The lXmu libraries are installed on my system.

Now the error is:

Making all in mri_em_register make[2]: Entering directory `/tmp/dev/mri_em_register' /bin/sh ../libtool --tag=CC --mode=link g++ -I../include -I../include/dicom -I/usr/local/cuda/include -DFS_CUDA -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib -o mri_em_register_cuda mri_em_register_cuda-mri_em_register.o em_register_cuda.o ../utils/libutils_cuda.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -L/usr/local/cuda/lib -lcuda -lcudart -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: warning: library `/tmp/packages/mni/current/lib/ libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/ libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la' was moved. g++ -I../include -I../include/dicom -I/usr/local/cuda/include -DFS_CUDA -o mri_em_register_cuda mri_em_register_cuda-mri_em_register.o em_register_cuda.o -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib ../utils/libutils_cuda.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -L/usr/local/cuda/lib -lcuda -lcudart -lz -lcrypt -ldl -lpthread /tmp/packages/mni/current/lib/libvolume_io.a -L/usr/pubsw/packages/mni/current/lib /tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib /usr/bin/ld: Warning: size of symbol `min' changed from 37 in em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `umin' changed from 37 in em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `llmin' changed from 46 in em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `ullmin' changed from 46 in em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `max' changed from 37 in em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `umax' changed from 37 in em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `llmax' changed from 46 in em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `ullmax' changed from 46 in em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `rsqrt' changed from 67 in em_register_cuda.o to 42 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `rsqrtf' changed from 45 in em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `erfinv' changed from 2130 in em_register_cuda.o to 926 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `erfinvf' changed from 45 in em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `erfcinv' changed from 1636 in em_register_cuda.o to 805 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `erfcinvf' changed from 45 in em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `sinpi' changed from 402 in em_register_cuda.o to 260 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `sinpif' changed from 45 in em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `rcbrt' changed from 352 in em_register_cuda.o to 220 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: Warning: size of symbol `rcbrtf' changed from 45 in em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o) /usr/bin/ld: warning: i386:x86-64 architecture of input file `em_register_cuda.o' is incompatible with i386 output */usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(libutils_cuda_a-polevl.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(mriframegpu.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(devicemanagement.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(gcamorphenergygpu.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(mrilabels_cuda.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(libutils_cuda_a-pgmstubs.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(libutils_cuda_a-const.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(gcamfots_cuda.o)' is incompatible with i386 output /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils_cuda.a(gcamregisterlevel_cuda.o)' is incompatible with i386 output* em_register_cuda.o: In function `__gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<int const, cudaDeviceProp> > >::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' em_register_cuda.o: In function `__gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<void (* const)(), cudaFuncAttributes> > >::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' em_register_cuda.o: In function `__gnu_cxx::new_allocator<thrust::detail::device::generic::detail::element_pair<float, long> >::allocate(unsigned long, void const*)': /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88: undefined reference to `operator new(unsigned long)' collect2: ld returned 1 exit status make[2]: *** [mri_em_register_cuda] Error 1 make[2]: Leaving directory `/tmp/dev/mri_em_register' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/tmp/dev' make: *** [all] Error 2

It seems that there are some files that aren't compatible with 32 bits...

2011/5/25 Yaroslav Halchenko yoh@psychology.rutgers.edu

lacking -lXmu ?

On Wed, 25 May 2011, Jordi Delgado wrote:

...

../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL -L/usr/X11R6/lib -lX11 -lm ../glut/libglut.a -lz -lm -lcrypt -ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib libtool: link: warning: library `/tmp/packages/mni/current/lib/[1]libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[2]libminc.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[3]libvolume_io.la' was moved. libtool: link: warning: library `/tmp/packages/mni/current/lib/[4]libminc.la' was moved. g++ -o mris_show mris_show.o -L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib -L/usr/X11R6/lib ../utils/libutils.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU /usr/lib/libGL.so -lXext -lX11 ../glut/libglut.a -lz -lcrypt -ldl -lpthread /tmp/packages/mni/current/lib/libvolume_io.a -L/usr/pubsw/packages/mni/current/lib /tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib /usr/bin/ld: warning: i386:x86-64 architecture of input file `../utils/libutils.a(pgmstubs.o)' is incompatible with i386 output ../glut/libglut.a(glut_cmap.o): In function `__glutSetupColormap': /tmp/dev/glut/glut_cmap.c:253: undefined reference to `XmuLookupStandardColormap'

-- Yaroslav O. Halchenko Postdoctoral Fellow, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.