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Well, you are not supposed to check *EVERYTHING*! The idea is to have
as complete coverage of the code options as possible. Then the nominal
behavior of the code is expected when operating within that region. You
stepped out of the boundaries or, depending how one wants to see it,
the coverage was incomplete. This situation is quite typical for
virtually every computational tool.<br>
<br>
The question remains whether after all patching and fixing is done your
solution is correct. I am not sure Jeans problem includes smlrho or a
zero density solution. ;)<br>
<br>
Tomek<br>
--<br>
Seyit Hocuk wrote:
<blockquote cite="mid:49F87F77.4000000@astro.rug.nl" type="cite">
<pre wrap="">Thanks Tomek,
You really have a good understanding of these things. I always worry
about unknown unknowns, as I like to call them. You have to be very
carefull. Like a colleague of mine says "Even one dot matters a lot". I
wish I had all the time to check everything.
Seyit
Tomasz Plewa wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Seyit -
The following has potential to mask real problems:
- use of thresholds ("small" parameters)
- use of hybrid energy formulation (eint_switch or eintSwitch)
- simulation passing a critical (crash) point upon restart
There perhaps a few more of this kind. The last case, for example,
likely indicates that either the code restart does not really work or
else the code memory becomes clogged and results in accessing invalid
data (flushed out upon restart). The former is generally harmful, the
latter is an implementation problem, both needs fixing.
FLASH is currently relatively densely populated with knobs, switches,
and special application-related features potentially masking bugs. I
expect the number of such extra features to grow with the growing
number of applications. This is perhaps not very different from other
codes. Every use of such features should be scrutinized,
well-justified, and documented. Otherwise it is (very) difficult to
trust the results. For example, responsibility for using thresholds
could be delegated to the user by setting their default values to
zero. Adding a paragraph discussing practice of using any extra
features already in quickstart section would not hurt.
Obviously the code might be crashing for many various reasons. It is a
complex machinery and can be easily misused (e.g. overly relaxed
refinement criteria). In a sense, for real applications it does have a
steep learning curve.
Tomek
--
Seyit Hocuk wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Thanks Klaus, for you long and useful explanations.
I had two problems looking similar. One was crashing due to
negative/zero values when using cooling/heating. And the other was
showing of all these warnings. Jeans' refinement was also problematic,
although I am not using that anymore, though great that you solved it.
And a great way by patching a diff file, I didn't know that was possible
:), so simple. Anybody else that uses or starts with Jeans standard
setup, should use Klaus' great patch!
The first problem, I had already figured it out by the way. Like you
also mentioned, there were some mistakes with lb and blocklist(lb) or
blockID and blocklist(blockID), resulting in trying to cool/heat some
parent/ancestor blocks, which can be negative and thus crashing.
The second warnings problem in sanitize, I did the two things like you
said, but I still have a lot of warnings that go below my small values,
no more negative though! This could be a natural thing, due to
cooling/shocks/adiabatic cooling or any other physical thing. Lowering
small doesn't solve this. Whatever that value is, I always have some
cells with the minimum values somehow. This can change suddenly from one
timestep to another timestep. I experience that it is very dependant on
the switch parameter, i.e., changing the way internal energy is
calculated. And I do have quite regular crashes (non convergence in
subroutine rieman) that might be related to this. Sometimes one or few
values just go crazy without any reason and by changing almost anything
just slightly (switch, hybrid_rieman, refmax/min, treshold, etc.) somhow
avoids it after restart.
Anyway, I think you solved to suppress the warnings that were coming
from "sanitizing" non-LEAF blocks. However since I still have a lot of
these annoying warnings, I completely commented the call statements for
sanitize. I will follow your suggestion on using Convert...ForMesh..., a
long name blah ;).
Kind Regards,
Seyit
Klaus Weide wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Tue, 14 Apr 2009, Seyit Hocuk wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Anshu,
Thanks for your reply. Of the solutions you proposed for the warnings (not on
the crash), I have a few remarks.
</pre>
</blockquote>
<pre wrap="">[Anshu:]
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">To reduce or suppress the
annoying messages, you could to either of two things:
1) Remove or comment out the line '#define DEBUG_CONSCONV'
in gr_sanitizeDataAfterInterp.F90. You should then see only
messages with one line per block / variable on standard output, no
dumping of the blocks contents.
2) Change gr_sanitizeDataAfterInterp so it only checks leaf blocks, not
leaf and parent blocks. That is, you might suppressing the checking
or the output if (nodetype(block)==2) .
</pre>
</blockquote>
<pre wrap="">Doing 1) still gives the warnings although like you say at a reduced amount.
With 2) you must mean if "nodetype(block)==1" for the leaf/child blocks.
</pre>
</blockquote>
<pre wrap="">Seyit,
That part of Anshu's message should have read:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">2) Change gr_sanitizeDataAfterInterp so it only checks leaf blocks, not
leaf and parent blocks. That is, you might suppress the checking
or the output if (nodetype(block)==2) .
</pre>
</blockquote>
</blockquote>
<pre wrap="">"Suppressing checking/output if (nodetype(block)==2)" was intended to mean
"doing the checking/output only if (nodetype(block)==1)". Sorry if this
was unclear (I originally wrote that part of the msg.)
</pre>
<blockquote type="cite">
<pre wrap="">However, that also does not completely remove the issue. The values can still
fall below the "small" values. I will still stick with the old
"convertToConsvdForMeshCalls" parameter.
</pre>
</blockquote>
<pre wrap="">I recommend that you disable convertToConsvdForMeshCalls, enable
convertToConsvdInMeshInterp (as per default), and see my previous
message from earlier today for a way to avoid misleading warnings;
in particular, change gr_hgSolve.F90 as indicated there.
If, after doing that, you again see warnings about min. dens (or ener, or
eint) values below their "small" lower thresholds, then this would be
reason for real concern - except PERHAPS if it happens only occasionally
and/or there is only slight undershooting of the thresholds, not negative
values. Your should then try to understand why interpolation during guard
cell filling would generate such values in your simulations, rather than
just trying to find a combination of runtime parameters that avoids the
checks being done.
Klaus
</pre>
</blockquote>
<pre wrap="">
Klaus Weide wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Flash Users,
This message is to explain, and help circumvent, some of the problems
that came up earlier this month with the Jeans problem ins FLASH 3.1.1.
Some of this will probably apply to other problems that were brought
up in the same context. In particular, private copies of
Grid_markRefineDerefine should be checked for errors similar to those
described below (near the end).
Seyit,
After applying all three runtime parameter changes, I was indeed also
able to reproduce the warning messages you had reported getting from
Jeans.
As you already seem to have found out yourself, the
Grid_markRefineDerefine.F90 provided with the Jeans problem is buggy.
A patch is attached. The original version resulted (with your changed
runtime parameters) in a pattern where a region of the domain was left
at a coarser refinement than the remainder, without a physical reason.
This showed up some further problems that become obscured after
Grid_markRefineDerefine is fixed. Let me therefore first discuss
those problems.
On Thu, 9 Apr 2009, Seyit Hocuk wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I also set convertToConsvdForMeshCalls to .True. in runtime
parameters instead of using convertToConsvdInMeshInterp, which should
have worked better because it is supposed to avoid spurius things in
paramesh3+. However convertToConsvdInMeshInterp calls at some point
gr_sanitizeDataAfterInterp, which creates all the weirdness. It is my
humble opinion that something goes wrong with conservation there.
</pre>
</blockquote>
<pre wrap="">It is not (runtime parameter) convertToConsvdInMeshInterp or
(subroutine) gr_sanitizeDataAfterInterp that created any problems.
gr_sanitizeDataAfterInterp (despite its name) only checks and reports
some problems with data, it does not modify any data; and it happens
to be called only when convertToConsvdInMeshInterp is TRUE. Now
gr_sanitizeDataAfterInterp was checking maybe a bit too aggressively.
That is, as Anshu has already written, it was checking guard cells in
PARENT blocks for plausible values even though the values in those
cells cannot impact the propagation of solutions *on LEAF blocks* at
all. And, as has just been also pointed out on FLASH-USERS, FLASH (as
provided) only cares about evolving solutions on leaf blocks.
At the point where the checking occurs, these guard cells have indeed
just been updated by PARAMESH, by copying values from a neighboring
block; so they should have valid data IF the neighbor did. But if
this neighbor of the PARENT (nodetype==2) block is an ANCESTOR
(nodetype==3) block, its data may not be valid. (It can be shown that
in THIS situation at a refinement boundary, the resulting PARENT cell
values do not impact solutions on the child (nodetype==1 aka LEAF)
blocks, even though in other cases PARENT cell values can and do
impact child solutions via interpolation/prolongation.)
Normally during most simulations, ANCESTOR blocks always contain
reasonably-looking values for all variables in their interior cells,
even though FLASH doesn't explicitly evolve ANCESTOR (or PARENT)
blocks in its solvers. These values either come from the initial
values established when Simulation_initBlock was called during
initialization, or from higher-resolution children via
LEAF->PARENT->ANCESTOR restriction done before checkpoints or plot
files are written. They may therefore be out of date with respect to
the current simulation time, but will not trigger
gr_sanitizeDataAfterInterp warnings.
However, this does not apply to the Jeans simulation in question, as
far as density DENS_VAR is concerned, because of a side effect of the
Multigrid solver. For certain kinds of boundary conditions, this
solver temporarily modifies the density values in blocks by
subtracting an offset, and later undoes this change by adding the same
value. There is, however, an inconsistency in the sets of blocks to
which these changes are applied: the subtraction is applied to all
blocks, the addition only to leaf blocks. I would like to emphasize
that this inconsistency causes no differences in results as long as
one only expects meaningful solution data in leaf blocks; and the only
negative effects are unnecessary WARNINGs from gr_sanitizeDataAfterInterp
as described above.
The following one-line change will make the addition apply to the same
set of blocks as the subtraction, and will thus avoid those warnings:
--- source/Grid/GridSolvers/Multigrid/gr_hgSolve.F90 (revision 10484)
+++ source/Grid/GridSolvers/Multigrid/gr_hgSolve.F90 (working copy)
@@ -185,7 +185,7 @@
! when using periodic/Neumann boundary conditions).
do m = 1, gr_hgMeshRefineMax
- call gr_hgLevelAddScalar(m, gr_iSource, gr_hgAvgSource,
MG_NODES_LEAF_ONLY) !oK
+ call gr_hgLevelAddScalar(m, gr_iSource, gr_hgAvgSource,
MG_NODES_ALL_NODES) !oK
enddo
! Leave boundary zones properly updated.
(Ultimately gr_sanitizeDataAfterInterp checking should be changed so
that it
only checks blocks (and cells) where valid data can always be expected.)
- * - * -
Finally, attached is a patch that fixes a few things specific to the
Jeans
simulation:
- Initialize internal energy properly in Simulation_initBlock.
- Fix inconsistent use of lb vs gr_blkList(lb), a common mistake.
- Changed LEAF -> ACTIVE_BLKS, the logic involving delta_max_par
requires it.
- Make sure delta_max_par, delta_max array elements are initialized.
Apply in the top directory (one level above source) with
patch -p0 < forSeyit.diff
Klaus
</pre>
</blockquote>
<pre wrap="">
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
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