Dear list,
In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to compile it locally with a new CUDA version. We get all the way to the configure command described on http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page which is:
./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1 --with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages --enable-fermi-gpu --libdir=/usr/lib64
Then there are no errors about any libraries, but instead errors about "undefined reference" in the files utils/mri.c and utils/mriio.c (see error below). I searched in the archives and couldn't find anything about this. Any ideas?
Cheers,
Mel
make[2]: Entering directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm'
/bin/sh ../libtool --tag=CC --mode=link g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l ib -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map,ld_map.txt -Wl,--no-demangle -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig htToolkit -o mri_gdfglm mri_gdfglm.o fsgdf.o ../utils/libutils.a ../fsgdf/libfsgdf.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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib
libtool: link: g++ -I../include -fdata-sections -ffunction-sections -Wl,--gc-sections -fopenmp -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mri_gdfglm mri_gdfglm.o fsgdf.o /usr/lib64/libuuid.so -L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l ib -L/usr/lib64 -L/usr/X11R6/lib64 -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib -L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig htToolkit ../utils/libutils.a ../fsgdf/libfsgdf.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 ../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKAlgorithms.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKCommon.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNumerics.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKMetaIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKniftiio.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKNrrdIO.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkpng.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitksys.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitktiff.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkv3p_netlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkzlib.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkgdcm.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkopenjpeg.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg8.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg12.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libitkjpeg16.a /data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight Toolkit/libITKDICOMParser.a -lrt -lz -lm -lcrypt -ldl -lpthread -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib -fopenmp
../utils/libutils.a(mri.o): In function `MRIfree':
/data2/Ganz/FSdev/freesurfer/utils/mri.c:5802: undefined reference to `delete_general_transform'
../utils/libutils.a(mri.o): In function `MRIcopyHeader':
/data2/Ganz/FSdev/freesurfer/utils/mri.c:6069: undefined reference to `copy_general_transform'
/data2/Ganz/FSdev/freesurfer/utils/mri.c:6072: undefined reference to `get_linear_transform_ptr'
/data2/Ganz/FSdev/freesurfer/utils/mri.c:6073: undefined reference to `get_inverse_linear_transform_ptr'
/data2/Ganz/FSdev/freesurfer/utils/mri.c:6067: undefined reference to `delete_general_transform'
../utils/libutils.a(mriio.o): In function `corRead':
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:1611: undefined reference to `input_transform_file'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:1612: undefined reference to `get_linear_transform_ptr'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:1613: undefined reference to `get_inverse_linear_transform_ptr'
../utils/libutils.a(mriio.o): In function `mincRead':
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2316: undefined reference to `start_volume_input'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2321: undefined reference to `get_volume_n_dimensions'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2335: undefined reference to `get_volume_n_dimensions'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2346: undefined reference to `get_volume_sizes'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2355: undefined reference to `get_volume_nc_data_type'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2386: undefined reference to `get_volume_separations'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2425: undefined reference to `convert_voxel_to_world'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2475: undefined reference to `get_voxel_to_world_transform'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2476: undefined reference to `get_linear_transform_ptr'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2456: undefined reference to `input_more_of_volume'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2463: undefined reference to `get_volume_voxel_value'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2485: undefined reference to `delete_volume_input'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:2486: undefined reference to `delete_volume'
../utils/libutils.a(mriio.o): In function `mghRead':
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:11472: undefined reference to `input_transform_file'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:11473: undefined reference to `get_linear_transform_ptr'
/data2/Ganz/FSdev/freesurfer/utils/mriio.c:11474: undefined reference to `get_inverse_linear_transform_ptr'
collect2: error: ld returned 1 exit status
Makefile:562: recipe for target 'mri_gdfglm' failed
make[2]: *** [mri_gdfglm] Error 1
make[2]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm'
Makefile:1048: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/indirect/data2/Ganz/FSdev/freesurfer'
Makefile:957: recipe for target 'all' failed
make: *** [all] Error 2