buildqa-Mac:/tmp % bash

The default interactive shell is now zsh.

To update your account to use zsh, please run `chsh -s /bin/zsh`.

For more details, please visit https://support.apple.com/kb/HT208050.

buildqa-Mac:/tmp> sw_vers

ProductName:	Mac OS X

ProductVersion:	10.15.2

BuildVersion:	19C57

buildqa-Mac:/tmp> echo $PATH | tr -s ':' '\n' 

/usr/local/bin

/usr/bin

/bin

/usr/sbin

/sbin

/opt/X11/bin

/Users/buildqa/bin

buildqa-Mac:/tmp> ls /opt/X11/bin

X@               cvt*             freetype-config* lndir*           showrgb*         xclipboard*      xev*             xkbcomp*         xman*            xsetpointer*

Xephyr*          cxpm*            fslsfonts*       luit*            smproxy*         xclock*          xeyes*           xkbevd*          xmessage*        xsetroot*

Xfake*           editres*         fstobdf*         makedepend*      startx*          xcmsdb*          xfd*             xkbprint*        xmh*             xsm*

Xnest*           fc-cache*        gccmakedep*      mkfontdir*       sxpm*            xcompmgr*        xfindproxy*      xkbvleds*        xmodmap*         xstdcmap*

Xorg*            fc-cat*          glxgears*        mkfontscale*     twm*             xconsole*        xfontsel*        xkbwatch*        xmore*           xterm*

Xquartz*         fc-list*         glxinfo*         oclock*          ucs2any*         xcursorgen*      xfs*             xkeystone*       xpr*             xvinfo*

Xvfb*            fc-match*        gtf*             png-fix-itxt*    uxterm*          xcutsel*         xfsinfo*         xkill*           xprop*           xwd*

appres*          fc-pattern*      iceauth*         pngfix*          viewres*         xditview*        xgamma*          xload*           xrandr*          xwininfo*

atobm*           fc-query*        ico*             quartz-wm*       x11perf*         xdm*             xgc*             xlogo*           xrdb*            xwud*

bdftopcf*        fc-scan*         koi8rxterm*      resize*          x11perfcomp*     xdmshell*        xhost*           xlsatoms*        xrefresh*

bdftruncate*     fc-validate*     libpng-config@   sessreg*         xauth*           xdpr*            xinit*           xlsclients*      xscope*

bitmap*          font_cache*      libpng16-config* setxkbmap*       xbacklight*      xdpyinfo*        xinput*          xlsfonts*        xset*

bmtoa*           fonttosfnt*      listres*         showfont*        xcalc*           xedit*           xkbbell*         xmag*            xsetmode*

buildqa-Mac:/tmp> export FREESURFER_HOME=/Applications/freesurfer/7.1.0

buildqa-Mac:/tmp> ls $FREESURFER_HOME

ASegStatsLUT.txt*              SetUpFreeSurfer.sh*            etc/                           sources.csh*

DefectLUT.txt*                 Simple_surface_labels2009.txt* fsafd/                         sources.sh*

FreeSurferColorLUT.txt*        WMParcStatsLUT.txt*            fsfast/                        subjects/

FreeSurferEnv.csh*             average/                       lib/                           tkmeditParcColorsCMA*

FreeSurferEnv.sh*              bin/                           matlab/                        trctrain/

Freeview.app/                  build-stamp.txt*               mni/                           uninstall.sh*

SegmentNoLUT.txt*              diffusion/                     python/

SetUpFreeSurfer.csh*           docs/                          sessions/

buildqa-Mac:/tmp> source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-darwin-macOS-7.1.0-20200511-813297b --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer/7.1.0

FSFAST_HOME       /Applications/freesurfer/7.1.0/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /Applications/freesurfer/7.1.0/subjects

MNI_DIR           /Applications/freesurfer/7.1.0/mni

buildqa-Mac:/tmp> echo $PATH | tr -s ':' '\n'

/Applications/freesurfer/7.1.0/bin

/Applications/freesurfer/7.1.0/fsfast/bin

/Applications/freesurfer/7.1.0/mni/bin

/usr/local/bin

/usr/bin

/bin

/usr/sbin

/sbin

/opt/X11/bin

/Users/buildqa/bin

buildqa-Mac:/tmp> open -a $FREESURFER_HOME/Freeview.app

<...pop up window asking to accept network connections, then freeview should open in a separate window … then exit freeview...>

buildqa-Mac:/tmp> otool -L /Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview 

/Applications/freesurfer/7.1.0/Freeview.app/Contents/MacOS/freeview:

	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 23.0.0)

	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit (compatibility version 1.0.0, current version 275.0.0)

	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)

	@rpath/QtWidgets.framework/Versions/5/QtWidgets (compatibility version 5.12.0, current version 5.12..7)

	/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)

	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.250.1)

	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 50.1.0)

	/System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 946.0.0)

	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)

	@rpath/QtGui.framework/Versions/5/QtGui (compatibility version 5.12.0, current version 5.12.7)

	@rpath/QtCore.framework/Versions/5/QtCore (compatibility version 5.12.0, current version 5.12.7)

	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.4)

	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit (compatibility version 45.0.0, current version 1671.60.107)

	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1575.17.0)

	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics (compatibility version 64.0.0, current version 1265.9..0)

	/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation (compatibility version 300.0.0, current version 1575.17.0)

	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

On Jun 14, 2020, at 18:34, fsbuild <fsbuild@contbay.com> wrote:

        External Email - Use Caution

Hello Alex,

Did you try the install with the 7.1.0 release using the .pkg file installer from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.pkg

If you did not go thru all the security exemptions (not related to your firewall settings) on Catalina, then something may be blocked from running. The install procedure to follow using the .pkg installer is under,
https://surfer.nmr.mgh.harvard.edu/fswiki//FS7_mac

I did this on my mac running Catalina and had no issues running freeview..

- R.
On Jun 14, 2020, at 17:45, Alex White <alexander.l.white@gmail.com> wrote:

        External Email - Use Caution

Hi Ruopeng

I tried deleting that .plist file, but it did not work, even after restarting the machine. The same PETSC crash occurred when I try to start Freeview either through the terminal or clicking on the icon.

Thanks for your continued help,
Alex

On Jun 14, 2020, at 2:29 PM, Wang, Ruopeng <RWANG4@mgh.harvard.edu> wrote:

Can you delete this file and wait for a minute and then try starting freeview again?
/Users/USERNAME/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist

Replace USERNAME with your actual username.

On Jun 14, 2020, at 1:47 PM, Alex White <alexander.l.white@gmail.com> wrote:

        External Email - Use Caution

Hello Ruopeng,

Thanks for the quick reply!

I tried launching Freeview by double-clicking on the app icon, and I tried installing the latest build. The same crash occurs (full output copied again below.

Also, I do have XQuartz 2.7.11 and it can run xeyes. And yes, FREESURFER_HOME and SetUpFreesurfer.sh both reference the current version 7.1.0. I didn’t see any LD_LIBRARY_PATH in my shell init file. Here’s what’s in my .bashrc file:

% cat .bashrc

#set freesurfer directories and set up script
export FREESURFER_HOME=/Applications/freesurfer/7.1.0
export SUBJECTS_DIR=$FREESURFER_HOME/subjects
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Any other ideas?

Thanks,
Alex

Crash output:

~ % freeview

[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 http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760
[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 darwin15. named gse7359200.local by alexlw Sun Jun 14 10:46:00 2020
[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2..3.3/src/petsc/lib/darwin15.6.0-c-opt
[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019
[0]PETSC ERROR: Configure options --with-debugging=no --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 0

On Jun 14, 2020, at 6:56 AM, Wang, Ruopeng <RWANG4@mgh.harvard.edu> wrote:

HI Alex,

Have you tried launching freeview by double-clicking freeview.app bundle?

Can you also try the latest build from here?
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,
Ruopeng

On Jun 14, 2020, at 12:07 AM, Alex White <alexander.l.white@gmail.com> wrote:

        External Email - Use Caution

Hello freesurfer team!

I can’t get Freeview to start up on my Mac (Catalina v 10.15.15).

It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer: freesurfer-darwin-macOS-7.1.0-20200511-813297b

Typing “freeview” into the terminal generates the following error:

[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 http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760
[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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020
[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt
[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019
[0]PETSC ERROR: Configure options --with-debugging=no --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 0

I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution.

Help?

Thank you,
Alex White

PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email.

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