Hi Victor, thanks, can you send the config.log for the original issue where configure fails and “--with-mni-dir=“ isn’t specified.
best, Andrew
On March 12, 2018 at 10:07:33 AM, Victor Hansen (victor.hansen@nru.dkmailto:victor.hansen@nru.dk) wrote:
Hello Andrew
Attached is our config.log I will try to build an older version too. Thank you -- Best regards Victor Hansen IT support Neurological Research Unit, Rigshospitalet nru.dk
On Wed, 2018-03-07 at 17:45 +0000, Hoopes, Andrew wrote: 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.hansen@nru.dkmailto:victor.hansen@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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