On Sep 10, 2019, at 13:52, TRISTAN J PAUTSCH <[email protected]> wrote:
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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 <[email protected] <mailto:[email protected]>>
*Sent:*Thursday, August 29, 2019 10:27 AM
*To:*fsbuild <[email protected] <mailto:[email protected]>>
*Cc:*[email protected]
<mailto:[email protected]><[email protected]
<mailto:[email protected]>>
*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 <[email protected]>
*Sent:*Tuesday, August 27, 2019 4:25 PM
*To:*TRISTAN J PAUTSCH <[email protected]>
*Cc:*[email protected] <[email protected]>
*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 <[email protected]> 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 <[email protected] <mailto:[email protected]>>
*Sent:*Friday, August 23, 2019 11:38 AM
*To:*Freesurfer support list <[email protected]
<mailto:[email protected]>>
*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:*[email protected]
<[email protected]> on behalf of Ruopeng Wang
<[email protected]>
*Sent:*Thursday, August 22, 2019 5:00 PM
*To:*Freesurfer support list <[email protected]>
*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 <[email protected]
<mailto:[email protected]>> 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:*[email protected]
<mailto:[email protected]><[email protected]
<mailto:[email protected]>> on behalf of
Ruopeng Wang <[email protected]
<mailto:[email protected]>>
*Sent:*Thursday, August 22, 2019 8:16 AM
*To:*Freesurfer support list <[email protected]
<mailto:[email protected]>>
*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 <[email protected]
<mailto:[email protected]>> 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:*[email protected]
<mailto:[email protected]><[email protected]
<mailto:[email protected]>> on behalf of
TRISTAN J PAUTSCH <[email protected]
<mailto:[email protected]>>
*Sent:*Tuesday, August 20, 2019 2:35 PM
*To:*[email protected]
<mailto:[email protected]><[email protected]
<mailto:[email protected]>>
*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
seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSCERROR:
or tryhttp://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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