[FLASH-USERS] [EXT] Segmentation Fault (LaserSlab example)

[BolañOs, Simon]

Hi Marissa,
Thank you for your email.
I don't really understand  "executable file is not an executable"  since when I ran ./flash4, it managed to do a part of the initialization and wrote the first check file (lasslab_hdf5_chk_0000).
The setup and the compilation were a success. It is only when I ran that It crashes.
Doing this with the Sedov example, I can compile and run successfully even with the shortcut +hdf5TypeIO .
By the way, thank you for the hint for the bash file it is pretty useful.
Cheers,
Simon.
________________________________
From: Marissa B. P. Adams <madams at pas.rochester.edu>
Sent: Wednesday, August 11, 2021 10:24
To: BolañOs, Simon <sbolanos at UCSD.EDU>
Cc: flash-users at flash.uchicago.edu <flash-users at flash.uchicago.edu>
Subject: Re: [EXT] [FLASH-USERS] Segmentation Fault (LaserSlab example)

Hi Simon!

As the error notes: "executable file is not an executable" so something is off with your flash4, perhaps. Can you ls -ltr in your object/ directory where you've performed the command ./flash4?  Do you see the permissions as being executable?

When you set-up did it set-up "SUCCESS"fully? I am a fan of making my own shell scripts for set-ups and then making my own object directory (e.g. emacs LaserSlab-TestProblem.sh -nw contains the c&p below; then I make it an executable chmod a+x LaserSlab-TestProblem.sh; then I just do ./LaserSlab-TestProblem.sh; this way everything is saved). Here is my example set-up command for the LaserSlab problem:


./setup -auto LaserSlab -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio \

          species=cham,targ +mtmmmt +laser +uhd3t +mgd mgd_meshgroups=6 \

          -parfile=example.par -site=mbpadams -objdir=LaserSlab

Try simplifying your HDF5 shortcuts in the set-up command and make sure that there is no space in "+uhd3t". Is there a reason you're forcing the use of serial HDF5? You can also try setting this up with no HDF5 related flags; it should (1) set-up (2) make and (3) run successfully. If the same thing happens, can you make the Sedov/ problem?

If that doesn't work then maybe there is an issue with the Makefile.h you're using (flags probably) or something off with the installation of the libraries you're using.

These are just my initial thoughts and I hope they are helpful in your debugging.

Have a lovely day,
Marissa


On Wed, Aug 11, 2021 at 12:55 PM BolañOs, Simon <sbolanos at ucsd.edu<mailto:sbolanos at ucsd.edu>> wrote:
Hello everyone,
When executing the Laser Slab example of Section 34.7.5, I got a Segmentation Fault, displayed below. Is someone got such a similar error during execution? How can I fix such an error?
By the way here are the module that I turn on: ./setup -auto LaserSlab     -2d -nxb=16 -nyb=16 +hdf5 +io +serialIO species=cham,targ +mtmmmt +laser +u    hd3t +mgd mgd_meshgroups=6 -parfile=example.par

Error message :


Finished with Grid_initDomain, no restart

 Ready to call Hydro_init

 [Hydro_init]: Using non-Cartesian Geometry!

 Hydro initialized

 Gravity initialized

 Initial dt verified

 *** Wrote checkpoint file to lasslab_hdf5_chk_0000 ****

 *** Wrote plotfile to lasslab_hdf5_plt_cnt_0000 ****

 Initial plotfile written

 Driver init all done


Program received signal SIGSEGV: Segmentation fault - invalid memory reference.


Backtrace for this error:


Could not print backtrace: executable file is not an executable

#0  0x104270b17

#1  0x10426fbab

#2  0x193edec43

zsh: segmentation fault  ./flash4

Thank you in advance for your help,
Simon.


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