Hi Victor,

Can you send over the config.log? Also, it’s probably worth noting that the 
cuda dev builds are currently failing due to recent mrisurf.c changes (working 
on fixing this now), so if you’re trying to resolve this as soon as possible, 
it might make sense to checkout and build an older version.

best
Andrew



On March 7, 2018 at 12:13:12 PM, Victor Hansen 
(victor.han...@nru.dk<mailto:victor.han...@nru.dk>) wrote:

Hello Bruce

I am the one inputting the commands - thanks for your tip about MNI libraries, 
I managed to point it towards the right location for them.
However, the "make" step is now complaining about the PetSC libraries: 
https://paste.ubuntu.com/p/68G4sBB7DK/
I have tried to point it towards the local libraries with --with-petsc= but 
then ./configure complains that it can't find them at all.
Thank you for your help.
--
Best regards
Victor Hansen
IT support
Neurological Research Unit, Rigshospitalet
nru.dk

On Wed, 2018-03-07 at 10:24 -0500, Bruce Fischl wrote:

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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