Re: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution
In fact, I think I have narrowed the issue completely down to PETSC,
irrespective of FreeSurfer/FreeView.
In a Hail Mary attempt, I downloaded the PETSC source code and compiled it from
scratch; I was going to try and replace the very out of date FreeSurfer version
(2.3.x) with the latest (3.11.x). It includes a builtin post-compile check
mechanism for testing the libraries, and wouldn't you know it, I get the exact
same "signal number 11 SEGV: Segmentation Violation" error when running that
check as I do with FreeView.
As such, I will take this error to the PETSC mailing list (or whatever else
might be available), as I'm no longer convinced the issue is directly connected
to FreeSurfer (which explains why literally everything else in FS still works).
Thank you everyone who replied in an attempt to help out, it is greatly
appreciated.
Tristan
From: TRISTAN J PAUTSCH
Sent: Tuesday, September 10, 2019 3:56 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume
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
on behalf of Ruopeng Wang
Sent: Tuesday, September 10, 2019 3:46 PM
To: 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 <mailto:fsbu...@contbay.com>
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: TRISTAN J PAUTSCH <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
<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 mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 <mailto:fsbu...@contbay.com>
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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.
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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
on behalf of Ruopeng Wang
Sent: Tuesday, September 10, 2019 3:46 PM
To: 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 <mailto:fsbu...@contbay.com>
Sent: Tuesday, September 10, 2019 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: TRISTAN J PAUTSCH <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
<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 mailto:tpaut...@wisc.edu>>
Sent: Thursday, August 29, 2019 10:27 AM
To: fsbuild mailto:fsbu...@contbay.com>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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 <mailto:fsbu...@contbay.com>
Sent: Tuesday, August 27, 2019 4:25 PM
To: TRISTAN J PAUTSCH <mailto:tpaut...@wisc.edu>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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
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
*Sent:* Tuesday, September 10, 2019 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Cc:* TRISTAN J PAUTSCH
*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 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 mailto:tpaut...@wisc.edu>>
*Sent:*Thursday, August 29, 2019 10:27 AM
*To:*fsbuild mailto:fsbu...@contbay.com>>
*Cc:*freesurfer@nmr.mgh.harvard.edu
<mailto: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
*Sent:*Tuesday, August 27, 2019 4:25 PM
*To:*TRISTAN J PAUTSCH
*Cc:*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 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 ult
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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. 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
wrote:External Email - Use
CautionThank 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 ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC
(16x32GB DIMMs)From:TRISTAN J PAUTSCH
tpaut...@wisc.eduSent:Thursday, August 29, 2019 10:27
AMTo:fsbuild
fsbu...@contbay.comCc:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:Re:
[Freesurfer] freeview crash -- petsc error when opening volumeThank you
for the reply, I will try this when time permits!TristanFrom:fsbuild
fsbu...@contbay.comSent:Tuesday, August 27, 2019 4:25
PMTo:TRISTAN J PAUTSCH
tpaut...@wisc.eduCc:freesurfer@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] freeview
crash -- petsc error when opening volumeHello 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
ishttps://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=sharingIt
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,
# 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-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,
seecmake_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 tpaut...@wisc.edu
wrote:External Email - Use
CautionSome 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.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:TRISTAN J PAUTSCH
tpaut...@wisc.eduSent:Friday, August 23, 2019 11:38
AMTo:Freesurfer support list
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] freeview
crash -- petsc error when opening volumeGood 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
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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 Sent: Thursday, August 29, 2019 10:27 AM To: fsbuild Cc: 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 Sent: Tuesday, August 27, 2019 4:25 PM To: TRISTAN J PAUTSCH Cc: 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 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 mailto:tpaut...@wisc.edu>> Sent: Friday, August 23, 2019 11:38 AM To: Freesurfer support list 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 on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 5:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview crash -- petsc error when opening vol
Re: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution Thank you for the reply, I will try this when time permits! Tristan From: fsbuild Sent: Tuesday, August 27, 2019 4:25 PM To: TRISTAN J PAUTSCH Cc: 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 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 mailto:tpaut...@wisc.edu>> Sent: Friday, August 23, 2019 11:38 AM To: Freesurfer support list 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 on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 5:00 PM To: Freesurfer support list 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 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 als
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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 Sent: Friday, August 23, 2019 11:38 AM To: Freesurfer support list 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 on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 5:00 PM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ruopeng Wang mailto:rpw...@nmr.mgh.harvard.edu>> Sent: Thursday, August 22, 2019 8:16 AM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J PAUTSCH 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> 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 CL
Re: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution 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 on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 5:00 PM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Ruopeng Wang mailto:rpw...@nmr.mgh.harvard.edu>> Sent: Thursday, August 22, 2019 8:16 AM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J PAUTSCH 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> 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 Re
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 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 > on behalf of Ruopeng Wang > > Sent: Thursday, August 22, 2019 8:16 AM > To: Freesurfer support list > 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 > <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> >> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J >> PAUTSCH > <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> >> 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 >> >> <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 xxx by xxx Tue Aug >> 20 13:44:15 2019 >> [0]PETSC ERROR: Libraries linked from >> /
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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 on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 8:16 AM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J PAUTSCH 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> 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 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 xxx by xxx 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.m
Re: [Freesurfer] freeview crash -- petsc error when opening volume
External Email - Use Caution Absolutely, Ruopeng, happy to provide. Would the best avenue for sharing these files be the FTP drop (into transfer/incoming) or some other avenue? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 8:16 AM To: Freesurfer support list 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 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> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of TRISTAN J PAUTSCH 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> 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 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 xxx by xxx 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 > on behalf of TRISTAN J PAUTSCH > > Sent: Tuesday, August 20, 2019 2:35 PM > To: 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 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 xxx by xxx 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 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freeview crash -- petsc error when opening volume
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 on behalf of TRISTAN J PAUTSCH Sent: Tuesday, August 20, 2019 2:35 PM To: 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 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 xxx by xxx 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 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 xxx by xxx 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
