We are building up our testing infrastructure and as it currently stands it may still be a little too catered to our specific build environment. If freesurfer builds for you than I would skip the 'make check' stage. The best sanity check would be to make a copy of the bert subject folder, re-recon that subject, and compare that with the original bert shipped with freesurfer
On 02/28/2017 01:10 AM, Francis Tyson Thomas wrote: > Hi, > > I have been trying to build the freesurfer dev version with GPU support > as per the information I had from my previous try a couple of months ago > that Richard help me to successfully complete and I have not been > successful in that. > > I followed the instructions > from > https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page > > with slight changes, > > After running, > cd ~/freesurfer > ./setup_configure > > I edited the configure file that it generated and then commented out, > # with_cuda="" > and I changed from CUDA_LIBS="-L$CUDA_DIR/lib $LIB_CUDA -lcudart" to > CUDA_LIBS="-L$CUDA_DIR/lib64 $LIB_CUDA -lcudart" > > then I executed, ./configure --disable-Werror > --with-pkgs-dir=/home/username/centos6-x86_64-packages > --prefix=/home/username/fs_install --disable-xawplus-apps > --disable-tcltk-apps --enable-fermi-gpu --with-cuda="/usr/local/cuda" > > Subsequently when I ran make -j4 it worked without any errors. But after > that when I run make check I get errors and it fails. > > I had sent a previous email regarding the same in another thread but it > looks like it has not shown up. So I'm re-sending this now. Infact I > have recloned the freesurfer dev version to try it once again and all I > get is new errors. Following are the errors now, > > Testsuite summary for Freesurfer dev > ============================================================================ > # TOTAL: 1 > # PASS: 0 > # SKIP: 0 > # XFAIL: 0 > # FAIL: 1 > # XPASS: 0 > # ERROR: 0 > ============================================================================ > See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log > Please report to freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > ============================================================================ > make[5]: *** [test-suite.log] Error 1 > make[5]: Leaving directory > `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' > make[4]: *** [check-TESTS] Error 2 > make[4]: Leaving directory > `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' > make[3]: *** [check-am] Error 2 > make[3]: Leaving directory > `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' > make[2]: *** [check-recursive] Error 1 > make[2]: Leaving directory `/media/data1/tyson/freesurfer/utils/test' > make[1]: *** [check-recursive] Error 1 > make[1]: Leaving directory `/media/data1/tyson/freesurfer/utils' > make: *** [check-recursive] Error 1 > > If you want the log files, let me know and I'll send it as well. > > The idea behind trying to build this was see how freesurfer v6 dev > version works with GPU. Also would it be possible to use the GPU > binaries of mri_em_register and the other register binary and combine it > with the current opnmp implemenation in freesurfer v6? > > My objective all along has been to reduce it from the current best > performance of 4hrs and 38mins to something even lower like 2hrs or > lesser on a per subject basis since the subjects are pushed to the > server dynamically. > > Thanks, > Tyson > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
