External Email - Use Caution
I'd be willing to try pretty much anything at this point...what would be the
best way to go about doing this?
Also, what exactly is PETSC? The error seems obviously related to it, and
Googling the issue brings up many results that aren't even related to
FreeSurfer, rather PETSC. Does FreeSurfer perhaps contain an old version of
PETSC?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu>
Sent: Tuesday, September 10, 2019 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
Hi Tristan,
Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x?
Best,
Ruopeng
On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote:
External Email - Use Caution
Thank you for the reply.
Just to clarify, everything builds successfully and there are no errors (that
I've been able to find) for running 99% of FS commands; I installed all the
deps listed in the makefile and followed the instructions. As with my first
message to the list, the only issue I appear to have is when trying to open
surface files on top of volumes in freeview.
I've attached the requested logs.
Thank you!
Tristan
________________________________
From: fsbuild <fsbu...@contbay.com><mailto:fsbu...@contbay.com>
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: TRISTAN J PAUTSCH <tpaut...@wisc.edu><mailto:tpaut...@wisc.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
Hello Tristan,
Please check to see that what is listed in the makefile.wiki under the section
for Ubuntu is installed on your machine. 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”. 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
<tpaut...@wisc.edu><mailto:tpaut...@wisc.edu> wrote:
External Email - Use Caution
Thank you so much again for the detailed reply.
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 Server
CPU: 4x Xeon Platinum 8164
RAM: 512GB DDR4 ECC (16x32GB DIMMs)
________________________________
From: TRISTAN J PAUTSCH <tpaut...@wisc.edu<mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
Thank you for the reply, I will try this when time permits!
Tristan
________________________________
From: fsbuild <fsbu...@contbay.com><mailto:fsbu...@contbay.com>
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH <tpaut...@wisc.edu><mailto:tpaut...@wisc.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
Hello Tristan,
Please try rebuilding the dev branch on your Ubuntu 18 machine using the
makefile listed from the wiki, (wiki page,
https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) where the download link to
makefile is
https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharing
It should go in the same subdirectory that contains the ./freesurfer tree
There are some comments in there which recommend the following be installed for
Ubuntu, so please check these are installed before building,
# sudo apt-get install build-essential
# sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
# sudo apt-get install libblas-dev liblapack-dev
# sudo apt-get install ocl-icd-opencl-dev
# sudo apt-get install libxmu-dev libxi-dev
# sudo apt-get install libopencv-dev
# Ubuntu 16: sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
# Ubuntu 18: sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8 <----
# sudo apt-get install xorg xorg-dev libx11-dev
# sudo apt-get install tcl tcl-dev tk tk-dev
# sudo apt-get install qt5-default qtcreator
# sudo apt-get install libqt5x11extras5-dev
# sudo apt-get install git-annex
# sudo apt-get install python3-dev
I’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 cmake_make_install_ubuntu18.tgz
I’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
<tpaut...@wisc.edu><mailto:tpaut...@wisc.edu> wrote:
External Email - Use Caution
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 high
I 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.
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.
Tristan
________________________________
From: TRISTAN J PAUTSCH <tpaut...@wisc.edu<mailto:tpaut...@wisc.edu>>
Sent: Friday, August 23, 2019 11:38 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
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?
Tristan
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu><mailto:rpw...@nmr.mgh.harvard.edu>
Sent: Thursday, August 22, 2019 5:00 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
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.
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?
Ruopeng
On Aug 22, 2019, at 12:20 PM, TRISTAN J PAUTSCH
<tpaut...@wisc.edu<mailto:tpaut...@wisc.edu>> wrote:
External Email - Use Caution
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=magenta
We can also replicate the error by opening freeview and opening all the above
files sequentially through the GUI.
Thank you!
Tristan
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu<mailto:rpw...@nmr.mgh..harvard.edu>>
Sent: Thursday, August 22, 2019 8:16 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
Hi Tristan,
Would it be possible to send us the files and the command-line you run?
Best,
Ruopeng
On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH
<tpaut...@wisc.edu<mailto:tpaut...@wisc.edu>> wrote:
External Email - Use Caution
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:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of TRISTAN J PAUTSCH
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Sent: Tuesday, August 20, 2019 2:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution
Greetings all, I'll try to keep this succinct.
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
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org<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 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 0
Segmentation fault (core dumped)
---
I've seen a number of other posts on the mailing list about this, but all of
them I could find either end abruptly without a solution or with an unanswered
request for more info.
Happy to provide any additional information or anything that may aid in the
resolution of this issue.
Thanks everyone,
~T
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