Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus
Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
$LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind markus.gschwind@gmail.com wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/ vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ 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
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Hm okay thanks - I’m curious what happens when you run:
cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>: Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, I gave this to the system admin as I do not ave the sudo rights.
I’ll come back!
Best, Markus
On 15 Sep 2017, at 20:06, Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hm okay thanks - I’m curious what happens when you run:
cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschwind@gmail.com mailto:markus.gschwind@gmail.com> wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@mgh.harvard.edu>: Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschwind@gmail.com mailto:markus.gschwind@gmail.com> wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Andrew,
after the System admin executed your proposed commands, it stays the same, Freeview aborts.
Is there anything else we could try?
Thank you and best wishes,
Markus
2017-09-15 20:06 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hm okay thanks - I’m curious what happens when you run:
cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind markus.gschwind@gmail.com wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
$LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0- openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6. 32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind markus.gschwind@gmail.com wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/v tk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ 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
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall of vtk might work, because those shared objects that we distribute are usually sym-linked
Can you also send the fs buildstamp? You can get this by running the command ‘bugr’ after sourcing freesurfer
Andrew
On Sep 19, 2017, at 11:02 AM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Dear Andrew,
after the System admin executed your proposed commands, it stays the same, Freeview aborts.
Is there anything else we could try?
Thank you and best wishes,
Markus
2017-09-15 20:06 GMT+02:00 Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>: Hm okay thanks - I’m curious what happens when you run:
cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>: Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschwind@gmail.commailto:markus.gschwind@gmail.com> wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Andrew,
Thank you!
Here is the output of bugr
[gschwind@login1 ~]$ bugr Cut-and-paste the following info into your FreeSurfer problem report:
FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.9 (Final) Kernel info: Linux 2.6.32-696.1.1.el6.x86_64 x86_64
I'll tell the system admin to reinstall your new vtk libraries.
I'll come back to you.
Thanks again, Markus
2017-09-19 19:56 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall of vtk might work, because those shared objects that we distribute are usually sym-linked
Can you also send the fs buildstamp? You can get this by running the command ‘bugr’ after sourcing freesurfer
Andrew
On Sep 19, 2017, at 11:02 AM, Markus Gschwind markus.gschwind@gmail.com wrote:
Dear Andrew,
after the System admin executed your proposed commands, it stays the same, Freeview aborts.
Is there anything else we could try?
Thank you and best wishes,
Markus
2017-09-15 20:06 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hm okay thanks - I’m curious what happens when you run:
cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
then do you get the same error from freeview?
-Andrew
On Sep 15, 2017, at 12:10 PM, Markus Gschwind markus.gschwind@gmail.com wrote:
Dear Andrew,
The command gives this result:
[gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
$LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjd k-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.3 2-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link
Thanks for your help!!
Markus
2017-09-15 17:49 GMT+02:00 Hoopes, Andrew AHOOPES@mgh.harvard.edu:
Hi Markus,
What is the output when you run the following: (this will list libraries you have access to)
/sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so
best, Andrew
On Sep 15, 2017, at 3:33 AM, Markus Gschwind markus.gschwind@gmail.com wrote:
Hi experts,
I am installing freeusrfer on our cluster which is running Centos6.
[gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Freeview aborts without any other complaint.
[gschwind@login1 ~]$ freeview Abort
When running freeview.bin it complains about a libraries error:
[gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory
I searched the archives and found this info to be given,
[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/v tk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li b/vtk-5.6/libvtkverdict.so.5.6.0
I then integrated this into bashrc
export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
however, the problem persists.
Any help is highly appreciated!
Thanks you! Markus _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Markus Gschwind