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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