External Email - Use Caution        

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-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of fsbuild 
<fsbu...@contbay.com>
Sent: Thursday, November 1, 2018 5:26:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: k...@akita-noken.jp
Subject: Re: [Freesurfer] Third party dependencies directory not found when 
building from source


        External Email - Use Caution

​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 <k...@akita-noken.jp> wrote:

       External Email - Use Caution

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.
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