Dear Simon, DuMuX users,
Here's the testing procedure (gcc/6.3.0 --- cmake/3.5.2 ---
open-mpi/1.5.6 --- dumux/3.0 --- dune/2.6).
I "build" the overall dumux installation repo (the one containing also
the dune modules folders) as following (cmake.opts is the classic one) :
*$ ./dune-common/bin/dunecontrol --opts=dumux/cmake.opts all*
Then I go into the dumux folder and run cmake :
*$ cd dumux**
**$ mkdir build-cmake && cd build-cmake**
**$ cmake ..*
Then I go into the test folder of interest
(/dumux/test/porousmediumflow/richards/implicit/lens/) and try to
compile the tests that can be found in the CMakeLists.txt file :
*$ make test_richards_lens_box*
---> compiles fine
*$ make test_richards_lens_box_parallel_ug*
---> compiles fine
*$ make test_richards_lens_box_parallel_alu*
---> compiles fine
I try then to run those tests on the cluster by running the following
command :
*$ submit "mpirun -n 4 /path/to/problem/file /path/to/input/file"*
Reassuringly,*the tests seem to run fine on the cluster*, however, some
questions :
*=> *Where can I find *documentation on the command line arguments
passed via the CMakeLists.txt file*
(/dumux/test/porousmediumflow/richards/implicit/lens/CMakeLists.txt/)
*?* I am thinking about " --script fuzzy" "--zeroThreshold {"process
rank":100}" etc.
*=>* Is the Grid.Overlap=0 parameter only needed for the YaspGrid type ?
More generally, *where can I find documentation about the different
grids and their use ? *
Thanks for your help,
Joan
On 26/04/2019 15:12, Simon Scholz wrote:
Dear Joan,
I am no expert in running things in parallel, but your setup seems
fine to me. What DuMuX version are you using? I am assuming it is
release/3.0 with dune 2.6, correct?
In general it is possible to run a simulation using the box-method in
parallel with DuMuX. We test this e.g. with the richards tests located in
/test/porousmediumflow/richards/implicit/lens
Maybe you can try and build those (parallel) tests and see if they run
with the setup on you cluster. If this works then they can serve as a
guideline. If this does not work my last idea would be to check the
grid that you are using. Maybe you can try to change to using ALU or
UG and see if the problem persists.
My best,
Simon
On 25.04.19 20:07, Joan Delort Ylla wrote:
Dear DuMuX users,
I am using a CCS model that includes hydrogen impurities and biofilm
growth and transport.
I inherit from the 2pncNIMin problem.
To be able to easily compute pressure gradients (needed for biofilm
attachment/detachment) *I switched from the CCTpfa method to the Box
method*.
My application compiles, links and executes fine (please note that
until now a succesful simulation would take about 2h of clock time on
40 cores).
*I run my simulations *on a cluster*in parallel* using
open-mpi/1.5.6, a typical job submission being :
$ submit "mpirun -n 40 /path/to/problem/file /path/to/input/file"
*At first* I got the following error message (at runtime):
*Dune reported error: Dune::InvalidStateException
[BoxFVGridGeometry:/path/to/dumux/root/dumux/dumux/discretization/box/fvgridgeometry.hh:125]:
The box discretization method only works with zero overlap for
parallel computations. Set the parameter "Grid.Overlap" in the
input file. ---> Abort!*
*Which I solved* by adding the following to my input file:
[Grid]
#other parameters
Overlap = 0
*However*, after doing so, the first time step of the simulation will
run forever and output the following error:*
*
*Assemble: r(x^k) = dS/dt + div F - q; M = grad r^MSolve: M
deltax^k = r^[[KCould not build any aggregates. Probably no
connected nodes.*
So here is my question :*
Is it possible to run a simulation in parallel with the Box
discretization method ? *And if so, where should I look for a way to
do it ?
Thanks for your help, and I'll be happy to provide you with any extra
information you might need.
Joan
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--
_______________________________________________________________________
Simon Scholz
Department of Hydromechanics and Modelling of Hydrosystems (LH2)
Simon Scholz phone: +49 711 685 67015
IWS, University of Stuttgart fax: +49 711 685 60430
Pfaffenwaldring 61 email:simon.sch...@iws.uni-stuttgart.de
D-70569 Stuttgart url:www.hydrosys.uni-stuttgart.de
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