New subject: freeview crash -- petsc error when opening volume

10 Sep 2019


      External Email - Use Caution
Hello Tristan,
Please check to see that what is listed in the makefile.wiki under the section for Ubuntu is installed on your machine. &nbsp; I would also try building with the instructions in the makefile if you have not already done so; that works on my Ubuntu 18.04 system, although I am not running the server distribution, e.g., type “make -f makefile.wiki help”. &nbsp; The makefile based build will also save logs for the cmake command, build and install pass, so you could send me those directly - look for ./freesurfer/{cmake.log, make.log, install.log}
- R.
On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Thank you so much again for the detailed reply.&nbsp;I attempted your suggestion, following the instructions from the wiki to a T and compiled everything from scratch, and I still get the same PETSC error from my first post. To be thorough, I again tested on multiple machines, experiencing the same error on each.I also realized I've never posted the specs of the system on which I've been attempting all of this, so in case it's relevant to anyone else, here they are:OS: Ubuntu 18.04 ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC (16x32GB DIMMs)From:&nbsp;TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt;Sent:&nbsp;Thursday, August 29, 2019 10:27 AMTo:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Cc:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] freeview crash -- petsc error when opening volume&nbsp;Thank you for the reply, I will try this when time permits!TristanFrom:&nbsp;fsbuild &lt;fsbuild@contbay.com&gt;Sent:&nbsp;Tuesday, August 27, 2019 4:25 PMTo:&nbsp;TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt;Cc:&nbsp;freesurfer@nmr.mgh.harvard.edu &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] freeview crash -- petsc error when opening volume&nbsp;Hello Tristan,Please try rebuilding the dev branch on your Ubuntu 18 machine using the makefile listed from the wiki, (wiki page,&nbsp;https://surfer.nmr.mgh.harvard.edu/fswiki/CMake)%C2%A0where the download link to makefile is&nbsp;https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=s... should go in the same subdirectory that contains the ./freesurfer treeThere are some comments in there which recommend the following be installed for Ubuntu, so please check these are installed before building,&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install build-essential&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install libblas-dev liblapack-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install ocl-icd-opencl-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install libxmu-dev libxi-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install libopencv-dev&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;# Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9&nbsp; &nbsp; &nbsp;&nbsp;# Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 &lt;----&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install xorg xorg-dev libx11-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install tcl tcl-dev tk tk-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install qt5-default qtcreator&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install libqt5x11extras5-dev&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install git-annex&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;# sudo apt-get install python3-devI’ve attached an archive containing that makefile along with the cmake output/build logs from my Ubuntu 18.04 machine so you can see what it looks like for me, see&nbsp;cmake_make_install_ubuntu18.tgzI’ve run all the freeview tutorial commands using the 6.0.0 release on my Ubuntu 18.04 machine, but have not been able to reproduce a petsc error so far.- R.On Aug 27, 2019, at 11:27, TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Some final bits of troubleshooting information for future readers, since I'm assuming this issue will now get lost in the sauce...I'll probably try compiling everything from scratch at some point, but my hopes aren't particularly highI manually compiled the missing libs to get the CentOS7 version of FS-dev freeview running on Ubuntu 18, and ultimately the same errors occur. As well, I replicated this behavior on a separate Ubuntu 18 machine in the environment, this time using a different lab's T1/brainmask/surface files. It would definitely seem like there is some sort of hard incompatibility with newer versions of freeview and loading surface files on top of volumes in Ubuntu 18.&nbsp;For what it's worth, it's not evident that any other part of FS has an issue; all CLI tools seem to work just fine.TristanFrom:&nbsp;TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt;Sent:&nbsp;Friday, August 23, 2019 11:38 AMTo:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] freeview crash -- petsc error when opening volume&nbsp;Good morning Ruopeng, thank you for your continued assistance!Unfortunately, I get the same error using the CentOS6 dev version.. I tried the CentOS7 dev version, however this led to a series of library errors, the majority of which are unsolvable on Ubuntu 18 without individually compiling each necessary library (sym-linking newer libraries does not work).I wanted to ensure I provide the most details possible, so I also installed FS 5.3.0 and tested the files...interestingly, they opened just fine, no errors at all.This leads me to believe there is some strange incompatibility between Ubuntu 18 and the 6.x/dev version of FS (at least when it comes to surface files), specifically related to PETSC. Is there anything else I can do to help troubleshoot?TristanFrom:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Ruopeng Wang &lt;rpwang@nmr.mgh.harvard.edu&gt;Sent:&nbsp;Thursday, August 22, 2019 5:00 PMTo:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] freeview crash -- petsc error when opening volume&nbsp;Hi Tristan,Thanks for the files. I have no problem loading them with the latest dev build and stable 6..0 build. I do not have an Ubuntu system, though.&nbsp;If I’m not mistaken you use dev version of freeview binary along with stable 6.0 FS binary. Is that correct? Is there any chance you can try installing the whole FS dev package?RuopengOn Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ruopeng,I've uploaded the files to the FTP drop (transfer/incoming/freesurfer_data.tar.gz). The command my user is running against these files is:freeview -v brainmask.mgz T1.mgz -f lh.white:edgecolor=yellow lh.pial:edgecolor=magenta rh.white:edgecolor=yellow rh.pial:edgecolor=magentaWe can also replicate the error by opening freeview and opening all the above files sequentially through the GUI.Thank you!TristanFrom:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Ruopeng Wang &lt;rpwang@nmr.mgh.harvard.edu&gt;Sent:&nbsp;Thursday, August 22, 2019 8:16 AMTo:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] freeview crash -- petsc error when opening volume&nbsp;Hi Tristan,Would it be possible to send us the files and the command-line you run?&nbsp;Best,RuopengOn Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH &lt;tpautsch@wisc.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adding more details provided by my user:The crash only happens when loading surface files, either via the -f flag from the CLI or directly through the GUI. Could this be an issue with the surface files or the manner in which they are created?From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard..edu&gt; on behalf of TRISTAN J PAUTSCH &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;Sent:&nbsp;Tuesday, August 20, 2019 2:35 PMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;[Freesurfer] freeview crash -- petsc error when opening volume&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Greetings all, I'll try to keep this succinct.&nbsp;I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview instructions. All dependencies have ostensibly been satisfied, all libs from 'ldd freeview.bin' installed. Freeview launches fine and stays open when launched alone, however attempting to open a volume (either through the GUI or directly via the CLI) causes a crash and the following error about 5-8 seconds after launching (brain images begin to populate, then crash):---[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see&nbsp;http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...: or try&nbsp;http://valgrind.org%C2%A0on linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run&nbsp;[0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a linux-gnu named xxxxxxx by xxxxxxx Tue Aug 20 13:44:15 2019[0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0Segmentation fault (core dumped)---I've seen a number of other posts on the mailing list about this, but all of them&nbsp;I could find&nbsp;either end abruptly without a solution or with an unanswered request for more info.&nbsp;Happy to provide any additional information or anything that may aid in the resolution of this issue.&nbsp;Thanks everyone,~T_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer