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I got further into to the install this time but now I'm getting the following errors. Any thoughts? I tried running with sudo but that doesn't work either. ----- Installing stable binaries /usr/bin/install: cannot remove ‘/bin/dtifit’: Permission denied /usr/bin/install -p -m 0775 dtifit /bin/ /usr/bin/install: cannot remove ‘/bin/ccops’: Permission denied /usr/bin/install -p -m 0775 ccops /bin/ /usr/bin/install: cannot remove ‘/bin/medianfilter’: Permission denied /usr/bin/install -p -m 0775 medianfilter /bin/ /usr/bin/install: cannot remove ‘/bin/make_dyadic_vectors’: Permission denied /usr/bin/install -p -m 0775 make_dyadic_vectors /bin/ /usr/bin/install: cannot remove ‘/bin/vecreg’: Permission denied /usr/bin/install -p -m 0775 vecreg /bin/ /usr/bin/install: cannot remove ‘/bin/xfibres’: Permission denied /usr/bin/install -p -m 0775 xfibres /bin/ /usr/bin/install: cannot remove ‘/bin/probtrackx’: Permission denied /usr/bin/install -p -m 0775 probtrackx /bin/ /usr/bin/install: cannot remove ‘/bin/pvmfit’: Permission denied /usr/bin/install -p -m 0775 pvmfit /bin/ /usr/bin/install: cannot remove ‘/bin/dtigen’: Permission denied /usr/bin/install -p -m 0775 dtigen /bin/ /usr/bin/install: cannot remove ‘/bin/eddy_combine’: Permission denied /usr/bin/install -p -m 0775 eddy_combine /bin/ /usr/bin/install: cannot remove ‘/bin/eddy_correct’: Permission denied /usr/bin/install -p -m 0775 eddy_correct /bin/ /usr/bin/install: cannot remove ‘/bin/zeropad’: Permission denied /usr/bin/install -p -m 0775 zeropad /bin/ /usr/bin/install: cannot remove ‘/bin/maskdyads’: Permission denied /usr/bin/install -p -m 0775 maskdyads /bin/ /usr/bin/install: cannot remove ‘/bin/probtrack’: Permission denied /usr/bin/install -p -m 0775 probtrack /bin/ /usr/bin/install: cannot remove ‘/bin/fdt_rotate_bvecs’: Permission denied /usr/bin/install -p -m 0775 fdt_rotate_bvecs /bin/ /usr/bin/install: cannot remove ‘/bin/bedpost’: Permission denied /usr/bin/install -p -m 0775 bedpost /bin/ /usr/bin/install: cannot remove ‘/bin/bedpostx’: Permission denied /usr/bin/install -p -m 0775 bedpostx /bin/ /usr/bin/install: cannot remove ‘/bin/bedpostx_postproc.sh’: Permission denied /usr/bin/install -p -m 0775 bedpostx_postproc.sh /bin/ /usr/bin/install: cannot remove ‘/bin/bedpostx_preproc.sh’: Permission denied /usr/bin/install -p -m 0775 bedpostx_preproc.sh /bin/ /usr/bin/install: cannot remove ‘/bin/bedpostx_single_slice.sh’: Permission denied /usr/bin/install -p -m 0775 bedpostx_single_slice.sh /bin/ /usr/bin/install: cannot remove ‘/bin/bedpostx_datacheck’: Permission denied /usr/bin/install -p -m 0775 bedpostx_datacheck /bin/ /bin/rm: cannot remove ‘Fdt’: Permission denied ln: failed to create symbolic link ‘Fdt’: File exists ln -s Runtcl Fdt make[3]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[3]: Entering directory `/home/area51/fslbuild/fsl/src/fdt' make[4]: Entering directory `/home/area51/fslbuild/fsl/src/fdt' Installing stable header files /usr/bin/install: cannot remove ‘/include/fdt/Bingham_Watson_approx.h’: Permission denied /usr/bin/install -p -m 0664 Bingham_Watson_approx.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ccopsOptions.h’: Permission denied /usr/bin/install -p -m 0664 ccopsOptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/commonopts.h’: Permission denied /usr/bin/install -p -m 0664 commonopts.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/diff_pvmoptions.h’: Permission denied /usr/bin/install -p -m 0664 diff_pvmoptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/diffmodels.h’: Permission denied /usr/bin/install -p -m 0664 diffmodels.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/dtifitOptions.h’: Permission denied /usr/bin/install -p -m 0664 dtifitOptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/fibre.h’: Permission denied /usr/bin/install -p -m 0664 fibre.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/particle.h’: Permission denied /usr/bin/install -p -m 0664 particle.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/probtrackx.h’: Permission denied /usr/bin/install -p -m 0664 probtrackx.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/probtrackxOptions.h’: Permission denied /usr/bin/install -p -m 0664 probtrackxOptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ptx_meshmask.h’: Permission denied /usr/bin/install -p -m 0664 ptx_meshmask.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ptx_nmasks.h’: Permission denied /usr/bin/install -p -m 0664 ptx_nmasks.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ptx_seedmask.h’: Permission denied /usr/bin/install -p -m 0664 ptx_seedmask.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ptx_simple.h’: Permission denied /usr/bin/install -p -m 0664 ptx_simple.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/ptx_twomasks.h’: Permission denied /usr/bin/install -p -m 0664 ptx_twomasks.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/pvmfitOptions.h’: Permission denied /usr/bin/install -p -m 0664 pvmfitOptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/streamlines.h’: Permission denied /usr/bin/install -p -m 0664 streamlines.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/tractOptions.h’: Permission denied /usr/bin/install -p -m 0664 tractOptions.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/tractOpts.h’: Permission denied /usr/bin/install -p -m 0664 tractOpts.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/tractvols.h’: Permission denied /usr/bin/install -p -m 0664 tractvols.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/tractvolsx.h’: Permission denied /usr/bin/install -p -m 0664 tractvolsx.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/vecreg.h’: Permission denied /usr/bin/install -p -m 0664 vecreg.h /include/fdt/ /usr/bin/install: cannot remove ‘/include/fdt/xfibresoptions.h’: Permission denied /usr/bin/install -p -m 0664 xfibresoptions.h /include/fdt/ make[4]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[4]: Entering directory `/home/area51/fslbuild/fsl/src/fdt' Installing stable library archives make[4]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[4]: Entering directory `/home/area51/fslbuild/fsl/src/fdt' Installing tcl scripts /usr/bin/install: cannot remove ‘/tcl/fdt.tcl’: Permission denied /usr/bin/install -p -m 0775 fdt.tcl /tcl/ couldn't open "tclIndex": permission denied make[4]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[4]: Entering directory `/home/area51/fslbuild/fsl/src/fdt' Installing (userguide) documents /bin/rm: cannot remove ‘/doc/fdt’: Permission denied make[4]: *** [docinstall] Error 1 make[4]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[3]: *** [install-non-src-exe-files] Error 2 make[3]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[2]: *** [install-non-src-files] Error 2 make[2]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make[1]: *** [master-install-script] Error 2 make[1]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' make: *** [install] Error 2 On Mon, Mar 16, 2015 at 9:14 AM, Moises Hernandez <[log in to unmask]> wrote: > Hi, > > Nvidia nvcc compiler contains a weird bug when using the function "sqrt" > combined with a precision conversion in CUDA 6.0 and CUDA 6.5. That is > causing the error: > ptxas fatal : Unresolved extern function 'sqrtf' > > You can: > > 1. Use CUDA toolkit 7.0 or CUDA toolkit 5.5 > 2. or edit the file fsl/src/fdt/CUDA/diffmodels_utils.h > and change line 82: > > #define d2lambda_gpu(d) (sqrt(double(d))) > with > #define d2lambda_gpu(d) (sqrt(d)) > > > Best, > Moises. > > > On 15 March 2015 at 21:10, area51 <[log in to unmask]> wrote: > >> In followup to Benjamin's question, I'm also trying to install >> bedpostx_gpu on my system. Wondering if anyone has a solution. >> >> I'm running Ubuntu 14.04 on my Macbook Pro. I'm trying to build >> bedpostx_gpu from the source files. My CUDA is 6.5. I tried the following: >> >> 1. cd into $FSLDEVDIR/src/fdt >> 2. export COMPILE_GPU=1 >> 3. export CUDA="/usr/local/cuda" >> 4. make install >> >> The following code tries to execute: >> >> /usr/local/cuda-6.5/bin/nvcc --shared --compiler-options '-fPIC' -o >> CUDA/libbedpostx_cuda.so CUDA/init_gpu.cu CUDA/samples.cu CUDA/ >> diffmodels.cu CUDA/runmcmc.cu CUDA/xfibres_gpu.cu -O3 >> -gencode=arch=compute_20,code=\"sm_20,compute_20\" >> -gencode=arch=compute_35,code=\"sm_35,compute_35\" -lcudart -lcuda >> -lcurand -I. -L/usr/local/cuda-6.5/lib64 -L/usr/local/cuda-6.5/lib >> -ICUDA/options -I/usr/local/cuda-6.5/include/thrust >> -I/home/area51/fslbuild/fsl/extras/include/newmat >> -I/home/area51/fslbuild/fsl/include >> -I/home/area51/fslbuild/fsl/extras/include/boost -maxrregcount=64 >> >> >> I GET THE FOLLOWING ERRORS: >> >> ptxas warning : Too big maxrregcount value specified 64, will be ignored >> ptxas warning : Too big maxrregcount value specified 64, will be ignored >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(49): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(65): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(91): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(75): >> warning: variable "tmp" was set but never used >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(202): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(203): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(205): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(206): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(208): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(209): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(211): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(49): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(65): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(91): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(75): >> warning: variable "tmp" was set but never used >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(202): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(203): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(205): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(206): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(208): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(209): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(211): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(49): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(65): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(91): >> warning: "cc" clobber ignored >> >> /home/area51/fslbuild/fsl/extras/include/boost/boost/detail/sp_counted_base_gcc_x86.hpp(75): >> warning: variable "tmp" was set but never used >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(202): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(203): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(205): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(206): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(208): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(209): warning: >> statement is unreachable >> >> /home/area51/fslbuild/fsl/include/miscmaths/nonlin.h(211): warning: >> statement is unreachable >> >> ptxas warning : Too big maxrregcount value specified 64, will be ignored >> ptxas fatal : Unresolved extern function 'sqrtf' >> make[2]: *** [libbedpostx_cuda.so] Error 255 >> make[2]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' >> make[1]: *** [master-install-script] Error 2 >> make[1]: Leaving directory `/home/area51/fslbuild/fsl/src/fdt' >> make: *** [install] Error 2 >> > > -- Ausaf A. Bari MD PhD Clinical Fellow Functional Neurosurgery Toronto Western Hospital University of Toronto Phone: 647-624-1929 Email: [log in to unmask]