[cig-commits] r15273 - in doc/snac: . figures
echoi at geodynamics.org
echoi at geodynamics.org
Mon Jun 15 13:49:52 PDT 2009
Author: echoi
Date: 2009-06-15 13:49:51 -0700 (Mon, 15 Jun 2009)
New Revision: 15273
Added:
doc/snac/figures/scaling_efficiency1.pdf
doc/snac/figures/scaling_speedup1.pdf
doc/snac/figures/scaling_walltime1.pdf
Modified:
doc/snac/snac.lyx
doc/snac/snac.pdf
Log:
Added a chapter for SNAC's parallel performance and the corresponding figures.
Added: doc/snac/figures/scaling_efficiency1.pdf
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Modified: doc/snac/snac.lyx
===================================================================
--- doc/snac/snac.lyx 2009-06-15 20:09:57 UTC (rev 15272)
+++ doc/snac/snac.lyx 2009-06-15 20:49:51 UTC (rev 15273)
@@ -7139,50 +7139,50 @@
SNAC writes binary output files, and it is necessary to convert them to
a file format that external visualization tools can handle.
Two such converting programs are provided.
- One is for the open source Open Visualization Data Explorer, better known
- as OpenDX.
- The other generates Visualization Tool Kit (VTK) files.
- OpenDX with documentation is available from the OpenDX website
+ One generates Visualization Tool Kit (VTK) files.
+ The other is for the open source Open Visualization Data Explorer, better
+ known as OpenDX.
+ There are several programs that can visualize VTK files: ParaView
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-www.opendx.org
+www.paraview.org
\end_layout
\end_inset
-.
- There are several programs that can visualize VTK files: ParaView
+, MayaVi2
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-www.paraview.org
+https://svn.enthought.com/enthought/wiki/MayaVi
\end_layout
\end_inset
-, MayaVi2
+, or VisIt
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-https://svn.enthought.com/enthought/wiki/MayaVi
+https://wci.llnl.gov/codes/visit/
\end_layout
\end_inset
-, or VisIt
+.
+ OpenDX with documentation is available from the OpenDX website
\begin_inset Flex URL
status collapsed
\begin_layout Plain Layout
-https://wci.llnl.gov/codes/visit/
+www.opendx.org
\end_layout
\end_inset
@@ -7222,10 +7222,126 @@
\end_layout
\begin_layout Section
-Converting to OpenDX files
+Converting to VTK files
\end_layout
\begin_layout Standard
+A program called
+\family typewriter
+snac2vtk
+\family default
+ is provided to convert the binary outputs from SNAC to ascii files in the
+ XML VTK Structured Grid format (.vts).
+
+\family typewriter
+snac2vtk
+\family default
+ is compiled during the building procedure and installed in
+\family typewriter
+${SNAC_BINDIR}
+\family default
+.
+ The usage is
+\end_layout
+
+\begin_layout LyX-Code
+snac2vtk path-to-outputs [time1 time2].
+\end_layout
+
+\begin_layout Standard
+The only required argument is a path to output files including
+\family typewriter
+sim.0
+\family default
+, which contains critical information to process data.
+ The last two optional arguments are used to set the range of time steps
+ for data conversion.
+\end_layout
+
+\begin_layout Standard
+
+\family typewriter
+snac2vtk
+\family default
+ automatically generates Parallel VTK Structured Grid files (.pvts) for each
+ time step so that there is no need for an extra step to combine data even
+ for the parallel cases.
+ It is the group of .pvts files that need to be loaded in ParaView or another
+ visualization tools for VTK.
+ However, .vts files should not be removed because .pvts files only refer
+ to .vts files rather than contain actual data.
+\end_layout
+
+\begin_layout LyX-Code
+> snac2vtk ./
+\family roman
+(the last time step only)
+\end_layout
+
+\begin_layout Standard
+or
+\end_layout
+
+\begin_layout LyX-Code
+> snac2vtk ./ 10
+\family roman
+(from 10th to the last time step)
+\end_layout
+
+\begin_layout Standard
+or
+\end_layout
+
+\begin_layout LyX-Code
+> snac2vtk ./ 1 1001
+\family roman
+(from 1 to 1001th time step)
+\end_layout
+
+\begin_layout Paragraph*
+Example list of SNAC output files in the VTK format: 8 processors and 51
+ outputs per processor.
+\end_layout
+
+\begin_layout LyX-Code
+snac.0.000001.vts snac.0.000003.vts snac.0.000005.vts ....
+ snac.0.000101.vts
+\end_layout
+
+\begin_layout LyX-Code
+snac.1.000001.vts snac.1.000003.vts snac.1.000005.vts ....
+ snac.1.000101.vts
+\end_layout
+
+\begin_layout LyX-Code
+snac.2.000001.vts snac.2.000003.vts snac.2.000005.vts ....
+ snac.2.000101.vts
+\end_layout
+
+\begin_layout LyX-Code
+
+\end_layout
+
+\begin_layout LyX-Code
+snac.7.000001.vts snac.7.000003.vts snac.7.000005.vts ....
+ snac.7.000101.vts
+\end_layout
+
+\begin_layout LyX-Code
+snac.000001.pvts snac.000003.pvts snac.000005.pvts ....
+ snac.000101.pvts
+\end_layout
+
+\begin_layout Section
+Converting to OpenDX files
+\end_layout
+
+\begin_layout Standard
+It is recommended to use VTK files for post-processing.
+ The conversion tools for the DX file format will not be updated any more.
+\end_layout
+
+\begin_layout Standard
To convert binary files into ascii OpenDX files, you need to run the program
\family typewriter
@@ -7426,115 +7542,149 @@
and make cross-sections.
\end_layout
+\begin_layout Chapter
+\begin_inset CommandInset label
+LatexCommand label
+name "cha:parallel performance"
+
+\end_inset
+
+Parallel Performance
+\end_layout
+
\begin_layout Section
-Converting to VTK files
+Method
\end_layout
\begin_layout Standard
-A program called
-\family typewriter
-snac2vtk
-\family default
- is provided to convert the binary outputs from SNAC to ascii files in the
- XML VTK Structured Grid format (.vts).
-
-\family typewriter
-snac2vtk
-\family default
- is compiled during the building procedure and installed in
-\family typewriter
-${SNAC_BINDIR}
-\family default
-.
- The usage is
-\end_layout
+We solve the problem of a 3-D elastic bar with a given initial geometry
+ deforming by its own weight to acquire SNAC's hard scaling data (i.e., the
+ size of problem is fixed while the number of processors is varied).
+ All the boundaries except the top surface is fixed such that the top surface
+ is warped downward due to gravity.
+ The file I/O has been reduced to a minimal level.
+ The
+\begin_inset Formula $32^{3}$
+\end_inset
-\begin_layout LyX-Code
-snac2vtk path-to-outputs [time1 time2].
-\end_layout
+-element case problem was run until the 1000-th step.
+ To save time, however, the
+\begin_inset Formula $64^{3}$
+\end_inset
-\begin_layout Standard
-The only required argument is a path to output files including
-\family typewriter
-sim.0
-\family default
-, which contains critical information to process data.
- The last two optional arguments are used to set the range of time steps
- for data conversion.
+-element and
+\begin_inset Formula $128^{3}$
+\end_inset
+
+-element cases were run until 200-th and 50-th step, respectively.
+
\end_layout
\begin_layout Standard
-
+These tests were performed on
\family typewriter
-snac2vtk
+ranger
\family default
- automatically generates Parallel VTK Structured Grid files (.pvts) for each
- time step so that there is no need for an extra step to combine data even
- for the parallel cases.
- It is the group of .pvts files that need to be loaded in ParaView or another
- visualization tools for VTK.
- However, .vts files should not be removed because .pvts files only refer
- to .vts files rather than contain actual data.
+ at Texas Advanced Computing Center of University of Texas, Austin, by Dr.
+ Colin Stark at Lamont Doherty Earth Observatory of Columbia University.
\end_layout
-\begin_layout LyX-Code
-> snac2vtk ./
-\family roman
-(the last time step only)
+\begin_layout Section
+Results
\end_layout
\begin_layout Standard
-or
-\end_layout
+The total wall clock times taken for each case is shown in the left panel
+ of Fig.
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:parallel performance"
-\begin_layout LyX-Code
-> snac2vtk ./ 10
-\family roman
-(from 10th to the last time step)
+\end_inset
+
+ as a function of the number of cores.
+ The plots of speedup and efficiency (the middle and right panels of Fig.
+
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:parallel performance"
+
+\end_inset
+
+) show the acceptable performance of SNAC up to 4096 cores.
+ The performance of the
+\begin_inset Formula $32^{3}$
+\end_inset
+
+-element case becomes notably poor for 2048 cores or more.
+ This is because the size of subdomain becomes too small to benefit from
+ parallel processing.
+ These results suggest that the parallel overhead will dominate the computation
+ time if the subdomains become too small and the empirical lower limit for
+ the subdomain size is
+\begin_inset Formula $3^{3}$
+\end_inset
+
+ elements.
+ Also, a good scaling is expected to hold for even larger numbers of cores
+ if the problem size is sufficiently large.
+
\end_layout
\begin_layout Standard
-or
-\end_layout
+\begin_inset Float figure
+wide false
+sideways false
+status open
-\begin_layout LyX-Code
-> snac2vtk ./ 1 1001
-\family roman
-(from 1 to 1001th time step)
-\end_layout
+\begin_layout Plain Layout
+\begin_inset Graphics
+ filename figures/scaling_walltime1.pdf
+ scale 30
-\begin_layout Paragraph*
-Example list of SNAC output files in the VTK format: 8 processors and 51
- outputs per processor.
-\end_layout
+\end_inset
-\begin_layout LyX-Code
-snac.0.000001.vts snac.0.000003.vts snac.0.000005.vts ....
- snac.0.000101.vts
-\end_layout
-\begin_layout LyX-Code
-snac.1.000001.vts snac.1.000003.vts snac.1.000005.vts ....
- snac.1.000101.vts
-\end_layout
+\begin_inset Graphics
+ filename figures/scaling_speedup1.pdf
+ scale 30
-\begin_layout LyX-Code
-snac.2.000001.vts snac.2.000003.vts snac.2.000005.vts ....
- snac.2.000101.vts
+\end_inset
+
+
+\begin_inset Graphics
+ filename figures/scaling_efficiency1.pdf
+ scale 30
+
+\end_inset
+
+
\end_layout
-\begin_layout LyX-Code
+\begin_layout Plain Layout
+\begin_inset Caption
+\begin_layout Plain Layout
+(left) Wall clock time as a function of the number of cores.
+ Speedup (middle) and efficiency (right) up to 4096 cores.
+\begin_inset CommandInset label
+LatexCommand label
+name "fig:parallel performance"
+
+\end_inset
+
+
\end_layout
-\begin_layout LyX-Code
-snac.7.000001.vts snac.7.000003.vts snac.7.000005.vts ....
- snac.7.000101.vts
+\end_inset
+
+
\end_layout
-\begin_layout LyX-Code
-snac.000001.pvts snac.000003.pvts snac.000005.pvts ....
- snac.000101.pvts
+\end_inset
+
+
\end_layout
\begin_layout Chapter
Modified: doc/snac/snac.pdf
===================================================================
(Binary files differ)
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