<div dir="ltr"><div class="gmail_quote"><div dir="ltr">Hi Donald,<div><br></div><div><br></div><div>the $ gcc -march..... gave me:</div><div>-march=corei7-avx</div><div><br></div><div>The workaround with -marchx86-64 (hyphen) worked fine and its now running on the Ubuntu 1.04 VMWare.</div>
<div>Thank you.</div><div><br></div><div>I have two other questions:</div><div><br></div><div>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/".</div>
<div>The path looks a bit strange, but I filled in the line. It looks like this:</div><div><br></div><div>/opt/mrtrix/lib</div><div>NumberOfThreads: 4 </div><div><br></div><div>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?</div>
<div><br></div><div>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.</div><div><br></div><div>I thank you for your help,</div>
<div>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.</div><div><br></div><div>Thanks again,</div><div><br></div><div>Ralf</div><div><br></div>
<div><br><hr style="font-size:16px;font-family:'Times New Roman'"><div style="direction:ltr;font-size:16px;font-family:'Times New Roman'"><br></div><div style="font-size:16px;font-family:'Times New Roman'">
</div><div style="font-size:16px;font-family:'Times New Roman'">
<div dir="ltr">Hi Ralf,<div><br></div><div>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:</div>
<div><br></div><div>$ gcc -march=native -Q --help=target | grep march</div><div><br></div><div>Can you run this and report back on the output?</div><div><br></div><div>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. </div>
<div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div><div>PS: could be that you need to put 'x86_64' - I can never remember whether it's an underscore or a hyphen...</div><div><br></div><div><br>
</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 8 January 2014 15:22, Ralf <span dir="ltr"><<a href="https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=mailto%3aluetzken%40med.ovgu.de" target="_blank">luetzken@med.ovgu.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>I tried to compile MRTrix on Ubuntu 12.04.</div>
<div>I installed all the compile-time and Run-time dependencies<br><div>The package manager didn't find nvidia-glx, the other stuff was properly installed.</div><div>After unpacking and starting building, the following error message popped up:</div>
<div><br></div><div><div><font face="Times" size="3">root@ubuntu-virtual-machine:/home/ubuntu/Desktop/mrtrix-0.2.11# ./build</font></div><div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">[CC] src/dwi/tractography/tracker/sd_prob.o[CC] src/min_max.o</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">ERROR: [CC] src/min_max.o</font></div><div><font face="Times" size="3"><br></font></div>
<div><font face="Times" size="3">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</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">failed with output:</font></div><div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">/tmp/cc85kt0Q.s: Assembler messages:</font></div>
<div><font face="Times" size="3">/tmp/cc85kt0Q.s:83: Error: no such instruction: `vfmadd312ss 512(%r13),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/cc85kt0Q.s:113: Error: no such instruction: `vfmadd312ss 512(%r13),%xmm0,%xmm1'</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">STOP</font></div><div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">ERROR: [CC] src/dwi/tractography/tracker/sd_prob.o</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">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</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">failed with output:</font></div><div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s: Assembler messages:</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:449: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:465: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:481: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:497: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:513: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:529: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:545: Error: no such instruction: `vfmadd312ss -72(%rbp),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2047: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm6'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2063: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm2'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2079: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm1'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2095: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm3'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2111: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm6'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2127: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm1'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2143: Error: no such instruction: `vfmadd312ss -648(%rbp),%xmm0,%xmm7'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2169: Error: no such instruction: `vfmsub312sd -656(%rbp),%xmm1,%xmm2'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2176: Error: no such instruction: `vfmsub312sd -656(%rbp),%xmm3,%xmm1'</font></div>
<div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2261: Error: no such instruction: `vfmsub312sd -656(%rbp),%xmm1,%xmm2'</font></div><div><font face="Times" size="3">/tmp/ccqC5s0Q.s:2268: Error: no such instruction: `vfmsub312sd -656(%rbp),%xmm3,%xmm1'</font></div>
<div><font face="Times" size="3"><br></font></div><div><font face="Times" size="3">STOP</font></div><div><font size="1"><span style="font-size:13px"><span style="font-family:Tahoma"></span><pre style="margin-bottom:14pt;margin-top:14pt">
Im not an Linux expert and I hope somebody can help.</pre><pre style="margin-bottom:14pt;margin-top:14pt">Thanks,</pre><pre style="margin-bottom:14pt;margin-top:14pt"></pre><pre style="margin-bottom:14pt;margin-top:14pt">
Ralf Luetzkendorf</pre><div><br></div></span></font></div></div></div></div><br>_______________________________________________<br>Mrtrix-discussion mailing list<br><a href="https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=mailto%3aMrtrix-discussion%40www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="https://exmail.med.uni-magdeburg.de/owa/redir.aspx?C=drDYToFPV022xkMIufFr5gpZK3Lh4NAIwC0rOHGR61Hq-xYMVMegDSMyPeUS3MMQ5pYGsQINHk0.&URL=http%3a%2f%2fwww.nitrc.org%2fmailman%2flistinfo%2fmrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br>
</font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div><div><i><font color="#990000"><b>T:</b> <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a></font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="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" title="Cmd+Klicken, um Link zu folgen" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i></div>
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