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Thank you to all who are providing input for these issues. After ensuring the correct versions of gcc, g++, and gfortran were installed and being used, I am able to complete the `make` command. However, when I conduct `make test`, I receive the following output:

56% tests passed, 57 tests failed out of 130

Total Test time (real) = 200.72 sec

The following tests FAILED: 2 - test_TriangleFile_readWrite (Failed) 4 - utils_test (Failed) 5 - voronoi_test (Failed) 6 - border_values_test (Failed) 9 - soapbubble_test (Failed) 10 - lineprof_test (Failed) 13 - mri_annotation2label_test (Failed) 15 - mri_aparc2aseg_test (Failed) 16 - mri_binarize_test (Failed) 18 - mri_ca_label_test (Failed) 20 - mri_ca_normalize_test (Failed) 22 - mri_ca_register_test (Failed) 25 - mri_concat_test (Failed) 28 - mri_convert_test (Failed) 29 - mri_coreg_test (Failed) 30 - mri_diff_test (Failed) 32 - mri_em_register_test (Failed) 36 - mri_fuse_segmentations_test (Failed) 37 - mri_fwhm_test (Failed) 39 - mri_label2label_test (Failed) 40 - mri_label2vol_test (Failed) 42 - mri_matrix_multiply_test (Failed) 43 - mri_mc_test (Failed) 47 - mri_normalize_test (Failed) 49 - mri_relabel_hypointensities_test (Failed) 53 - mri_robust_template_test (Failed) 58 - mri_segment_test (Failed) 61 - mri_surf2surf_test (Failed) 62 - mri_surf2vol_test (Failed) 63 - mri_surfcluster_test (Failed) 68 - mris_anatomical_stats_test (Failed) 70 - mris_ca_label_test (Failed) 72 - mris_convert_test (Failed) 73 - mris_convert_gifti_test (Failed) 75 - mris_curvature_test (Failed) 76 - mris_curvature_stats_test (Failed) 77 - mris_diff_test (Failed) 78 - mris_divide_parcellation_test (Failed) 81 - mris_fix_topology_test (Failed) 84 - mris_inflate_posix_test (Failed) 86 - mris_jacobian_posix_test (Failed) 87 - mris_label2annot_test (Failed) 89 - mris_make_surfaces_test (Failed) 91 - mris_register_test (Failed) 93 - mris_smooth_posix_test (Failed) 95 - mris_sphere_test (Failed) 96 - mris_sphere_posix_test (Failed) 97 - mris_surface_stats_test (Failed) 99 - mris_volmask_test (Failed) 106 - talairach_avi_test (Failed) 110 - mri_concatenate_gcam_test (Failed) 112 - mri_glmfit_test (Failed) 116 - mri_seg_diff_test (Failed) 118 - mri_segcentroids_test (Failed) 120 - mri_warp_convert_test (Failed) 123 - mris_expand_test (Failed) 127 - mris_transform_test (Failed) Errors while running CTest Makefile:85: recipe for target 'test' failed make: *** [test] Error 8

I have installed the datafiles in the annex repo. Do you have any suggestions for alleviating these failures?

I must add that I, too, am performing this build from source in hopes to be able to use CUDA (I have 9.1) and my GPUs (GeForce Titan X) when running freesurfer. I understand that CUDA is not directly supported, but do you believe that building from source is the best option to try to get Freesurfer to work with the CUDA software and GPU’s on my system?

I could not get them to work together from the prebuilt software and I have concerns about downloading CUDA 5.0 on my Ubuntu 18.04 system, since the archived CUDA 5.0 download on NVIDIA only has options for up to Ubuntu 11.10.

If you have other suggestions besides building from source to get Freesurfer to use my GPUs for processing, I’m open to them. Otherwise, any advise you have re: my current `make test` issues are much appreciated!

Many thanks, Christian McDaniel

P.S. Kazuhiro, I tried your 8-step procedure above, but on step 2 I got an error building vxl that it could not find the '-lgeotiff' flag used in one of the cmake commands. I tried debugging but found no help online. Any advice?

___________________________________________

Christian McDaniel President, Deep Learning @ UGA Data Scientist, UGA CVIOG ITOS Data Analytics Team Master’s Student, Institute for Artificial Intelligence Boyd GSRC University of Georgia Athens, GA ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild fsbuild@contbay.com Sent: Thursday, November 1, 2018 5:26:06 PM To: freesurfer@nmr.mgh.harvard.edu Cc: knam@akita-noken.jp Subject: Re: [Freesurfer] Third party dependencies directory not found when building from source

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​Hello Kazuhiro,

With the old configure/automake tools, I used the following configure command on a CentOS7 machine (release 7.4.17-8) to build with the 5.0.35 Cuda distribution with the CentOS6 packages archive. (My cuda 5 distribution was installed under /home/osboxes/unzip/centos6-x86_64-packages/CUDA/5.0.35-rh5).

$ ./configure —disable-Werror —enable-fermi-gpu —with-cuda=/home/osboxes/unzip/centos6-x86_64-packages/CUDA/5.0.35-rh5 —with-pkgs-dir=/home/osboxes/unzip/centos6-x86_64-packages

My understanding is you need to use the —enable-fermi-gpu configure option.

I have not yet tried building with cuda in the new cmake build with the new packages archive (see previous thread postings with Christian). Please be aware that the automake build may no longer be as up to date as the cmake build, and we also do not technically support building with cuda.

On Nov 1, 2018, at 09:52, Nakamura Kazuhiro knam@akita-noken.jp wrote:

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Hi, I'm Kazuhiro. I also met trouble for compilation of freesurfer stable6 repository under my Ubuntu 18.04 LTS machine.

Even the binary package of freesurfer6.0(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz) can work under Ubuntu 18.04, option of '-use-gpu' required cuda runtime library of ver 5.0(libcudart.so.5.0).

I have tried to link cuda runtime library of Ubuntu 18.04 (ver9.1) to ver5.0 filename. (ln -s libcudart.so.9.0 libcudart.so.5.0 ) It cannot work well.