2063: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm2'
>> /tmp/ccqC5s0Q.s:2079: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:2095: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm3'
>> /tmp/ccqC5s0Q.s:2111: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm6'
>> /tmp/ccqC5s0Q.s:2127: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm1'
>> /tmp/ccqC5s0Q.s:2143: Error: no such instruction: `vfmadd312ss
>> -648(%rbp),%xmm0,%xmm7'
>> /tmp/ccqC5s0Q.s:2169: Error: no such instruction: `vfmsub312sd
>> -656(%rbp),%xmm1,%xmm2'
>> /tmp/ccqC5s0Q.s:2176: Error: no such instruction: `vfmsub312sd
>> -656(%rbp),%xmm3,%xmm1'
>> /tmp/ccqC5s0Q.s:2261: Error: no such instruction: `vfmsub312sd
>> -656(%rbp),%xmm1,%xmm2'
>> /tmp/ccqC5s0Q.s:2268: Error: no such instruction: `vfmsub312sd
>> -656(%rbp),%xmm3,%xmm1'
>>
>> STOP
>>
>>
>> Im not an Linux expert and I hope somebody can help.
>>
>> Thanks,
>>
>>
>> Ralf Luetzkendorf
>>
>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org<https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=mailto%3aMrtrix-discussion%40www.nitrc.org>
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion<https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=http%3a%2f%2fwww.nitrc.org%2fmailman%2flistinfo%2fmrtrix-discussion>
>>
>>
>
>
> --
> *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
> <https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=http%3a%2f%2fwww.kcl.ac.uk%2fmedicine%2fresearch%2fdivisions%2fimaging%2fdepartments%2fbiomedengineering>*
>

-- 
*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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