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I have re-configured/built using:<br>
<br>
./configure PETSC_ARCH=gnu_shared
-download-{spooles,parmetis,superlu_dist,prometheus,mpich,ml,hypre,metis}
--with-shared-libraries<br>
<br>
make PETSC_ARCH=gnu_shared all<br>
<br>
make PETSC_ARCH=gnu_shared test<br>
<br>
<br>
Using the same test problem (src/ksp/ksp/examples/tutorials/ex2.c),
on the 100x100 case I get:<br>
<br>
sg-macbook-prolocal:tutorials sg$ make PETSC_ARCH=gnu_shared
runex2spooles<br>
Norm of error 2.21422e-12 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make PETSC_ARCH=gnu_shared
runex2superlu<br>
Norm of error 7.66145e-13 iterations 1<br>
<br>
One the 500x500 case I get:<br>
<br>
sg-macbook-prolocal:tutorials sg$ make PETSC_ARCH=gnu_shared
runex2spooles<br>
Norm of error 2.69468e-10 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make PETSC_ARCH=gnu_shared
runex2superlu<br>
Norm of error 419.953 iterations 1<br>
<br>
otool shows:<br>
<br>
sg-macbook-prolocal:tutorials sg$ otool -L ex2<br>
ex2:<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libpetsc.dylib
(compatibility version 0.0.0, current version 0.0.0)<br>
/usr/X11/lib/libX11.6.dylib (compatibility version 10.0.0,
current version 10.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libmpichcxx.dylib
(compatibility version 0.0.0, current version 3.0.0)<br>
/usr/local/lib/libstdc++.6.dylib (compatibility version 7.0.0,
current version 7.17.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libparmetis.dylib
(compatibility version 0.0.0, current version 0.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libmetis.dylib
(compatibility version 0.0.0, current version 0.0.0)<br>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
(compatibility version 1.0.0, current version 1.0.0)<br>
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
(compatibility version 1.0.0, current version 1.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libmpichf90.dylib
(compatibility version 0.0.0, current version 3.0.0)<br>
/usr/local/lib/libgfortran.3.dylib (compatibility version 4.0.0,
current version 4.0.0)<br>
/usr/local/lib/libquadmath.0.dylib (compatibility version 1.0.0,
current version 1.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libpmpich.dylib
(compatibility version 0.0.0, current version 3.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libmpich.dylib
(compatibility version 0.0.0, current version 3.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libopa.1.dylib
(compatibility version 2.0.0, current version 2.0.0)<br>
/Users/sg/petsc-3.3-p5/gnu_shared/lib/libmpl.1.dylib
(compatibility version 3.0.0, current version 3.0.0)<br>
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 159.1.0)<br>
/usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0,
current version 1.0.0)<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/26/12 3:08 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote
cite="mid:CAMYG4Gmn8uwypwzoGRmjaOhDRL7Mbkdqn6ii5VORh_wxok2PrA@mail.gmail.com"
type="cite">
<div dir="ltr"><br>
<div class="gmail_extra">On Wed, Dec 26, 2012 at 4:38 PM, Sanjay
Govindjee <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu" target="_blank">s_g@berkeley.edu</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">I have a
macbook pro (Mac OS X 10.7.5)<br>
<br>
% uname -a<br>
Darwin sg-macbook-prolocal.local 11.4.2 Darwin Kernel
Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012;
root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64<br>
<br>
I configured using:
<div class="im"><br>
<br>
./configure --with-cc=icc --with-fc=ifort
-download-{spooles,parmetis,superlu_dist,prometheus,mpich,ml,hypre,metis}<br>
<br>
</div>
so everything was built together.</blockquote>
<div><br>
</div>
<div style="">Since</div>
<div style=""><br>
</div>
<div style=""> a) you have tried other compilers</div>
<div style=""><br>
</div>
<div style=""> b) we cannot reproduce it</div>
<div style=""><br>
</div>
<div style=""> c) we are building the library during
configure</div>
<div style=""><br>
</div>
<div style="">I would guess that some outside library, in
your default link path, is contaminating</div>
<div style="">the executable with symbols which override
some of those in SuperLU. The SuperLU</div>
<div style="">people are not super careful about naming.
Could you</div>
<div style=""><br>
</div>
<div style=""> 1) Try this same exercise using
--with-shared-libraries</div>
<div style=""><br>
</div>
<div style=""> 2) Once you do that, use otool -L on the
executable so we can see where everything comes from</div>
<div style=""><br>
</div>
<div style=""> Thanks,</div>
<div style=""><br>
</div>
<div style=""> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb">
<div class="h5">
On 12/26/12 1:34 PM, Hong Zhang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Sanjay:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
hmmm....I guess that is good news -- in that
superlu is not broken. However,<br>
for me<br>
not so good news since I seems that there is nasty
bug lurking on my<br>
machine.<br>
<br>
Any suggestions on chasing down the error?<br>
</blockquote>
How did you install your supelu_dist with petsc-3.3?<br>
What machine do you use?<br>
<br>
Hong<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
On 12/26/12 1:23 PM, Hong Zhang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
Sanjay:<br>
I get<br>
petsc-3.3/src/ksp/ksp/examples/tutorials>mpiexec
-n 2 ./ex2<br>
-ksp_monitor_short -ksp_type preonly -pc_type
lu<br>
-pc_factor_mat_solver_package superlu_dist -m
500 -n 500<br>
Norm of error 1.92279e-11 iterations 1<br>
<br>
Hong<br>
<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
I have done some more testing of the problem,
continuing with<br>
src/ksp/ksp/examples/tutorials/ex2.c.<br>
<br>
The behavior I am seeing is that with smaller
problems sizes superlu_dist<br>
is<br>
behaving properly<br>
but with larger problem sizes things seem to
go wrong and what goes wrong<br>
is<br>
apparently consistent; the error appears both
with my intel build as well<br>
as<br>
with my gcc build.<br>
<br>
I have two run lines:<br>
<br>
runex2superlu:<br>
-@${MPIEXEC} -n 2 ./ex2
-ksp_monitor_short -m 100 -n 100<br>
-ksp_type<br>
preonly -pc_type lu
-pc_factor_mat_solver_package superlu_dist<br>
<br>
runex2spooles:<br>
-@${MPIEXEC} -n 2 ./ex2
-ksp_monitor_short -m 100 -n 100<br>
-ksp_type<br>
preonly -pc_type lu
-pc_factor_mat_solver_package spooles<br>
<br>
From my intel build, I get<br>
<br>
sg-macbook-prolocal:tutorials sg$ make
runex2superlu<br>
Norm of error 7.66145e-13 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make
runex2spooles<br>
Norm of error 2.21422e-12 iterations 1<br>
<br>
From my GCC build, I get<br>
sg-macbook-prolocal:tutorials sg$ make
runex2superlu<br>
Norm of error 7.66145e-13 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make
runex2spooles<br>
Norm of error 2.21422e-12 iterations 1<br>
<br>
If I change the -m 100 -n 100 to -m 500 -n
500, I get for my intel build<br>
<br>
sg-macbook-prolocal:tutorials sg$ make
runex2superlu<br>
Norm of error 419.953 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make
runex2spooles<br>
Norm of error 2.69468e-10 iterations 1<br>
<br>
From my GCC build with -m 500 -n 500, I get<br>
<br>
sg-macbook-prolocal:tutorials sg$ make
runex2superlu<br>
Norm of error 419.953 iterations 1<br>
sg-macbook-prolocal:tutorials sg$ make
runex2spooles<br>
Norm of error 2.69468e-10 iterations 1<br>
<br>
<br>
Any suggestions will be greatly appreciated.<br>
<br>
-sanjay<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 12/23/12 6:42 PM, Matthew Knepley wrote:<br>
<br>
<br>
On Sun, Dec 23, 2012 at 9:37 PM, Sanjay
Govindjee <<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu"
target="_blank">s_g@berkeley.edu</a>><br>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
I decided to go with
ksp/ksp/exampeles/tutorials/ex2.c; I was
unsure how<br>
to convert the run lines for
snes/examples/ex5.c to work with a direct<br>
solver as I am not versed in SNES options.<br>
<br>
Notwithstanding something strange is
happening only on select examples.<br>
With ksp/ksp/exampeles/tutorials/ex2.c and
the run line:<br>
<br>
-@${MPIEXEC} -n 2 ./ex2 -ksp_monitor_short
-m 20 -n 20 -ksp_type preonly<br>
-pc_type lu -pc_factor_mat_solver_package
superlu_dist<br>
<br>
I get good results (of the order):<br>
<br>
Norm of error 1.85464e-14 iterations 1<br>
<br>
using both superlu_dist and spooles.<br>
<br>
My BLAS/LAPACK: -llapack -lblas (so native
to my machine).<br>
<br>
If you can guide me on a run line for the
snes ex5.c I can try that too.<br>
I'll also try to construct a GCC build later
to see if that is an issue.<br>
</blockquote>
<br>
Same line on ex5, but ex2 is good enough.
However, it will not tell us<br>
anything new. Try another build.<br>
<br>
Matt<br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
-sanjay<br>
<br>
<br>
On 12/23/12 5:58 PM, Matthew Knepley wrote:<br>
<br>
On Sun, Dec 23, 2012 at 8:08 PM, Sanjay
Govindjee <<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu"
target="_blank">s_g@berkeley.edu</a>><br>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
Not sure what you mean by where is your
matrix? I am simply running<br>
ex6<br>
in the ksp/examples/tests directory.<br>
<br>
The reason I ran this test is because I
was seeing the same behavior<br>
with<br>
my finite element code (on perfectly
benign problems).<br>
<br>
Is there a built-in test that you use to
check that superlu_dist is<br>
working properly with petsc?<br>
i.e. something you know that works with
with petsc 3.3-p5?<br>
</blockquote>
<br>
1) Run it on a SNES ex5 (or KSP ex2), which
is a nice Laplacian<br>
<br>
2) Compare with MUMPS<br>
<br>
Matt<br>
<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
-sanjay<br>
<br>
<br>
<br>
On 12/23/12 4:56 PM, Jed Brown wrote:<br>
<br>
Where is your matrix? It might be ending
up with a very bad pivot. If<br>
the<br>
problem can be reproduced, it should be
reported to the SuperLU_DIST<br>
developers to fix. (Note that we do not
see this with other matrices.)<br>
You<br>
can also try MUMPS.<br>
<br>
<br>
On Sun, Dec 23, 2012 at 6:48 PM, Sanjay
Govindjee <<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu"
target="_blank">s_g@berkeley.edu</a>><br>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
I wanted to use SuperLU Dist to perform
a direct solve but seem to be<br>
encountering<br>
a problem. I was wonder if this is a
know issue and if there is a<br>
solution for it.<br>
<br>
The problem is easily observed using
ex6.c in<br>
src/ksp/ksp/examples/tests.<br>
<br>
Out of the box: make runex6 produces a
residual error of O(1e-11), all<br>
is well.<br>
<br>
I then changed the run to run on two
processors and add the flag<br>
-pc_factor_mat_solver_package spooles
this produces a residual error<br>
of<br>
O(1e-11), all is still well.<br>
<br>
I then switch over to
-pc_factor_mat_solver_package
superlu_dist and<br>
the<br>
residual error comes back as 22.6637!
Something seems very wrong.<br>
<br>
My build is perfectly vanilla:<br>
<br>
export PETSC_DIR=/Users/sg/petsc-3.3-p5/<br>
export PETSC_ARCH=intel<br>
<br>
./configure --with-cc=icc
--with-fc=ifort \<br>
<br>
-download-{spooles,parmetis,superlu_dist,prometheus,mpich,ml,hypre,metis}<br>
<br>
make PETSC_DIR=/Users/sg/petsc-3.3-p5/
PETSC_ARCH=intel all<br>
make PETSC_DIR=/Users/sg/petsc-3.3-p5/
PETSC_ARCH=intel test<br>
<br>
-sanjay<br>
</blockquote>
<br>
<br>
--<br>
-----------------------------------------------<br>
Sanjay Govindjee, PhD, PE<br>
Professor of Civil Engineering<br>
Vice Chair for Academic Affairs<br>
<br>
779 Davis Hall<br>
Structural Engineering, Mechanics and
Materials<br>
Department of Civil Engineering<br>
University of California<br>
Berkeley, CA 94720-1710<br>
<br>
Voice: <a moz-do-not-send="true"
href="tel:%2B1%20510%20642%206060"
value="+15106426060" target="_blank">+1
510 642 6060</a><br>
FAX: <a moz-do-not-send="true"
href="tel:%2B1%20510%20643%205264"
value="+15106435264" target="_blank">+1
510 643 5264</a><br>
<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu"
target="_blank">s_g@berkeley.edu</a><br>
<a moz-do-not-send="true"
href="http://www.ce.berkeley.edu/%7Esanjay"
target="_blank">http://www.ce.berkeley.edu/~sanjay</a><br>
-----------------------------------------------<br>
<br>
New Books:<br>
<br>
Engineering Mechanics of Deformable<br>
Solids: A Presentation with Exercises<br>
<br>
<br>
<a moz-do-not-send="true"
href="http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641"
target="_blank">http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641</a><br>
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href="http://ukcatalogue.oup.com/product/9780199651641.do"
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<a moz-do-not-send="true"
href="http://amzn.com/0199651647"
target="_blank">http://amzn.com/0199651647</a><br>
<br>
<br>
Engineering Mechanics 3 (Dynamics)<br>
<a moz-do-not-send="true"
href="http://www.springer.com/materials/mechanics/book/978-3-642-14018-1"
target="_blank">http://www.springer.com/materials/mechanics/book/978-3-642-14018-1</a><br>
<a moz-do-not-send="true"
href="http://amzn.com/3642140181"
target="_blank">http://amzn.com/3642140181</a><br>
<br>
-----------------------------------------------<br>
</blockquote>
<br>
<br>
<br>
--<br>
What most experimenters take for granted
before they begin their<br>
experiments is infinitely more interesting
than any results to which<br>
their<br>
experiments lead.<br>
-- Norbert Wiener<br>
<br>
<br>
</blockquote>
<br>
--<br>
What most experimenters take for granted
before they begin their<br>
experiments<br>
is infinitely more interesting than any
results to which their<br>
experiments<br>
lead.<br>
-- Norbert Wiener<br>
<br>
<br>
</blockquote>
</blockquote>
--<br>
-----------------------------------------------<br>
Sanjay Govindjee, PhD, PE<br>
Professor of Civil Engineering<br>
Vice Chair for Academic Affairs<br>
<br>
779 Davis Hall<br>
Structural Engineering, Mechanics and Materials<br>
Department of Civil Engineering<br>
University of California<br>
Berkeley, CA 94720-1710<br>
<br>
Voice: <a moz-do-not-send="true"
href="tel:%2B1%20510%20642%206060"
value="+15106426060" target="_blank">+1 510 642
6060</a><br>
FAX: <a moz-do-not-send="true"
href="tel:%2B1%20510%20643%205264"
value="+15106435264" target="_blank">+1 510 643
5264</a><br>
<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu" target="_blank">s_g@berkeley.edu</a><br>
<a moz-do-not-send="true"
href="http://www.ce.berkeley.edu/%7Esanjay"
target="_blank">http://www.ce.berkeley.edu/~sanjay</a><br>
-----------------------------------------------<br>
<br>
New Books:<br>
<br>
Engineering Mechanics of Deformable<br>
Solids: A Presentation with Exercises<br>
<a moz-do-not-send="true"
href="http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641"
target="_blank">http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641</a><br>
<a moz-do-not-send="true"
href="http://ukcatalogue.oup.com/product/9780199651641.do"
target="_blank">http://ukcatalogue.oup.com/product/9780199651641.do</a><br>
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href="http://amzn.com/0199651647"
target="_blank">http://amzn.com/0199651647</a><br>
<br>
<br>
Engineering Mechanics 3 (Dynamics)<br>
<a moz-do-not-send="true"
href="http://www.springer.com/materials/mechanics/book/978-3-642-14018-1"
target="_blank">http://www.springer.com/materials/mechanics/book/978-3-642-14018-1</a><br>
<a moz-do-not-send="true"
href="http://amzn.com/3642140181"
target="_blank">http://amzn.com/3642140181</a><br>
<br>
-----------------------------------------------<br>
<br>
</blockquote>
</blockquote>
<br>
-- <br>
-----------------------------------------------<br>
Sanjay Govindjee, PhD, PE<br>
Professor of Civil Engineering<br>
Vice Chair for Academic Affairs<br>
<br>
779 Davis Hall<br>
Structural Engineering, Mechanics and Materials<br>
Department of Civil Engineering<br>
University of California<br>
Berkeley, CA 94720-1710<br>
<br>
Voice: <a moz-do-not-send="true"
href="tel:%2B1%20510%20642%206060"
value="+15106426060" target="_blank">+1 510 642 6060</a><br>
FAX: <a moz-do-not-send="true"
href="tel:%2B1%20510%20643%205264"
value="+15106435264" target="_blank">+1 510 643 5264</a><br>
<a moz-do-not-send="true"
href="mailto:s_g@berkeley.edu" target="_blank">s_g@berkeley.edu</a><br>
<a moz-do-not-send="true"
href="http://www.ce.berkeley.edu/%7Esanjay"
target="_blank">http://www.ce.berkeley.edu/~sanjay</a><br>
-----------------------------------------------<br>
<br>
New Books:<br>
<br>
Engineering Mechanics of Deformable<br>
Solids: A Presentation with Exercises<br>
<a moz-do-not-send="true"
href="http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641"
target="_blank">http://www.oup.com/us/catalog/general/subject/Physics/MaterialsScience/?view=usa&ci=9780199651641</a><br>
<a moz-do-not-send="true"
href="http://ukcatalogue.oup.com/product/9780199651641.do"
target="_blank">http://ukcatalogue.oup.com/product/9780199651641.do</a><br>
<a moz-do-not-send="true"
href="http://amzn.com/0199651647" target="_blank">http://amzn.com/0199651647</a><br>
<br>
<br>
Engineering Mechanics 3 (Dynamics)<br>
<a moz-do-not-send="true"
href="http://www.springer.com/materials/mechanics/book/978-3-642-14018-1"
target="_blank">http://www.springer.com/materials/mechanics/book/978-3-642-14018-1</a><br>
<a moz-do-not-send="true"
href="http://amzn.com/3642140181" target="_blank">http://amzn.com/3642140181</a><br>
<br>
-----------------------------------------------<br>
<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
What most experimenters take for granted before they begin
their experiments is infinitely more interesting than any
results to which their experiments lead.<br>
-- Norbert Wiener
</div>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Sanjay Govindjee, PhD, PE
Professor of Civil Engineering
Vice Chair for Academic Affairs
779 Davis Hall
Structural Engineering, Mechanics and Materials
Department of Civil Engineering
University of California
Berkeley, CA 94720-1710
Voice: +1 510 642 6060
FAX: +1 510 643 5264
<a class="moz-txt-link-abbreviated" href="mailto:s_g@berkeley.edu">s_g@berkeley.edu</a>
<a class="moz-txt-link-freetext" href="http://www.ce.berkeley.edu/~sanjay">http://www.ce.berkeley.edu/~sanjay</a>
-----------------------------------------------
New Books:
Engineering Mechanics of Deformable
Solids: A Presentation with Exercises
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-----------------------------------------------
</pre>
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