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Commit 39ec32db authored by sfritschi's avatar sfritschi
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Updated scripts

parent e89b3562
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gen/perf.py
View file @ 39ec32db
...@@ -7,8 +7,8 @@ from netflow import * ...@@ -7,8 +7,8 @@ from netflow import *
from time import perf_counter from time import perf_counter
def main(): def main():
if len(sys.argv) != 4: if len(sys.argv) != 6:
raise AssertionError("Usage: python3 perf.py <n1> <n2> <n3>") raise AssertionError("Usage: python3 perf.py <2^min threads> <2^max threads> <n1> <n2> <n3>")
basenet = netflow.load_network_from('../netflow/network/network.h5') basenet = netflow.load_network_from('../netflow/network/network.h5')
print("Network statistics:") print("Network statistics:")
...@@ -18,13 +18,13 @@ def main(): ...@@ -18,13 +18,13 @@ def main():
print("Min. number of throats per pore: %d" % min(pore_throat_counts)) print("Min. number of throats per pore: %d" % min(pore_throat_counts))
print("Avg. number of throats per pore: %f" % (sum(pore_throat_counts) / len(pore_throat_counts))) print("Avg. number of throats per pore: %f" % (sum(pore_throat_counts) / len(pore_throat_counts)))
target = [int(sys.argv[1]), int(sys.argv[2]), int(sys.argv[3])] target = [int(sys.argv[3]), int(sys.argv[4]), int(sys.argv[5])]
print("Target size: {}".format(target)) print("Target size: {}".format(target))
cutoff = 0.5 * max([basenet.ub[i] - basenet.lb[i] \ cutoff = 0.5 * max([basenet.ub[i] - basenet.lb[i] \
for i in range(len(basenet.ub))]) for i in range(len(basenet.ub))])
i = 0 i = int(sys.argv[1])
max_ = 5 max_ = int(sys.argv[2])
speedups = [] speedups = []
threads = [] threads = []
...@@ -39,6 +39,7 @@ def main(): ...@@ -39,6 +39,7 @@ def main():
end = perf_counter() end = perf_counter()
elapsed = end - start elapsed = end - start
print("Elapsed: %e" % elapsed)
print("Generated network statistics:") print("Generated network statistics:")
print("Throats: %d" % len(dendro.throats)) print("Throats: %d" % len(dendro.throats))
print("Pores: %d" % len(dendro.pores)) print("Pores: %d" % len(dendro.pores))
......
gen/perf.sh
View file @ 39ec32db
#!/bin/bash #!/bin/bash
bsub -n 48 -W 00:30 -R fullnode python3 perf.py 4 4 4 # Targets Xeon Gold 6150 nodes with 36 cores/node
bsub -n 36 -W 01:00 -R fullnode python3 perf.py 0 5 3 3 3
gen/plots/strong_scaling.png
View replaced file @ e89b3562 View file @ 39ec32db
gen/plots/strong_scaling.png

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gen/plots/strong_scaling.png

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gen/plots/strong_scaling.png
gen/plots/strong_scaling.png
gen/plots/strong_scaling.png
gen/plots/strong_scaling.png
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netflow/netgen.py
View file @ 39ec32db
...@@ -805,11 +805,11 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \ ...@@ -805,11 +805,11 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
serialThresh = nthreads * 4 serialThresh = nthreads * 4
# Pores in interior that are not fully-connected yet # Pores in interior that are not fully-connected yet
poresRemain = pores[:n] poresRemain = pores[:n]
while (throatsLeft != 0): while (throatsUnrealized > 0):
if (not mute): if (not mute):
print("Throats left: %d Throats Unrealized: %d (%.2f%%)" % \ print("Throats left: %d Throats Unrealized: %d (%.2f%%)" % \
(throatsLeft, throatsUnrealized, throatsUnrealized / totalThroats * 100.)) (throatsLeft, throatsUnrealized, throatsLeft / totalThroats * 100.))
nRemain = len(poresRemain) nRemain = len(poresRemain)
if (nRemain > serialThresh): if (nRemain > serialThresh):
...@@ -938,12 +938,12 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \ ...@@ -938,12 +938,12 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
cellList.connPores[pore.index].clear() cellList.connPores[pore.index].clear()
poresRemain = nextPores poresRemain = nextPores
throatsUnrealized = throatCount // 2 # Counted all throats twice
throatsLeft = totalThroats - len(throats)
throatsLeft = throatCount // 2 # Counted all throats twice
throatsUnrealized = totalThroats - len(throats)
# Unrealized throats # Unrealized throats
nUnrealized = throatsUnrealized nUnrealized = throatsLeft
# Free memory (not needed anymore) # Free memory (not needed anymore)
del cellList del cellList
......
thesis/thesis.aux
View file @ 39ec32db
...@@ -48,10 +48,11 @@ ...@@ -48,10 +48,11 @@
\@writefile{lof}{\defcounter {refsection}{0}\relax }\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.\relax }}{5}{figure.caption.2}\protected@file@percent } \@writefile{lof}{\defcounter {refsection}{0}\relax }\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.\relax }}{5}{figure.caption.2}\protected@file@percent }
\newlabel{fig:cell}{{2}{5}{Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.\relax }{figure.caption.2}{}} \newlabel{fig:cell}{{2}{5}{Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.\relax }{figure.caption.2}{}}
\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Iterative Algorithm}{5}{subsection.3.2}\protected@file@percent } \@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Iterative Algorithm}{5}{subsection.3.2}\protected@file@percent }
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\newlabel{alg:connect}{{1}{6}{Connect pores in parallel\relax }{algorithm.1}{}} \newlabel{alg:connect}{{1}{6}{Connect pores in parallel\relax }{algorithm.1}{}}
\@writefile{lot}{\defcounter {refsection}{0}\relax }\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 1015 were not realized due to falling below the threshold of 1\%.\relax }}{7}{table.caption.3}\protected@file@percent } \@writefile{lot}{\defcounter {refsection}{0}\relax }\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 27 were not realized due to there being no possible candidates left for these remaining pores.\relax }}{7}{table.caption.3}\protected@file@percent }
\newlabel{table:iter}{{1}{7}{Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 1015 were not realized due to falling below the threshold of 1\%.\relax }{table.caption.3}{}} \newlabel{table:iter}{{1}{7}{Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 27 were not realized due to there being no possible candidates left for these remaining pores.\relax }{table.caption.3}{}}
\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{\numberline {A}PETSc Installation}{7}{appendix.A}\protected@file@percent } \@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{\numberline {A}PETSc Installation}{7}{appendix.A}\protected@file@percent }
\newlabel{appendix:install}{{A}{7}{PETSc Installation}{appendix.A}{}} \newlabel{appendix:install}{{A}{7}{PETSc Installation}{appendix.A}{}}
\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{\numberline {B}Base Network}{7}{appendix.B}\protected@file@percent } \@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{\numberline {B}Base Network}{7}{appendix.B}\protected@file@percent }
...@@ -61,3 +62,5 @@ ...@@ -61,3 +62,5 @@
\abx@aux@defaultrefcontext{0}{MEYER2021101592}{none/global//global/global} \abx@aux@defaultrefcontext{0}{MEYER2021101592}{none/global//global/global}
\abx@aux@defaultrefcontext{0}{petsc-web-page}{none/global//global/global} \abx@aux@defaultrefcontext{0}{petsc-web-page}{none/global//global/global}
\abx@aux@defaultrefcontext{0}{hypre-web-page}{none/global//global/global} \abx@aux@defaultrefcontext{0}{hypre-web-page}{none/global//global/global}
\@writefile{lof}{\defcounter {refsection}{0}\relax }\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Network consisting of 2636 pores and 4291 throats, inscribed within a cube extending $1.07\cdot 10^{-3}$m in each spatial direction. The pore-arrangement is obviously \emph {not uniform}, as can be seen by the clustering of pores in some regions, while others are mostly undisturbed. The \emph {porosity}, measured as the relative fraction of volume taken up by the void-space geometry, is roughly $32\%$.\relax }}{8}{figure.caption.4}\protected@file@percent }
\newlabel{fig:base}{{3}{8}{Network consisting of 2636 pores and 4291 throats, inscribed within a cube extending $1.07\cdot 10^{-3}$m in each spatial direction. The pore-arrangement is obviously \emph {not uniform}, as can be seen by the clustering of pores in some regions, while others are mostly undisturbed. The \emph {porosity}, measured as the relative fraction of volume taken up by the void-space geometry, is roughly $32\%$.\relax }{figure.caption.4}{}}
thesis/thesis.log
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thesis/thesis.out
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...@@ -7,5 +7,6 @@ ...@@ -7,5 +7,6 @@
\BOOKMARK [1][-]{section.3}{Parallel Network Generation}{}% 7 \BOOKMARK [1][-]{section.3}{Parallel Network Generation}{}% 7
\BOOKMARK [2][-]{subsection.3.1}{Cell Lists}{section.3}% 8 \BOOKMARK [2][-]{subsection.3.1}{Cell Lists}{section.3}% 8
\BOOKMARK [2][-]{subsection.3.2}{Iterative Algorithm}{section.3}% 9 \BOOKMARK [2][-]{subsection.3.2}{Iterative Algorithm}{section.3}% 9
\BOOKMARK [1][-]{appendix.A}{PETSc Installation}{}% 10 \BOOKMARK [2][-]{subsection.3.3}{Results}{section.3}% 10
\BOOKMARK [1][-]{appendix.B}{Base Network}{}% 11 \BOOKMARK [1][-]{appendix.A}{PETSc Installation}{}% 11
\BOOKMARK [1][-]{appendix.B}{Base Network}{}% 12
thesis/thesis.pdf
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thesis/thesis.synctex.gz
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thesis/thesis.tex
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...@@ -111,108 +111,99 @@ ...@@ -111,108 +111,99 @@
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\end{tikzpicture} \end{tikzpicture}
\caption{Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.} \caption{Cell lists visualized in 2D. The neighborhood of the pore highlighted in red is marked in blue. Because the cell-size is the maximally permissible throat length $L_m$, only the pores contained within the blue region must be considered during neighbor search. Finally, the periodic buffer layers, containing copies of pores on the opposite side from the interior, are painted in orange.}
\label{fig:cell} \label{fig:cell}
...@@ -224,7 +215,9 @@ ...@@ -224,7 +215,9 @@
\begin{equation} \begin{equation}
j^* = \argmin_{j \in \mathcal{N}(i)}\Bigr| ||\mathbf{p}_i - \mathbf{p}_j||_2 - L_t \Bigr| j^* = \argmin_{j \in \mathcal{N}(i)}\Bigr| ||\mathbf{p}_i - \mathbf{p}_j||_2 - L_t \Bigr|
\end{equation} \end{equation}
Where $\mathcal{N}(i)$ is the set of all pores in adjacent cells to pore $i$. Finding $j^*$ for different pores is \emph{embarrassingly parallel} and can therefore be computed by a large number of threads, storing their results in shared memory. Each thread works on an even chunk of the pores located \emph{inside} the domain. Subsequently, these ideal matches are connected, while avoiding \textbf{conflicts} of pores seeking a neighbor that is already fully-connected. Finally we repeat the two steps from above, now only considering pores that still have throats left in \emph{random} order (for improved \textbf{load balancing}), until only a specified \textbf{fraction of total feasible throats} are left e.g. $1\%$. Empirically, this process converges very fast and consistently, for different target sizes of the full domain, after merely 3-4 iterations. The first iteration alone leaves only $\approx 18\%$ of all possible throats left, see Table ~\ref{table:iter}. The procedure is summarized as pseudo-code in Algorithm ~\ref{alg:connect}. Where $\mathcal{N}(i)$ is the set of all pores in adjacent cells to pore $i$. Finding $j^*$ for different pores is \emph{embarrassingly parallel} and can therefore be computed by a large number of threads, storing their results in shared memory. Each thread works on an even chunk of the pores located \emph{inside} the domain. Subsequently, these ideal matches are connected, while avoiding \textbf{conflicts} of pores seeking either a neighbor that is already fully-connected or that was previously connected to them. Finally we repeat the two steps from above, now only considering pores that still have throats left in \emph{random} order (for improved \textbf{load balancing}), until \textbf{no more connections} can be found. Empirically, this process converges very fast and consistently, for different target sizes of the full domain, after merely 7-8 iterations. The first iteration alone leaves only $\approx 18\%$ of all possible throats left, see Table ~\ref{table:iter}. Final iterations may be performed serially if only few pores remain as to avoid costly spawning of threads without speed gain. The procedure is summarized as pseudo-code in Algorithm ~\ref{alg:connect}.
\subsection{Results}
\hspace{0.5cm}The parallel algorithm achieves
\end{multicols} \end{multicols}
\begin{algorithm}[ht] \begin{algorithm}[ht]
...@@ -233,9 +226,8 @@ ...@@ -233,9 +226,8 @@
\State Initialize $cellList$ using $pores$ and compute $totalThroats$ \State Initialize $cellList$ using $pores$ and compute $totalThroats$
\State $poresRemain \gets pores$ \State $poresRemain \gets pores$
\State $throatsLeft \gets totalThroats$ \State $throatsLeft \gets totalThroats$
\State $iterCount \gets 0$ \State $throatsUnrealized \gets totalThroats$
\State $throatThreshold \gets \lfloor 0.01 * totalThroats\rfloor$ \Comment{at most 1\% of $totalThroats$} \While{$throatsUnrealized > 0$}
\While{$iterCount < maxIters$ \textbf{and} $throatsLeft > throatThreshold$}
\State Spawn $nthreads$ threads \State Spawn $nthreads$ threads
\State Compute best matches for all pores in $poresRemain$ using threads \State Compute best matches for all pores in $poresRemain$ using threads
\State Store result in shared memory location $poreMatchTable$ \State Store result in shared memory location $poreMatchTable$
...@@ -251,7 +243,6 @@ ...@@ -251,7 +243,6 @@
\State $poresRemain \gets nextPores$ \State $poresRemain \gets nextPores$
\State Count throats that are still left: $nextThroats$ \State Count throats that are still left: $nextThroats$
\State $throatsLeft \gets nextThroats$ \State $throatsLeft \gets nextThroats$
\State $iterCount \gets iterCount + 1$
\EndWhile \EndWhile
\end{algorithmic} \end{algorithmic}
\label{alg:connect} \label{alg:connect}
...@@ -259,16 +250,19 @@ ...@@ -259,16 +250,19 @@
\begin{table}[ht] \begin{table}[ht]
\centering \centering
\caption{Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 1015 were not realized due to falling below the threshold of 1\%.} \caption{Sample run of parallel pore-connecting algorithm using 4 threads. The generated network is 3 times as large as the base network in all directions. The maximal feasible number of throats is 103464, of which 27 were not realized due to there being no possible candidates left for these remaining pores.}
\begin{tabular}{|c|c|c|} \begin{tabular}{|c|c|c|}
\hline \hline
\textbf{Iteration} & \textbf{Throats left} & \textbf{Rel. percentage} \\ \textbf{Iteration} & \textbf{Throats left} & \textbf{Rel. percentage} \\
\hline \hline
0 & 103464 & 100.00\% \\ 0 & 103464 & 100.0\% \\
1 & 18676 & 18.1\% \\ 1 & 18690 & 18.1\% \\
2 & 5191 & 5.0\% \\ 2 & 4329 & 4.2\% \\
3 & 1996 & 1.9\% \\ 3 & 1096 & 1.1\% \\
4 & 1015 & 0.98\% \\ 4 & 282 & 0.3\% \\
5 & 73 & 0.1\% \\
6 & 30 & 0.03\% \\
7 & 27 & 0.026\% \\
\hline \hline
\end{tabular} \end{tabular}
\label{table:iter} \label{table:iter}
...@@ -295,7 +289,16 @@ ...@@ -295,7 +289,16 @@
\section{Base Network} \section{Base Network}
\label{appendix:base} \label{appendix:base}
Throughout this paper we rely on existing networks obtained via tomographic scans to serve as a basis for \textbf{generation} of larger networks and \textbf{simulation} of network flow. Their statistics are detailed in the figures below. Throughout this thesis we rely on existing networks obtained via tomographic scans to serve as a \emph{basis} for \textbf{generation} of larger networks and \textbf{simulation} of network flow. The statistics of the base network mentioned previously are detailed in Figure ~\ref{fig:base}.
\begin{figure}[ht]
\vspace{-0.5cm}
\centering
\includegraphics[width=0.8\textwidth]{plots/base.png}
\caption{Network consisting of 2636 pores and 4291 throats, inscribed within a cube extending $1.07\cdot 10^{-3}$m in each spatial direction. The pore-arrangement is obviously \emph{not uniform}, as can be seen by the clustering of pores in some regions, while others are mostly undisturbed. The \emph{porosity}, measured as the relative fraction of volume taken up by the void-space geometry, is roughly $32\%$.}
\label{fig:base}
\end{figure}
\newpage \newpage
\centering \centering
......
visualize/print_pores.py
View file @ 39ec32db
...@@ -14,7 +14,7 @@ def print_point(x, y): ...@@ -14,7 +14,7 @@ def print_point(x, y):
if __name__ == '__main__': if __name__ == '__main__':
nInterior = 10 nInterior = 10
nRest = 40 nRest = 34
interiorX = np.random.uniform(-2, 1, (nInterior, 1)) interiorX = np.random.uniform(-2, 1, (nInterior, 1))
interiorY = np.random.uniform(-1, 2, (nInterior, 1)) interiorY = np.random.uniform(-1, 2, (nInterior, 1))
...@@ -41,5 +41,13 @@ if __name__ == '__main__': ...@@ -41,5 +41,13 @@ if __name__ == '__main__':
# Up/down side # Up/down side
if (y <= -1.): if (y <= -1.):
print_point(x, y + 4.) print_point(x, y + 4.)
if (x <= -1.):
print_point(x + 4., y + 4.)
elif (x >= 1.):
print_point(x - 4., y + 4.)
elif (y >= 1.): elif (y >= 1.):
print_point(x, y - 4.) print_point(x, y - 4.)
if (x <= -1.):
print_point(x + 4., y - 4.)
elif (x >= 1.):
print_point(x - 4., y - 4.)
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