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 <ahoo...@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.gschw...@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 <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-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 <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. >> >> > _______________________________________________ > 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 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.
