Hi Mel (and Victor?)
the missing functions are all from the MNI lib. Not sure what you are
missing. Maybe Andrew (ccd) knows?
cheers
Bruce
On Wed, 7 Mar 2018, Melanie Ganz wrote:
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/lib
-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/ce
ntos6-x86_64-packages/itk/current/lib/InsightToolkit -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/InsightToolkit/libITKIO.a
/data2/Ganz/FSdev/freesurfer/
centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packa
ges/itk/current/lib/InsightToolkit/libITKCommon.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insi
ghtToolkit/libITKNumerics.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaI
O.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a
/data2/Ganz/FSdev
/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_
64-packages/itk/current/lib/InsightToolkit/libitkpng.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib
/InsightToolkit/libitksys.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.
a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a
/data2/Ganz/FSde
v/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_6
4-packages/itk/current/lib/InsightToolkit/libitkgdcm.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib
/InsightToolkit/libitkopenjpeg.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitk
jpeg8.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a
/data2/Ganz/FS
dev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a
/data2/Ganz/FSdev/freesurfer/centos6-x
86_64-packages/itk/current/lib/InsightToolkit/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/lib
-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/InsightToolkit
../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/InsightToolkit/libITKIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkpng.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitksys.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkgdcm.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkopenjpeg.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg8.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/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
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