Author Archives: Mohsen Koohi Esfahani

Random Vertex Relabelling in LaganLighter

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To evaluate the impacts of locality-optimizing reordering algorithms, a baseline is required. To create the baseline a random assignment of IDs to vertices may be used to produce a representation of the graph with reduced locality [ DOI:10.1109/ISPASS57527.2023.00029, DOI:10.1109/IISWC53511.2021.00020 ].

To that end, we create the random_ordering() function in relabel.c file. It consists a number of iterations. In each iteration, concurrent threads traverse the list of vertices and assign them new IDs. The function uses xoshiro to produce random numbers.

The alg4_randomize tests this function for a number of graphs. For each dataset, an initial plot of degree distribution of Neighbor to Neighbor Average ID Distance (N2N AID) [DOI:10.1109/IISWC53511.2021.00020] is created. Also, after each iteration of random_ordering() the N2N AID distribution is plotted. This shows the impacts of randomization.

The complete results for all graphs can be seen in this PDF file. The results for some graphs are in the following.

The algorithm has been executed on a machine with two AMD 7401 CPUs, 128 cores, 128 threads. The report created by the launcher is in the following.

Technical Posts


LaganLighter

Minimum Spanning Forest of MS-BioGraphs

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We use MASTIFF to compute the weight of Minimum Spanning Forest (MST) of MS-BioGraphs while ignoring self-edges of the graphs.

– MS1

Using machine with 24 cores.

MSF weight: 109,915,787,546

– MS50

Using machine with 128 cores.

MSF weight: 416,318,200,808

MS-BioGraphs
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Technical Posts


LaganLighter

Topology-Based Thread Affinity Setting (Thread Pinning) in OpenMP

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In applications such as graph processing, it is important how threads are pinned on CPU cores as the threads that share resources (such as memory and cache) can accelerate the performance by processing consecutive blocks of input dataset, especially, when the dataset has a high-level of locality.

In LaganLighter, we read the CPU topology to specify how OpenMP threads are pinned. In omp.c file, the block starting with comment “Reading sibling groups of each node“, reads the “/sys/devices/system/cpu/cpu*/topology/thread_siblings” files to identify the sibling threads and three arrays ("node_sibling_groups_start_ID“, “sibling_group_cpus_start_offsets“, and “sibling_groups_cpus“) are used to store the sibling CPUs.

Then, in block starting with comment “Setting affinity of threads“, the sibling groups are read and based on the total number of threads requested by user, a number of threads with consecutive IDs are pinned to sibling CPUs.

For a machine with 24 cores, 48 hyperthreads, when 48 threads are requested, we have:

If 96 threads are created, we have:

Technical Posts


LaganLighter

An (Incomplete) List of Publicly Available Graph Datasets/Generators

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Short URL of this post: https://blogs.qub.ac.uk/DIPSA/graphs-list-2024

Real-World Graphs

Smaller Graphs

Synthetic Graph Generators

Technical Posts

QClique: Optimizing Performance and Accuracy in Maximum Weighted Clique – Euro-Par 2024

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30th International European Conference on Parallel and Distributed Computing (Euro-Par 2024)

DOI: 10.1007/978-3-031-69583-4_7
PDF Version

Abstract

The Maximum Weighted Clique(MWC) problem remains challenging due to its unfavourable time complexity.In this paper, we analyze the execution of exact search-based MWC algorithms and show that high-accuracy weighted cliques can be discovered in the early stages of the execution if searching the combinatorial space is performed systematically.

Based on this observation, we introduce QClique as an approximate MWC algorithm that processes the search space as long as better cliques are expected. QClique uses a tunable parameter to trade-off between accuracy vs. execution time and delivers 4.7-$82.3 time speedup in comparison to previous state-of-the-art MWC algorithms while providing 91.4% accuracy and achieves a parallel speedup of up to 56x on 128 threads.

Additionally, QClique accelerates the exact MWC computation by replacing the initial clique of the exact algorithm. For WLMC, an exact state-of-the-art MWC algorithm, this results in 3.3x on average.

Code

https://github.com/DIPSA-QUB/QClique

Selective Parallel Loading of Large-Scale Compressed Graphs with ParaGrapher – arXiv Version

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PDF version
DOI: 10.48550/arXiv.2404.19735

Comprehensive evaluation is one of the basis of experimental science. In High-Performance Graph Processing, a thorough evaluation of contributions becomes more achievable by supporting common input formats over different frameworks. However, each framework creates its specific format, which may not support reading large-scale real-world graph datasets. This shows a demand for high-performance libraries capable of loading graphs to (i) accelerate designing new graph algorithms, (ii) to evaluate the contributions on a wide range of graph algorithms, and (iii) to facilitate easy and fast comparison over different graph frameworks.

To that end, we present ParaGrapher, a high-performance API and library for loading large-scale and compressed graphs. ParaGrapher supports different types of requests for accessing graphs in shared- and distributed-memory and out-of-core graph processing. We explain the design of ParaGrapher and present a performance model of graph decompression, which is used for evaluation of ParaGrapher over three storage types.

Our evaluation shows that by decompressing compressed graphs in WebGraph format, ParaGrapher delivers up to 3.2 times speedup in loading and up to 5.2 times speedup in end-to-end execution in comparison to the binary and textual formats.

ParaGrapher is available online on https://blogs.qub.ac.uk/DIPSA/ParaGrapher/.

BibTex

@misc{paragrapher-arxiv,
  title = { Selective Parallel Loading of Large-Scale 
            Compressed Graphs with ParaGrapher}, 
  author = { {Mohsen} {Koohi Esfahani} and Marco D'Antonio and 
             Syed Ibtisam Tauhidi and Thai Son Mai and 
             Hans Vandierendonck},
  year = {2024},
  eprint = {2404.19735},
  archivePrefix = {arXiv},
  primaryClass = {cs.AR},
  doi = {10.48550/arXiv.2404.19735}
}

Related Posts & Source Code

ParaGrapher Web Page

An Evaluation of Bandwidth of Different Storage Types (HDD vs. SSD vs. LustreFS) for Different Block Sizes and Different Parallel Read Methods (mmap vs pread vs read)

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Short URL of this post: https://blogs.qub.ac.uk/DIPSA/HDD-vs-SSD-vs-LustreFS-2024

We evaluate read bandwidth of three storage types:

  • HDD: A 6TB Hitachi HUS726060AL 7200RPM SATA v3.1
  • SSD: A 4TB Samsung MZQL23T8HCLS-00A07 PCIe4 NVMe v1.4
  • LustreFS: A parallel file system with total 2PB with a SSD pool

and for three parallel read methods:

and for two block sizes:

  • 4 KB blocks
  • 4 MB blocks

The source code is available on ParaGrapher repository:

The OS cache of storage contents have been dropped after each evaluation
(sudo sh -c 'echo 3 >/proc/sys/vm/drop_caches').
The flushcache.c file (https://github.com/DIPSA-QUB/ParaGrapher/blob/main/test/flushcache.c) can be used with the same functionality for users without sudo access, however, it usually takes more time to be finished.

For LustreFS, we have repeated the evaluation of read and pread using O_DIRECT flag as this flag prevents client-side caching.

For HDD and SSD experiments, we have used a machine with Intel W-2295 3.00GHz CPU, 18 cores, 36 hyper-threads, 24MB L3 cache, 256 GB DDR4 2933Mhz memory, running Debian 12 Linux 6.1. For LustreFS, we have used a machine with 2TB 3.2GHz DDR4 memory, 2 AMD 7702 CPUs, in total, 128 cores, 256 threads.

The results of the evaluation using read_bandwidth.c are in the following table. The values are Bandwidth in MB/s. Also, 1-2 digits close to each number with a white background are are percentage of load imbalance between parallel threads.

Please click on the image to expand.

C vs. Java

We measure the bandwidth of SSD and HDD in C (mmap and pread) vs. Java (mmap and read). We use a machine with Intel W-2295 3.00GHz CPU, 18 cores, 36 hyper-threads, 24MB L3 cache, 256 GB DDR4 2933Mhz memory, running Debian 12 Linux 6.1 and the following codes:

The results are in the following.


For similar comparisons you may refer to:
– https://github.com/david-slatinek/c-read-vs.-mmap/tree/main
– https://eklausmeier.goip.de/blog/2016/02-03-performance-comparison-mmap-versus-read-versus-fread/

Technical Posts


ParaGrapher

MS-BioGraphs on IEEE DataPort

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MS-BioGraph sequence similarity graph datasets are now publicly available on IEEE DataPort: https://doi.org/10.21227/gmd9-1534.

To access the files, you need to register/login to IEEE DataPort and then visit the MS-BioGraphs page. By saving the page as an HTML file such as dp.html, you may download the datasets (as an example MS1) using the following script:

dsname="MS1"
html_file="dp.html"

urls=`cat $html_file  | sed  -e 's/\&/\&/g'  | grep -Eo "(http|https)://[a-zA-Z0-9./?&=_%:-]*" | grep amazonaws  | sort | uniq | grep -E "$dsname[-_\.]"`

for u in $urls; do
    wget $u
    if [ $? != 0 ]; then break; fi
done

# removing query strings
for f in $(find $1 -type f); do
    if [ $f = ${f%%\?*} ]; then continue; fi
    mv "${f}" "${f%%\?*}"
done

# liking offsets.bin to be found by ParaGrapher
ln -s ${dsname}_offsets.bin ${dsname}-underlying_offsets.bin

Instead of wget you may use axel -n 10 to use multiple connections (here, 10) for downloading each file (https://manpages.ubuntu.com/manpages/noble/en/man1/axel.1.html).

MS-BioGraphs

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ParaGrapher Integrated to LaganLighter

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Poplar source code has been integrated to LaganLighter and access to different WebGraph formats are available in LaganLighter:

  • PARAGRAPHER_CSX_WG_400_AP
  • PARAGRAPHER_CSX_WG_404_AP
  • PARAGRAPHER_CSX_WG_800_AP

For further details, please refer to
– LaganLighter source coder Repository: https://github.com/DIPSA-QUB/LaganLighter, particularly, the graph.c file.
– ParaGrapher source code repository: https://github.com/DIPSA-QUB/ParaGrapher particularly, the src/webgraph.c and src/WG*.java files.

Read more about ParaGrapher and LaganLighter.

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ParaGrapher Source Code For WebGraph Types

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ParaGrapher source code for accessing WebGraphs have been published. The supported graph types are:

ParaGrapher uses its asynchronous and parallel API to implement these graph types. The user needs to implement a callback function that is called by the API upon completion of reading a block of edges. Poplar uses a shared memory for interaction between its C library and the Java library that deploys the WebGraph framework.

For further details, please refer to Poplar source code repository: https://github.com/DIPSA-QUB/ParaGrapher, particularly, src/webgraph.c and src/WG*.java files.

ParaGrapher

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