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 <ahoo...@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/:/ /' <<< $LD_LIBRARY_PATH) | grep > libvtkverdict.so > > best, > Andrew > > On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschw...@gmail.com> > wrote: > > Hi experts, > > I am installing freeusrfer on our cluster which is running Centos6. > > [gschwind@login1 ~]$ 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 > > > 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. > >
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