Thanks again for the answers, I have now got it working. It was my
fault, I thought the name should be libcrypt.so and not as I found out
it should be libcrypt.so.1.
So the solution for OpenSUSE 12.3 (64 bit) is to copy e.g.
/lib64/libcrypt-2.14.1.so from an OpenSUSE 12.1 installation to
freesurfer_home/lib. and then make a symbolic link to that, like ln
-s libcrypt-2.14.1.so libcrypt.so.1 (also in freesurfer_home/lib).
Actually the LD_LIBRARY_PATH already included this directory (even two
times) while I have the command source
$FREESURFER_HOME/SetUpFreeSurfer.sh in the .profile (we are using bash
shell).
Thanks for the help
Claus
On 12-06-2013 19:13, Z K wrote:
Yes, I agree. Setting/appending to the LD_LIBRARY_PATH should be the
last thing you do just before issuing a freesurfer command. At the
moment Im unsure of the details regarding various Freesurfer scripts,
and their ability to retain environment variables, but I would guess
that information is preserved since knowledge FREESURFER_HOME and
SUBJECTS_DIR is so often required.
If the /etc/csh.cshrc.local works than that is a good method as well.
We will be looking into this Opensuse 12.3 libcrypt
incompatibility, but shy of a new release of freesurfer (which is very
unlikely) the solution will almost certainly involve using the older
version of libcrypt and setting the LD_LIBRARY_PATH.
-Zeke
On 06/12/2013 01:01 PM, Nick Jones wrote:
Hi Claus,
I don't know what to say, it worked for me.
Make sure the permissions on the library file are ok, and confirm that
the LD_LIBRARY_PATH path is set properly before launching the freesurfer
command (the system should check that first). I'm not sure if when
launching certain commands, freesurfer creates new shells that don't
have the variable set properly, which breaks it. I set mine at shell
invocation using /etc/csh.cshrc.local and so that may make the
difference, but as you say, it is risky to override the system libcrypt.so
Thanks
Nick
On 06/12/2013 02:53 AM, Claus Svarer wrote:
Thank you for all the answers, I am sure it has something to do with
this crypt shared library as when I replace the /lib64/libcrypt.so
with the OpenSuse 12.1 version tkmedit can start. This is though a bit
risky as there may be other routines including the operating system,
that uses the new updated library.
Unfortunately, the proposed solution about copying the libcrypt.so to
freesurfer/lib and then add that path to the $LD_LIBRARY_PATH does not
work. Any other idea about how to make the old libcrypt.so accessible
to freesurfer routines?
Thanks
Claus
On 11-06-2013 20:00, Z K wrote:
Thank you Nick for informing the list of this workaround.
-Zeke
On 06/11/2013 01:48 PM, Nick Jones wrote:
Regarding any license issue under Opensuse 12.3 and the libcrypt
incompatibility.
So grab a libcrypt from an older opensuse (one where freesurfer was
working, for me, I used libcrypt.so from 11.3, but 12.1 may be a better
candidate if it works). Place it somewhere ($FREESURFER_HOME/lib is a
good candidate), then add the location to the LD_LIBRARY_PATH
environment variable so that freesurfer finds the old libcrypt.
There is another workaround but you must contact Nick Schmansky, I
don't
remember the details.
Thanks
Nick
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