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<div class="moz-cite-prefix">Hi,<br>
Nek uses static memory allocation so you have the max memory
amount you can use. In this case the max number of elements
depends on the size of given element (lx1) and can be pretty high
for 2D runs but for 3D is bounded. There are possible compiler
options to increase memory limit (e.g. -mcmodel for gfortran), but
we usually do not bother bother about it as nek is well
parallelised and one can easily increase amount of global memory
by adding more nodes. That is the proper way to go. Otherwise you
would wait for result forever.<br>
regards<br>
Adam<br>
<br>
On 22/08/17 10:11, <a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
</div>
<blockquote type="cite"
cite="mid:mailman.2066.1503389492.6680.nek5000-users@lists.mcs.anl.gov">
<div dir="ltr">Hi Adam,
<div> </div>
<div> For running a 3D case , I am setting: parameter
(lelg=500). This gives some compilations errors as follows:</div>
<div><br>
</div>
<div>
<div>obj/bdry.o: In function `faceiv_..0':</div>
<div>/home/Nek5000/core/bdry.f:(.text+0x8b8c): relocation
truncated to fit: R_X86_64_32S against symbol `screv_'
defined in COMMON section in obj/postpro.o</div>
</div>
<div><br>
</div>
<div>This does not occur if lelg<300. Please let me know a
higher lelg can be used.</div>
<div><br>
</div>
<div>Thank you</div>
<div>Swarandeep </div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Aug 21, 2017 at 6:41 PM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex"><span
class="">
<div dir="ltr">Hi Adam,
<div><br>
</div>
<div> Yes, I had wrongly set it to <span
style="font-size:12.8px"> </span><span
style="font-size:12.8px">lx2=lx1. I corrected it and
now the running is correct. The base flow is held in
place and the perturbations are time stepped. Thank
you very much for this.</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"> However the
following line </span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"> call
gradm1(DTDX,DTDY,DTDZ,T)</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"> which works
for the base flow is not working for the
perturbation if I use the below lines:</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px"> call
gradm1(DTPDX,DTPDY,DTPDZ,TP)</span></div>
<div><span style="font-size:12.8px"> call
outpost(DTPDX,DTPDY,DTPDZ,PRP,<wbr>TP,0,'gdtprt') </span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Thank you</span></div>
<div><span style="font-size:12.8px">Swarandeep</span></div>
</div>
</span>
<div class="gmail_extra"><br>
<div class="gmail_quote"><span class="">On Mon, Aug 21,
2017 at 4:41 PM, <span dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.<wbr>gov</a>></span>
wrote:<br>
</span>
<div>
<div class="h5">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div
class="m_3081789329514160659m_-2614846919753584310moz-cite-prefix">Hi,<br>
The first problem I could see is pressure mesh
size. From the log file it seems you are using
P_n-P_n instead P_n-P_n-2. Only P_n-P_n-2 has
perturbation mode, so please check you SIZE
file and compare it with the SIZE file in
dfh_cav example. You should have lx2=lx1-2
instead of lx2=lx1. Is it the case?<br>
Regards<br>
Adam
<div>
<div class="m_3081789329514160659h5"><br>
<br>
<br>
On 18/08/17 15:06, <a
class="m_3081789329514160659m_-2614846919753584310moz-txt-link-abbreviated"
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div class="m_3081789329514160659h5">
<blockquote type="cite">
<div dir="ltr">Hi Adam,
<div> I have send the logfile to
your email: <a
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:adam@mech.kth.se"
target="_blank"
moz-do-not-send="true">adam@mech.kth.se</a>)</div>
<div><br>
</div>
<div>Swarandeep<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug
18, 2017 at 6:14 PM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933moz-cite-prefix">Strange.
Could you send me your log
file? (<a
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:adam@mech.kth.se" target="_blank" moz-do-not-send="true">adam@mech.kth.se</a>)<br>
Regards<br>
Adam
<div>
<div
class="m_3081789329514160659m_-2614846919753584310gmail-h5"><br>
<br>
<br>
On 18/08/17 14:40, <a
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div
class="m_3081789329514160659m_-2614846919753584310gmail-h5">
<blockquote type="cite">
<div dir="ltr">Hi Adam,
<div><br>
<div> Thank you
for the continued
support. I managed
to get the base
flow and then I
used it in a
perturbation
calculation
following the
dfh_cav case.
Peculiarly, I an
finding that the
basic state is
getting time
stepped and the
perturbations are
not (in contrast
to the dfh_cav
case). I have used
the same .par file
from the dfh_cav
case and has used
the follwoing
settings:</div>
<div><br>
</div>
<div>
<div>[PROBLEMTYPE]</div>
<div>perturbations
= yes</div>
<div>solveBaseflow
= no</div>
<div>variableProperties
= yes</div>
</div>
<div><br>
</div>
<div> Can you
please let me know
where I am am
mistaken.</div>
<div><br>
</div>
<div>Swarandeep</div>
<div><br>
</div>
<div> </div>
</div>
</div>
<div class="gmail_extra"><br>
<div
class="gmail_quote">On
Fri, Aug 18, 2017 at
4:52 PM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px
0px 0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex">
<div
bgcolor="#FFFFFF">
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286moz-cite-prefix">Hi,<br>
<br>
###.ma2 is the
binary version
of ###.map
file and you
need only one
of them (it is
a new
feature). The
map (or ma2)
is generated
by travis
during testing
by running
genmap, so we
do not keep it
in repository.<br>
regards<br>
adam
<div>
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933h5"><br>
<br>
On 18/08/17
10:49, <a
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286moz-txt-link-abbreviated"
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933h5">
<blockquote
type="cite">
<div dir="ltr">Hi
<div> I
could no find
the ###.ma2
file for the
dfh_cav
example. Hence
I suppose I
require the
###.box or the
###.map file
to proceed for
the base flow.
Please correct
me if I have
misunderstood.</div>
<div><br>
</div>
<div>Swarandeep</div>
</div>
<div
class="gmail_extra"><br>
<div
class="gmail_quote">On
Fri, Aug 18,
2017 at 1:03
AM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hi
Swarandeep,<br>
<br>
For computing
the base flow
you can use
the same mesh
and map file.
What you need
to change is
1) the
boundary
conditions
such that they
are valid for
the base flow
and 2) the
flags that you
run a
nonlinear
instead of a
linear case.<br>
<br>
As Clio was
saying, in
that
particular
case the base
flow was
computed using
a Newton
method. For
lower Rayleigh
numbers, you
should however
be able to
just run
(nonlinear)
DNS to reach
the steady
state.<br>
<br>
Best regards,<br>
Philipp<span><br>
<br>
On 2017-08-17
20:23, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</span>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex"><span>
Hi Clio and
Adam,<br>
<br>
Thanks
for the
information.<br>
<br>
I think in
order to
compute the
base flow I
need the
###.box file
as well as a
different
###.usr file
as I think the
boundary and
initial
conditions for
the ###.usr
file in the
short_tests/dfh_cav
directory is
applicable for
the
perturbations
only. Please
send me the
###.box and
the
corresponding
###.usr file
applicable for
the base flow
for dfh_cav
case.<br>
<br>
Swarandeep<br>
<br>
<br>
</span>
<div>
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286h5">
On Thu, Aug
17, 2017 at
7:03 PM, <<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi
Swarandeep,<br>
<br>
The
baseflow has
been computed
with a Newton
solver (which
is not<br>
available
in the nek
examples). The
additional
code had been<br>
implemented in
the version
1040 of
nek5000, and
there is no
.par<br>
file for
that. However,
in general, if
your case is
laminar, to<br>
compute a
baseflow, you
just need to
evaluate the
steady state
of<br>
your
nonlinear
case. For
that, you can
use the same
.par file, and<br>
just
change to the
nonlinear
solver
(perturbationmodes
= 0,<br>
perturbations
= no,
solveBaseflow
= yes).<br>
<br>
The non
dimensionalization
is based on
Hellums and
Churchill
(1962).<br>
<br>
The
equations are:<br>
<br>
Pr (du/dt
+ (U*nabla)u +
(u*nabla)U) =
1/sqrt(Ra)laplacian(u) -grad<br>
p + e_g
theta<br>
d theta/dt
+
(u*nabla)Theta
+
(U*nabla)theta
=<br>
1/sqrt(Ra)laplacian(theta)<br>
div(u)=0<br>
<br>
where u,
theta are
respectively
the velocity
and
temperature of
the<br>
perturbation,
U, Theta the
velocity and
temperature of
the baseflow.<br>
<br>
You can
find more
information in
the paper
"Saglietti,
Clio, et al.<br>
"Adjoint
optimization
of natural
convection
problems:
differentially<br>
heated
cavity."
Theoretical
and
Computational
Fluid Dynamics
(2016):<br>
1-17." on
which the
example is
based.<br>
<br>
Regards,<br>
<br>
clio<br>
<br>
<br>
Quoting <a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</div>
</div>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>:<span><br>
<br>
Hi
Adam,<br>
<br>
Thanks
for the
clarification.
Can you please
send me a
sample<br>
.par
file for<br>
the
baseflow for
the case of
"dfh_cav".
Also is it
possible to<br>
get
the<br>
equations
solved for
this
problem(dfh_cav).
I would like
to know<br>
the
way<br>
that
this has been
made
dimensionless.<br>
<br>
For
your kind
information I
briefly
describe my
case which I<br>
have
been used<br>
to
solve with the
regular
non-linear
framework
using older<br>
versions (.rea<br>
files). My
setup is as
follows:<br>
Geometry is a
3D cylindrical
annullus.<br>
Temperature
are fixed at
inner and
outer
cylinders.<br>
Gravity is
acting in -z
direction<br>
There
is a back
ground
rotation which
is constant.<br>
<br>
Please
let me know if
any other info
is required.
Thanks for the<br>
help.<br>
<br>
Swarandeep<br>
<br>
<br>
<br>
<br>
On
Thu, Aug 17,
2017 at 1:48
PM,<br>
<<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi
Swarandeep,<br>
<br>
Yes. You
generate
###.rea in the
standard way.
In the old<br>
version it was<br>
txt and
contained both
mesh
information
and runtime<br>
parameter. One
could<br>
split mesh
information
(###.re2,
binary file)
and runtime<br>
parameters<br>
(###.rea with
negative
number of
elements or
currently<br>
###.par) using<br>
reatore2 tool.
The map file
is generated
with genmap
(can be<br>
txt or<br>
binary). So
the procedure
is more or
less the same.
If you<br>
have ###.rea<br>
with mesh you
split it and
generate
###.re2. Next
you<br>
generate
###.map with<br>
genmap and
finally
###.par by
hand. Be
careful to use
tolls<br>
from the same<br>
release, as
they've been
changed
significantly
(e.g. binary<br>
###.map file).<br>
Regards<br>
Adam<br>
<br>
<br>
On
16/08/17
18:52, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
Hi
Adam,<br>
<br>
Thank
you very much
for the help.<br>
<br>
Does
the ###.map,
###.box file
and from them
the<br>
###.rea file<br>
(in the
dfh_cav case:
the ###.re2
files) are
created as<br>
done for the<br>
earlier
versions i.e.,
by using
genbox and
genmap. Please<br>
clarify.<br>
<br>
Swarandeep<br>
<br>
<br>
<br>
On
Wed, Aug 16,
2017 at 5:35
PM,<br>
<<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi,<br>
<br>
The simplest
way would be
to look into
existing
example<br>
under<br>
Nek5000/short_test/dfh_cav/<br>
It is a
differentially
heated cavity
case and
covers<br>
both direct
and<br>
adjoint
linear solver.
It is
compatible
with the
current<br>
git version
and<br>
uses ###.par
file instead
of ###.rea.<br>
Regards<br>
Adam<br>
<br>
<br>
<br>
<br>
<br>
On 11/08/17
11:05, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
This
information
might be
outdated (old
version) but<br>
previously the
base<br>
flow was
read in using
the restart
option in the
rea<br>
file.
The
disturbance<br>
you can
read in
yourself in
userchk.<br>
<br>
Philipp<br>
<br>
On
2017-08-11
10:49, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
Hi
Philipp,<br>
<br>
That was
very much
helpful. I
have a<br>
steady base
flow and<br>
temperature
state. Please
let me know
where to<br>
provide the
base flow.<br>
<br>
<br>
Thank you<br>
Swarandeep<br>
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<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286HOEnZb">
<div
class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286h5">______________________________<wbr>_________________<br>
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href="mailto:Nek5000-users@lists.mcs.anl.gov"
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<pre>______________________________<wbr>_________________
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<a class="m_3081789329514160659m_-2614846919753584310gmail-m_-538237651637850933m_-9042198792866845286moz-txt-link-freetext" href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users" target="_blank" moz-do-not-send="true">https://lists.mcs.anl.gov/mail<wbr>man/listinfo/nek5000-users</a>
</pre>
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______________________________<wbr>_________________<br>
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<br>
<pre>______________________________<wbr>_________________
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</pre>
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<p><br>
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______________________________<wbr>_________________<br>
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class="m_3081789329514160659m_-2614846919753584310mimeAttachmentHeader"></fieldset>
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<pre>______________________________<wbr>_________________
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<a class="m_3081789329514160659m_-2614846919753584310moz-txt-link-abbreviated" href="mailto:Nek5000-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true">Nek5000-users@lists.mcs.anl.go<wbr>v</a>
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______________________________<wbr>_________________<br>
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<pre wrap="">_______________________________________________
Nek5000-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Nek5000-users@lists.mcs.anl.gov">Nek5000-users@lists.mcs.anl.gov</a>
<a class="moz-txt-link-freetext" href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a>
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