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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