Re: [Freesurfer] Freeview on Mac not starting due PETSC error

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I am, albeit on a Linux (Ubuntu 18.04) server.

I first reported the issue back in August of last year: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63461.html

Last I remember I was waiting on further test instructions from "-R." (fsbuild): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66257.html

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of RWANG4@mgh.harvard.edu RWANG4@mgh.harvard.edu Sent: Thursday, July 2, 2020 6:11 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview on Mac not starting due PETSC error

We are still investigating. Are you experiencing the same crash?

Ruopeng

On Jul 2, 2020, at 4:13 PM, TRISTAN J PAUTSCH <tpautsch@wisc.edumailto:tpautsch@wisc.edu> wrote:

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Is this new freeview build platform agnostic? I'd be interested in trying, as this sounds like another instance of the issue I've been reporting:

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66267.html

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Sent: Wednesday, July 1, 2020 9:45 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview on Mac not starting due PETSC error

I’ll send you a new build to try shortly.

Ruopeng

On Jul 1, 2020, at 9:57 PM, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:

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Hi Ruopeng,

Unfortunately, still the same error (I did download the whole thing again yesterday, which fixed the issue last time, but not so this time):

$ 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#Sig... ERROR: or try http://valgrind.orghttp://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 MacBook-Pro.local by elizabethharis Thu Jul 2 11:55:28 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

Thanks, Liz

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 1 July 2020 at 10:31 pm To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview on Mac not starting due PETSC error

Hi Liz,

Can you try the latest build of freeview here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best, Ruopeng

On Jul 1, 2020, at 4:45 AM, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:

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Hiya.

I wasn’t sure if I should start a new thread or just add to this one (do let me know if I should start a new one).

I’m also getting the same error and also on Catalina (10.15.5). The first time it happened, I installed the complete FS pkg and it worked; I was using it earlier today, and now it’s decided to stop working again. So frustrating.

Btw, I have an up to date XQuartz app, I installed FS using the pkg option, open -a $FREESURFER_HOME/Freeview.app doesn’t do anything at all, nor does deleting the plist file.

Thought I would share that I feel your pain, Alex, and am looking forward to a fix (whenever it’s figured out what is actually going on—if it hasn’t already been figured out!) 😊

Thanks for the help, guys.

Best, Liz

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alex White <alexander.l.white@gmail.commailto:alexander.l.white@gmail.com> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 18 June 2020 at 7:47 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview on Mac not starting due PETSC error

External Email - Use Caution Ok, thank you! -Alex

On Jun 17, 2020, at 2:44 PM, Wang, Ruopeng <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> wrote:

Hi Alex,

Unfortunately I can’t replicate the issue on my Mac so it makes debugging a little harder. I will send you a new build that will write out a log file a bit later.

Best, Ruopeng

On Jun 15, 2020, at 8:19 PM, Alex White <alexander.l.white@gmail.commailto:alexander.l.white@gmail.com> wrote:

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Hi there

Sorry for confusing you two smart and nice people!

I’m still unable to get Freeview to open reliably.

It worked when I followed your instructions earlier today. I was able to load volumes and surfaces. Then I closed Freeview and was not able to restart it, either by clicking on the app icon in Finder (no crash report is generated), nor from the terminal.

When I enter "open -a $FREESURFER_HOME/Freeview.app”, a window briefly pops up asking if I want to allow incoming network connections, then that window disappears quickly, then nothing happens. No output in the terminal. If I just enter “Freeview” I get the the same PETSC error I’ve been having all along.

I rebooted my machine and still, it won’t work :(

So, something is preventing Freeview from launching almost every time, but not every time. Damn.

Let me know if you have any other ideas.

Thanks Alex

On Jun 15, 2020, at 12:55 PM, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> wrote:

Hello Alex,

While I'm (fsbuild) and not Ruopeng, I don't mind being mistaken for such a smart/nice guy ;-) . So I'm cc'ing back to the list so he and others can follow up.

It looks like you already have the commands to set FREESURFER_HOME and source the setup script in your $HOME/.bashrc file - as that information is printed out to the terminal after you run bash. So there should be no need to repeat typing those commands in the terminal window (though it should do no harm).

I guess one question would be if it works for yo to do:

1) reboot your machine 2) start a new terminal window 3) type "bash" .... see output from the freesurfer environment and then run the command ... 4) open -a $FREESURFER_HOME/Freeview.app

Then try loading a simple volume in freeview. (Under the freeview File pull down menu, select load volume, then you could try navigating to this file and select it, /Applications/freesurfer/7.1.0/subjects/bert/mri/brain.mgz - see screen shot below).

I think Ruopeng wanted to know if after the steps above, it also works for you to double click on Freeview.app in the Finder window and launch it (navigate with the Finder to /Applications/freesurfer/7.1.0).

You could try making bash your default shell with this command in the terminal window, so you don't have to type bash in step (3).

$ chsh -s /bin/bash

- R.

Alex White wrote:

Hello again Ruopeng,

I copied those commands into my terminal. To my amazement, Freeview opened successfully with the command open -a $FREESURFER_HOME/Freeview.app

It was also able to load a volume. And then I was able to start Freeview with the simpler command “freeview.” I can’t explain that.. The FREESURFER_HOME variable didn’t change, and my shell init script had already sourced SetUpFreesurfer.sh.

However, I restarted my machine and tried again, and then Freeview wouldn’t open with either command, even following the whole sequence of commands you suggested. Then I tried again, and it worked. For some reason it’s only working intermittently.

In response to your other question, when I double-clicked on the app bundle to start freeview, there was no crash report generated.

Below is the output to the commands you requested. Do you see anything suspicious?

Thanks a million! Alex

alexlw@gse7359200 ~ % bash -------- 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

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.

bash-3.2$ sw_vers ProductName: Mac OS X ProductVersion: 10.15.5 BuildVersion: 19F101

bash-3.2$ 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 /Users/alexlw/google-cloud-sdk/bin /Library/Frameworks/Python.framework/Versions/3.8/bin /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/alexlw/Library/Python/3.8/bin /Users/alexlw/Library/Python/3..8/bin /Users/alexlw/Library/Python/3.8/bin

bash-3.2$ ls /opt/X11/bin X bmtoa font_cache libpng-config resize x11perf xditview xfsinfo xkeystone xmore xstdcmap Xephyr cvt fonttosfnt libpng16-config sessreg x11perfcomp xdm xgamma xkill xpr xterm Xfake cxpm freetype-config listres setxkbmap xauth xdmshell xgc xload xprop xvinfo Xnest editres fslsfonts lndir showfont xbacklight xdpr xhost xlogo xrandr xwd Xorg fc-cache fstobdf luit showrgb xcalc xdpyinfo xinit xlsatoms xrdb xwininfo Xquartz fc-cat gccmakedep makedepend smproxy xclipboard xedit xinput xlsclients xrefresh xwud Xvfb fc-list glxgears mkfontdir startx xclock xev xkbbell xlsfonts xscope appres fc-match glxinfo mkfontscale sxpm xcmsdb xeyes xkbcomp xmag xset atobm fc-pattern gtf oclock twm xcompmgr xfd xkbevd xman xsetmode bdftopcf fc-query iceauth png-fix-itxt ucs2any xconsole xfindproxy xkbprint xmessage xsetpointer bdftruncate fc-scan ico pngfix uxterm xcursorgen xfontsel xkbvleds xmh xsetroot bitmap fc-validate koi8rxterm quartz-wm viewres xcutsel xfs xkbwatch xmodmap xsm

bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.0

bash-3.2$ ls $FREESURFER_HOME ASegStatsLUT..txt SetUpFreeSurfer.csh diffusion matlab tkmeditParcColorsCMA DefectLUT.txt SetUpFreeSurfer.sh docs mni trctrain FreeSurferColorLUT.txt Simple_surface_labels2009.txt etc python uninstall.sh FreeSurferEnv.csh WMParcStatsLUT.txt fsafd sessions FreeSurferEnv.sh average fsfast sources.csh Freeview.app bin lib sources.sh SegmentNoLUT.txt build-stamp.txt license.txt subjects

bash-3.2$ 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

bash-3.2$ 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 /Applications/freesurfer/7.1.0/bin /Applications/freesurfer/7.1.0/fsfast/bin /Applications/freesurfer/7.1.0/mni/bin /Users/alexlw/google-cloud-sdk/bin /Library/Frameworks/Python.framework/Versions/3.8/bin /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/alexlw/Library/Python/3.8/bin /Users/alexlw/Library/Python/3.8/bin /Users/alexlw/Library/Python/3.8/bin

bash-3.2$ open -a $FREESURFER_HOME/Freeview.app Freeview opens…sometimes

bash-3.2$ 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 8:49 PM, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> wrote:

Hello Alex,

See what you get for results on your Mac with the commands listed below. Your version of MacOS may be slightly different. It should work to cut and paste the commands below.

- R.

- - - - -

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.commailto:fsbuild@contbay.com> wrote:

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​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-darw...

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_machttps://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.commailto:alexander.l.white@gmail.com> wrote:

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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.edumailto: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.commailto:alexander.l.white@gmail.com> wrote:

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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#Sig... ERROR: or try http://valgrind.orghttp://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.edumailto: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.commailto: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#Sig... ERROR: or try http://valgrind.orghttp://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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