[FLASH-USERS] Flash not progressing after 'Initial dt verified'
Gabriel Pérez Callejo
gabriel.perez.callejo at uva.es
Tue Oct 15 06:18:37 EDT 2024
Hi Ryan,
Thanks for the quick response. I am attaching to this email the STDOUT,
STDERR and log files.
To answer your questions, the simulation does stall. The ps command
shows the parallel processes as active, as well as the mpirun, but no
progress is done, nothing is printed in the log, STDOUT or STDERR files,
and if I run a *top* command, the machine is not working on FLASH.
I have retried including +noio and -debug in my setup command, but it
works identically, same problem.
Best,
*Gabriel Pérez-Callejo*
Profesor Ayudante Doctor (Assistant Professor)
Departamento de Física Teórica, Atómica y Óptica
Universidad de Valladolid
Valladolid, Spain
+34 983 18 6513
El 15/10/24 a las 12:00, Ryan Farber escribió:
> Hi Gabriel,
>
> I have encountered (and am to some extent still trying to understand)
> a similar, possibly the same, issue (also with FLASH 4.8). I think the
> usual issue I encounter is caused due to running out of memory, but it
> may also be related to HDF5...
>
> Regarding your issue, does the run just stall? Such that ps aux | grep
> flash shows the process is running but the simulation makes no
> progress in outputting to your log file or STDOUT/STDERR file(s)?
>
> Or does the run die? [Some error is encountered / ps no longer shows
> the process or it's in a completing, i/o, or zombie state.]
>
> It would be helpful if you can attach your log file and your
> STDOUT/STDERR file(s). It would also be useful if you try using +noio
> to determine if you have an HDF5 issue, and -debug to provide a
> traceback if an exception is raised.
>
> It's interesting this happened for you just changing distributions.
> I'm hoping you re-installed openmpi, hdf5, etc. on the new OS rather
> than copying your installations from your old OS(?)
>
> Best wishes,
> --------
> Ryan
>
>
> On Tue, Oct 15, 2024 at 2:51 AM Gabriel Pérez Callejo
> <gabriel.perez.callejo at uva.es> wrote:
>
> Dear all,
>
> I have been using FLASH for a while in Ubuntu 18, and am moving
> now to use the linux distribution OpenSUSE. However, when running
> flash in parallel mode, I am encountering the following problem.
>
> I am testing the LaserSlab example, with FLASH4.6.2, using
> hdf5-1.10.7, hypre-2.11.2 and openmpi-4.0.5 (same as I used in
> Ubuntu 18).
>
> I am launching the simulation by using /"./setup -auto LaserSlab
> -2d +cylindrical -nxb=16 -nyb=16 +hdf5typeio species=cha//
> //m,targ +mtmmmt +laser +uhd3t +mgd mgd_meshgroups=6
> -parfile=example.par" /then moving to the /object/ directory,
> using /"make -j"/ and after SUCCESS running "/mpirun -np 3 flash4"/.
>
> Now, this is what I used to do in Ubuntu, but what I am finding in
> this case is that the calculation is initialized, but after
> printing /"Initial dt verified" /nothing else happens. The code
> does not move forward. I can see that the chk_0000 file has been
> generated, but not the plt_0000.
>
> Has anyone encountered this problem before? Does anyone have any
> suggestions on how to fix it?
>
> Best,
>
> --
> *Gabriel Pérez-Callejo*
> Profesor Ayudante Doctor (Assistant Professor)
> Departamento de Física Teórica, Atómica y Óptica
> Universidad de Valladolid
> Valladolid, Spain
> +34 983 18 6513
>
>
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>
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> https://flash.rochester.edu/mailman/listinfo/flash-users
>
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NOTE: Enabling curvilinear, cartesian_pm/cylindrical_pm/spherical_pm/polar_pm so far was F F F F
Grid_init: resolution based on runtime params:
lrefine dx dy
1 2.500E-04 2.500E-04
2 1.250E-04 1.250E-04
3 6.250E-05 6.250E-05
4 3.125E-05 3.125E-05
MaterialProperties initialized
Cosmology initialized
in eos_inittabulated, tableName = he-imx-005.cn4
in eos_inittabulated, groupName = -none-
[eos_tabBrowseIonmix4Tables] IONMIX4 file found: he-imx-005.cn4
[eos_tabBrowseIonmix4Tables] IONMIX4 file found: al-imx-003.cn4
in eos_inittabulated, tableName = he-imx-005.cn4
in eos_inittabulated, groupName = -none-
in eos_inittabulated, tableName = al-imx-003.cn4
in eos_inittabulated, groupName = -none-
in eos_inittabulated, tableName = al-imx-003.cn4
in eos_inittabulated, groupName = -none-
RadTrans initialized
[EnergyDeposition_init] INFO: Using ed_irradVar= 16 ed_irradVarName=lase
Source terms initialized
iteration, no. not moved = 0 0
refined: total leaf blocks = 2
refined: total blocks = 2
[amr_morton_process]: Initializing surr_blks using standard orrery implementation
INFO: Grid_fillGuardCells is ignoring masking.
iteration, no. not moved = 0 1
iteration, no. not moved = 1 0
refined: total leaf blocks = 5
refined: total blocks = 6
iteration, no. not moved = 0 1
iteration, no. not moved = 1 0
refined: total leaf blocks = 20
refined: total blocks = 26
iteration, no. not moved = 0 4
iteration, no. not moved = 1 0
refined: total leaf blocks = 44
refined: total blocks = 58
Finished with Grid_initDomain, no restart
Ready to call Hydro_init
[Hydro_init]: Using non-Cartesian Geometry!
Hydro initialized
Gravity initialized
Initial dt verified
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