External Email - Use Caution
Hello John,
You might be able to tell from the log what directory recon-all was cd'd
into when the creation of the soft link failed. You could try to cd
there as your userid (which I assume you used to run recon-all), and see
if you can manually create any soft link there. if you cannot do so,
there could be a problem with the directory permissions. The uersid
running recon-all should have permission to read, write, and execute on
subdirectories which typically means the permission on them is
set to be 755.
While do not officially support cuda, I would first check to see you
have the cuda libraries installed on you system. You could do a search
under /usr to see if you have it, e.g.
$ sudo find /usr -name "libcudart*"
- or with the package tools, look to see if any nvidia or cuda packages are
installed, e.g.,
$ rpm -qa | grep -i nvid
$ rpm -qa | grep -i cuda
If you don't find a libcudart.so.5 installed, then I think you will need
to install rev 7.5 of the cuda tools on your system as that should be
the version with libcudart.so.5
- R.
John Absher June 22, 2019 at 22:28
External Email - Use Caution
Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm
hoping someone can help me troubleshoot:
First, recon-all exits with error indicating that it is unable to create a
symbolic link:
[GHS\026278@vmcntdsktp10 fs_sample1]$ tail
/neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log
ICI = 216.7, FI = 1989.1, variation=32373.324
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC
2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The error occurs in CentOS 7 running on a virtual machine environment, with the
latest stable freesurfer release, 6.0.
The recon-all process was being run on the sample_001.mgz file to test the
installation, and ran for about 7 hours.
Second, when I tried to use the -use-gpu flag, the process seems to be missing
a library:
[GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i
./sample-001.mgz -use-gpu -all
Testing for CUDA device:
/usr/local/freesurfer/bin/mri_em_register_cuda:
error while loading shared libraries: libcudart.so.5.0: cannot open
shared object file: No such file or directory
Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC
2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh..harvard.edu/fswiki/BugReporting
[GHS\026278@vmcntdsktp10 fs_sample1]$
Can you suggest workarounds for one or both of these errors? Thanks,
John
Warm regards,
Please, note my new email address, john.abs...@prismahealth.org
John R. Absher, MD, FAAN
Division of Neurology, Department of Medicine
Prisma Health-Upstate
200 Patewood Drive, Suite 350B
City, SC 29615
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)
Inspire health. Serve with compassion. Be the difference.
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