Thanks R, those are very good points.
-Paul
________________________________
From: fsbuild <fsbu...@contbay.com>
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: r.lud...@eni-g.de <r.lud...@eni-g.de>; Wighton, Paul
<pwigh...@mgh.harvard.edu>; fsbu...@contbay.com <fsbu...@contbay.com>
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
External Email - Use Caution
The glibc version has changed in newer versions of Ubuntu. That and/or changes
to encryption related functions is likely preventing the license decoding from
working. Binary backwards compatibility cannot assure old binaries will
indefinitely run on newer releases of the operating system., e.g., CentOS6
binaries may not run on CentOS8. Freesurfer 5.3 was released in 2013 at the
time of Ubuntu 12 so I would not assume it will run on Ubuntu 18 and/or newer
versions. I don['t think LD_LIBRARY_PATH will help with statically linked
binaries - and sertting it to point to a version could break dynamically linked
binaries with RPATH strings. In general it is a bad idea to be running with
different versions of glibc on the same system.
There is an Ubuntu 12 VM running Freesurfer 5.3 available from
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz<https://secure-web.cisco.com/13_Z5mhms1Dpq_WEjE79lEciW_21298e4jPP1NTDsZfB8Igfsnnu3qYl3BeyM76R9HGTX5lxisLN47qGSSeHCN3PAWPWaLY0swK-cyJZamxaMUeok9Y0urSrvDuG7EXCubWSA3M94NvLmMuwxWo8LWS7hCY67NvQdwSYhtCSqCRyqvpp1Goknf5X8rRc0NCmHs7-L7zGrDXU1W5kOLf63Mk6ffRDL39v9CdhvyvDG9umhsQ0VhOFfdRF6EeAKHLTgPTCv-FmbijBEd2vF73cPSHsNyOyqNt9aB4ywSLhNzB1ro12Z78khyvHF8cXPQ3rz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz>
That VM still runs in VirtualBox on todays operating systems.
- R.
On Sep 13, 2022, at 13:28, Wighton, Paul <pwigh...@mgh.harvard.edu> wrote:
Hi Rüdiger,
This is really interesting.. I'm able to reproduce this issue in a docker
container. Anyone else who would like to reproduce or look into this issue can
use the following containers
- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04
(glibc v2.23) and everything works as expected in this container.
- The container `pwighton/freesurfer:5..3.0-HCP-focal` is based off of ubuntu
20.04 (glib2 v2.31) and I am experiencing the same issue you describe.
- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04
and has the latest version of FreeSurfer installed. Everything works as
expected in this container.
So the issue seems to be some interaction between the v5.3 license checking
code and the crypt() function provided by different versions of glibc, but that
is just speculation at this point.
I'm sorry I don't have any solution for this at the moment. You mention you
are using lmod, would it be possible to define LD_LIBRARY_PATH inside the
FreeSurfer 5.3 module to point to an older version of glibc?
-Paul
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ludwig, Rüdiger
<r.lud...@eni-g.de>
Sent: Tuesday, September 13, 2022 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu <freesur...@nmr..mgh.harvard.edu>
Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
Hello again,
I realized I might have missed some important information in my question about
freesurfer 5.3 license files a few days ago:
We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/''
for freesurfer 5.3
When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file
/opt/apps/freesurfer/5.3/license.txt
After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file
/opt/apps/freesurfer/5.3/license.txt
So the file is obviously read but rejected. We get the same result it with a
brand new license file, and one that still works for freesurfer 5.3 on our
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or
freesurfer 7.3
If you need any further information to help us, we am more than willing to
provide that.
Thank you so much in advance
Ruediger
---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max
Planck Society
Grisebachstr. 5
37077 Göttingen
Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
