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 <ahoo...@mgh.harvard.edu>: > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup the shared objects > mv libvtkverdict.so libvtkverdict.so.bk > mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk > # link them to 5.6 > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 > > then do you get the same error from freeview? > > -Andrew > > On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com> > wrote: > > Dear Andrew, > > The command gives this result: > > [gschwind@login1 ~]$ /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 <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 $FREESURFER_HOME/lib/vtk/lib/v >> tk-5.6/*libvtkverdict* >> -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 >> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li >> b/vtk-5.6/libvtkverdict.so >> -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 >> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li >> b/vtk-5.6/libvtkverdict.so.5.6 >> -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 >> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/li >> b/vtk-5.6/libvtkverdict.so.5.6.0 >> >> >> I then integrated this into bashrc >> >> export LD_LIBRARY_PATH=$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 >> >> >> 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.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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