Storage Format Selection and Optimization for Materialized Intermediate Results in Data-Intensive Flows

Modern organizations produce and collect large volumes of data, that need to be processed repeatedly and quickly for gaining business insights. For such processing, typically, Data-intensive Flows (DIFs) are deployed on distributed processing frameworks. The DIFs of different users have many computation overlaps (i.e., parts of the processing are duplicated), thus wasting computational resources and increasing the overall cost. The output of these computation overlaps (known as intermediate results) can be materialized for reuse, which helps in reducing the cost and saves computational resources if properly done. Furthermore, the way such outputs are materialized must be considered, as different storage layouts (i.e., horizontal, vertical, and hybrid) can be used to reduce the I/O cost. In this PhD work, we first propose a novel approach for automatically materializing the intermediate results of DIFs through a multi-objective optimization method, which can tackle multiple and conflicting quality metrics. Next, we study the behavior of different operators of DIFs that are the first to process the loaded materialized results. Based on this study, we devise a rule-based approach, that decides the storage layout for materialized results based on the subsequent operation types. Despite improving the cost in general, the heuristic rules do not consider the amount of data read while making the choice, which could lead to a wrong decision. Thus, we design a cost model that is capable of finding the right storage layout for every scenario. The cost model uses data and workload characteristics to estimate the I/O cost of a materialized intermediate results with different storage layouts and chooses the one which has minimum cost. The results show that storage layouts help to reduce the loading time of materialized results and overall, they improve the performance of DIFs. The thesis also focuses on the optimization of the configurable parameters of hybrid layouts. We propose ATUN-HL (Auto TUNing Hybrid Layouts), which based on the same cost model and given the workload and characteristics of data, finds the optimal values for configurable parameters in hybrid layouts (i.e., Parquet). Finally, the thesis also studies the impact of parallelism in DIFs and hybrid layouts. Our proposed cost model helps to devise an approach for fine-tuning the parallelism by deciding the number of tasks and machines to process the data. Thus, the cost model proposed in this thesis, enables in choosing the best possible storage layout for materialized intermediate results, tuning the configurable parameters of hybrid layouts, and estimating the number of tasks and machines for the execution of DIFs.Moderne Unternehmen produzieren und sammeln große Datenmengen, die wiederholt und schnell verarbeitet werden müssen, um geschäftliche Erkenntnisse zu gewinnen. Für die Verarbeitung dieser Daten werden typischerweise Datenintensive Prozesse (DIFs) auf verteilten Systemen wie z.B. MapReduce bereitgestellt. Dabei ist festzustellen, dass die DIFs verschiedener Nutzer sich in großen Teilen überschneiden, wodurch viel Arbeit mehrfach geleistet, Ressourcen verschwendet und damit die Gesamtkosten erhöht werden. Um diesen Effekt entgegenzuwirken, können die Zwischenergebnisse der DIFs für spätere Wiederverwendungen materialisiert werden. Hierbei müssen vor allem die unterschiedlichen Speicherlayouts (horizontal, vertikal und hybrid) berücksichtigt werden. In dieser Doktorarbeit wird ein neuartiger Ansatz zur automatischen Materialisierung der Zwischenergebnisse von DIFs durch eine mehrkriterielle Optimierungsmethode vorgeschlagen, der in der Lage ist widersprüchliche Qualitätsmetriken zu behandeln. Des Weiteren wird untersucht die Wechselwirkung zwischen verschiedenen peratortypen und unterschiedlichen Speicherlayouts untersucht. Basierend auf dieser Untersuchung wird ein regelbasierter Ansatz vorgeschlagen, der das Speicherlayout für materialisierte Ergebnisse, basierend auf den nachfolgenden Operationstypen, festlegt. Obwohl sich die Gesamtkosten für die Ausführung der DIFs im Allgemeinen verbessern, ist der heuristische Ansatz nicht in der Lage die gelesene Datenmenge bei der Auswahl des Speicherlayouts zu berücksichtigen. Dies kann in einigen Fällen zu falschen Entscheidung führen. Aus diesem Grund wird ein Kostenmodell entwickelt, mit dem für jedes Szenario das richtige Speicherlayout gefunden werden kann. Das Kostenmodell schätzt anhand von Daten und Auslastungsmerkmalen die E/A-Kosten eines materialisierten Zwischenergebnisses mit unterschiedlichen Speicherlayouts und wählt das kostenminimale aus. Die Ergebnisse zeigen, dass Speicherlayouts die Ladezeit materialisierter Ergebnisse verkürzen und insgesamt die Leistung von DIFs verbessern. Die Arbeit befasst sich auch mit der Optimierung der konfigurierbaren Parameter von hybriden Layouts. Konkret wird der sogenannte ATUN-HL Ansatz (Auto TUNing Hybrid Layouts) entwickelt, der auf der Grundlage des gleichen Kostenmodells und unter Berücksichtigung der Auslastung und der Merkmale der Daten die optimalen Werte für konfigurierbare Parameter in Parquet, d.h. eine Implementierung von hybrider Layouts. Schließlich werden in dieser Arbeit auch die Auswirkungen von Parallelität in DIFs und hybriden Layouts untersucht. Dazu wird ein Ansatz entwickelt, der in der Lage ist die Anzahl der Aufgaben und dafür notwendigen Maschinen automatisch zu bestimmen. Zusammengefasst lässt sich festhalten, dass das in dieser Arbeit vorgeschlagene Kostenmodell es ermöglicht, das bestmögliche Speicherlayout für materialisierte Zwischenergebnisse zu ermitteln, die konfigurierbaren Parameter hybrider Layouts festzulegen und die Anzahl der Aufgaben und Maschinen für die Ausführung von DIFs zu schätzen

Storage format selection and optimization for materialized intermediate results in data-intensive flows

Tesi en modalitat de cotuela: Universitat Politècnica de Catalunya i Technische Universität DresdenModern organizations produce and collect large volumes of data, that need to be processed repeatedly and quickly for gaining business insights. For such processing, typically, Data-intensive Flows (DIFs) are deployed on distributed processing frameworks. The DIFs of different users have many computation overlaps (i.e., parts of the processing are duplicated), thus wasting computational resources and increasing the overall cost. The output of these computation overlaps (known as intermediate results) can be materialized for reuse, which helps in reducing the cost and saves computational resources if properly done. Furthermore, the way such outputs are materialized must be considered, as different storage layouts (i.e., horizontal, vertical, and hybrid) can be used to reduce the I/O cost. In this PhD work, we first propose a novel approach for automatically materializing the intermediate results of DIFs through a multi-objective optimization method, which can tackle multiple and conflicting quality metrics. Next, we study the behavior of different operators of DIFs that are the first to process the loaded materialized results. Based on this study, we devise a rule-based approach, that decides the storage layout for materialized results based on the subsequent operation types. Despite improving the cost in general, the heuristic rules do not consider the amount of data read while making the choice, which could lead to a wrong decision. Thus, we design a cost model that is capable of finding the right storage layout for every scenario. The cost model uses data and workload characteristics to estimate the I/O cost of a materialized intermediate results with different storage layouts and chooses the one which has minimum cost. The results show that storage layouts help to reduce the loading time of materialized results and overall, they improve the performance of DIFs. The thesis also focuses on the optimization of the configurable parameters of hybrid layouts. We propose ATUN-HL (Auto TUNing Hybrid Layouts), which based on the same cost model and given the workload and characteristics of data, finds the optimal values for configurable parameters in hybrid layouts (i.e., Parquet). Finally, the thesis also studies the impact of parallelism in DIFs and hybrid layouts. Our proposed cost model helps to devise an approach for fine-tuning the parallelism by deciding the number of tasks and machines to process the data. Thus, the cost model proposed in this thesis, enables in choosing the best possible storage layout for materialized intermediate results, tuning the configurable parameters of hybrid layouts, and estimating the number of tasks and machines for the execution of DIFs.Las organizaciones producen y recopilan grandes volúmenes de datos, que deben procesarse de forma repetitiva y rápida para obtener información relevante para la empresa. Para tal procesamiento, por lo general, se emplean flujos intensivos de datos (DIFs por sussiglas en inglés) en entornos de procesamiento distribuido. Los DIFs de diferentes usuarios tienen elementos comunes (es decir, se duplican partes del procesamiento, lo que desperdicia recursos computacionales y aumenta el coste en general). Los resultados intermedios de varios DIFs pueden pues coincidir y se pueden por tanto materializar para facilitar su reutilización, lo que ayuda a reducir el coste y ahorrar recursos si se realiza correctamente. Además, la forma en qué se materializan dichos resultados debe ser considerada. Por ejemplo, diferentes tipos de diseño lógico de los datos (es decir, horizontal, vertical o híbrido) se pueden utilizar para reducir el coste de E/S. En esta tesis doctoral, primero proponemos un enfoque novedoso para materializar automáticamente los resultados intermedios de los DIFs a través de un método de optimización multi-objetivo, que puede considerar múltiples y contradictorias métricas de calidad. A continuación, estudiamos el comportamiento de diferentes operadores de DIF que acceden directamente a los resultados materializados. Sobre la base de este estudio, ideamos un enfoque basado en reglas, que decide el diseño del almacenamiento para los resultados materializados en función de los tipos de operaciones que los utilizan directamente. A pesar de mejorar el coste en general, las reglas heurísticas no consideran estadísticas sobre la cantidad de datos leídos al hacer la elección, lo que podría llevar a una decisión errónea. Consecuentemente, diseñamos un modelo de costos que es capaz de encontrar el diseño de almacenamiento adecuado para cada escenario dependiendo de las características de los datos almacenados. El modelo de costes usa estadísticas y características de acceso para estimar el coste de E/S de un resultado intervii medio materializado con diferentes diseños de almacenamiento y elige el de menor coste. Los resultados muestran que los diseños de almacenamiento ayudan a reducir el tiempo de carga de los resultados materializados y, en general, mejoran el rendimiento de los DIF. La tesis también presta atención a la optimización de los parámetros configurables de diseños híbridos. Proponemos así ATUN-HL (Auto TUNing Hybrid Layouts), que, basado en el mismo modelo de costes, las características de los datos y el tipo de acceso que se está haciendo, encuentra los valores óptimos para los parámetros de configuración en disponibles Parquet (una implementación de diseños híbridos para Hadoop Distributed File System). Finalmente, esta tesis estudia el impacto del paralelismo en DIF y diseños híbridos. El modelo de coste propuesto ayuda a idear un enfoque para ajustar el paralelismo al decidir la cantidad de tareas y máquinas para procesar los datos. En resumen, el modelo de costes propuesto permite elegir el mejor diseño de almacenamiento posible para los resultados intermedios materializados, ajustar los parámetros configurables de diseños híbridos y estimar el número de tareas y máquinas para la ejecución de DIF.Moderne Unternehmen produzieren und sammeln große Datenmengen, die wiederholt und schnell verarbeitet werden müssen, um geschäftliche Erkenntnisse zu gewinnen. Für die Verarbeitung dieser Daten werden typischerweise Datenintensive Prozesse (DIFs) auf verteilten Systemen wie z.B. MapReduce bereitgestellt. Dabei ist festzustellen, dass die DIFs verschiedener Nutzer sich in großen Teilen überschneiden, wodurch viel Arbeit mehrfach geleistet, Ressourcen verschwendet und damit die Gesamtkosten erhöht werden. Um diesen Effekt entgegenzuwirken, können die Zwischenergebnisse der DIFs für spätere Wiederverwendungen materialisiert werden. Hierbei müssen vor allem die unterschiedlichen Speicherlayouts (horizontal, vertikal und hybrid) berücksichtigt werden. In dieser Doktorarbeit wird ein neuartiger Ansatz zur automatischen Materialisierung der Zwischenergebnisse von DIFs durch eine mehrkriterielle Optimierungsmethode vorgeschlagen, der in der Lage ist widersprüchliche Qualitätsmetriken zu behandeln. Des Weiteren wird untersucht die Wechselwirkung zwischen verschiedenen Operatortypen und unterschiedlichen Speicherlayouts untersucht. Basierend auf dieser Untersuchung wird ein regelbasierter Ansatz vorgeschlagen, der das Speicherlayout für materialisierte Ergebnisse, basierend auf den nachfolgenden Operationstypen, festlegt. Obwohl sich die Gesamtkosten für die Ausführung der DIFs im Allgemeinen verbessern, ist der heuristische Ansatz nicht in der Lage die gelesene Datenmenge bei der Auswahl des Speicherlayouts zu berücksichtigen. Dies kann in einigen Fällen zu falschen Entscheidung führen. Aus diesem Grund wird ein Kostenmodell entwickelt, mit dem für jedes Szenario das richtige Speicherlayout gefunden werden kann. Das Kostenmodell schätzt anhand von Daten und Auslastungsmerkmalen die E/A-Kosten eines materialisierten Zwischenergebnisses mit unterschiedlichen Speicherlayouts und wählt das kostenminimale aus. Die Ergebnisse zeigen, dass Speicherlayouts die Ladezeit materialisierter Ergebnisse verkürzen und insgesamt die Leistung von DIFs verbessern. Die Arbeit befasst sich auch mit der Optimierung der konfigurierbaren Parameter von hybriden Layouts. Konkret wird der sogenannte ATUN-HLAnsatz (Auto TUNing Hybrid Layouts) entwickelt, der auf der Grundlage des gleichen Kostenmodells und unter Berücksichtigung der Auslastung und der Merkmale der Daten die optimalen Werte für konfigurierbare Parameter in Parquet, d.h. eine Implementierung von hybrider Layouts. Schließlich werden in dieser Arbeit auch die Auswirkungen von Parallelität in DIFs und hybriden Layouts untersucht. Dazu wird ein Ansatz entwickelt, der in der Lage ist die Anzahl der Aufgaben und dafür notwendigen Maschinen automatisch zu bestimmen. Zusammengefasst lässt sich festhalten, dass das in dieser Arbeit vorgeschlagene Kostenmodell es ermöglicht, das bestmögliche Speicherlayout für materialisierte Zwischenergebnisse zu ermitteln, die konfigurierbaren Parameter hybrider Layouts festzulegen und die Anzahl der Aufgaben und Maschinen für die Ausführung von DIFs zu schätzenPostprint (published version

Characterisation and purification of an aggrecanase made by injured synovium

Freshly dissected porcine synovial tissue in culture produces an enzymatic activity that cleaves cartilage aggrecan generating ARGS- and AGEG- bearing neo-epitope fragments. The aggrecanolytic activity was abolished when synovial tissue was cultured in the presence of cycloheximide. The enzyme(s) were sensitive to N-terminal inhibitory domain of tissue inhibitor of matrix metalloproteinase (N-TIMP-3) and general matrix metalloproteinase inhibitor (GM6001) suggesting they may belong to a disintegrin and metalloproteinase (ADAM) or ADAM with thrombospondin motifs (ADAMTS) family of enzymes. Cation exchange chromatography was used to partially purify aggrecanase(s) from synovial tissue culture medium (SYCM). Two active species have been separated from the partially purified material using size-exclusion chromatography. The smaller species had a molecular weight of 35-40 kDa while the larger enzyme had an apparent molecular weight greater than 2000 kDa. Low density lipoprotein receptor-related protein (LRP1) didn’t appear to be involved in the formation of higher molecular weight complex. The smaller species was further chromatographed on a SMART mono Q column. The sequential chromatography gave approximately 400-fold enrichment of the enzyme. The concentration of the enzyme was estimated by titration with recombinant N-TIMP-3, which was expressed and purified from E.coli. The N-TIMP-3 was electrostatically coupled to Ni2+ agarose beads. The beads were then used to affinity purify the enzyme from mono Q fractions. The affinity-purified material was electrophoresed and protein bands were selected for mass spectrometry. No ADAMTS enzyme was identified in the candidate bands. Further improvements will be made to the purification procedure to identify the synovial aggrecanase.Open Acces

Automatically configuring parallelism for hybrid layouts

Distributed processing frameworks process data in parallel by dividing it into multiple partitions and each partition is processed in a separate task. The number of tasks is always created based on the total file size. However, this can lead to launch more tasks than needed in the case of hybrid layouts, because they help to read less data for certain operations (i.e., projection, selection). The over-provisioning of tasks may increase the job execution time and induce significant waste of computing resources. The latter due to the fact that each task introduces extra overhead (e.g., initialization, garbage collection, etc.). To allow a more efficient use of resources and reduce the job execution time, we propose a cost-based approach that decides the number of tasks based on the data being read. The proposed cost-model can be utilized in a multi-objective approach to decide both the number of tasks and number of machines for execution.Peer ReviewedPostprint (author's final draft

Experimental Investigation and Statistical Modeling of FRP Confined RuC Using Response Surface Methodology

Scrap tires that are dumped to landfill is a serious problem in China and rest of the world. The use of rubber in concrete is an effective environmental approach to reduce the amount of scrap tires around the world. However, the loss in compressive strength of concrete is a major drawback of rubberized concrete. In this paper, the fiber reinforced polymer (FRP) confinement technique is used to overcome the drawbacks of rubberized concrete (RuC). A total of sixty six RuC cylinders were tested in axial compression. The cylinders were cast using recycled rubber to replace, a) 0-50 percent fine aggregate volume, b) 0-50 percent coarse aggregate volume, and c) 40-50 percent fine and coarse aggregate volume. Twenty seven cylinders of the latter mix were then confined with one, two and three layers of CFRP jackets. Concrete suffered a substantial reduction in compressive strength up to 80 percent by fine and coarse aggregate replacement with rubber content. However, CFRP jackets recovered and further enhanced the axial compressive strength of RuC up to 600% over unconfined RuC. SEM was performed to investigate the microstructural properties of RuC. Statistical models were developed on the basis of experimental tests for FRP confined RuC cylinders using response surface method. The effect of variable factors; unconfined concrete strength, rubber replacement type and number of FRP layers on confined compressive concrete strength was investigated. The regression analysis was performed to develop the response equations based on quadratic models. The predicted and experimental test results were found in good agreement as the variation between experimental and predicted values were less than 5%. Furthermore, the difference between predicted and adjusted R2 was found to be less than 0.2 which shows the significance of the statistical models. These proposed statistical models can provide a better understanding to design the experiments and the parameters affecting FRP-confined RuC cylinders

Pattern and Practice of Paediatric Neurosurgical Procedures- An analysis of one year initial experience at resource challenged setup of Children Hospital, Faisalabad.

patients presenting to Children Hospital, Faisalabad. Materials and Methods:  Retrospective case series of 778 consecutive cases admitted in Pediatric Neurosurgery Department, Children Hospital, Faisalabad over one year (October 2019- September 2020). Patients of age less than 15 years, any gender, admitted in Pediatric Neurosurgery ward for management were included and studied for their demographic data hospital stay, a procedure done and outcome. Results:  A total of 778 patients who required some neurosurgical intervention were admitted, 725 underwent various types of procedures and the remaining were treated conservatively. 320 (44.14%) were male and405 (55.86%) were female. The age range was 20 days to 13 years. The most common diagnosis was hydrocephalous, and then was Meningomyelocele (MMC). The first three common procedures performed included monitoring of Cerebrospinal fluid (CSF) in 36% of cases, Placement of shunt (21%), and placement of external ventricular drain (EVD) in 13% of cases of cerebrospinal fluid (CNS) infections in patients of hydrocephalous. Conclusion:  Pattern of presentation of pediatric neurosurgical cases take in almost all types of diseases like neural tube defects, hydrocephalous, cranial trauma, tumors, cysts, and infections but surgical procedures in routine practice in Faisalabad district cover mainly hydrocephalous and its complications. Endoscopic or advanced procedures are not commonly practiced due to multiple factors but existing constraints do not prevent the best management of pediatric neurosurgery patients

Resilient store: a heuristic-based data format selector for intermediate results

The final publication is available at link.springer.comLarge-scale data analysis is an important activity in many organizations that typically requires the deployment of data-intensive workflows. As data is processed these workflows generate large intermediate results, which are typically pipelined from one operator to the following. However, if materialized, these results become reusable, hence, subsequent workflows need not recompute them. There are already many solutions that materialize intermediate results but all of them assume a fixed data format. A fixed format, however, may not be the optimal one for every situation. For example, it is well-known that different data fragmentation strategies (e.g., horizontal and vertical) behave better or worse according to the access patterns of the subsequent operations. In this paper, we present ResilientStore, which assists on selecting the most appropriate data format for materializing intermediate results. Given a workflow and a set of materialization points, it uses rule-based heuristics to choose the best storage data format based on subsequent access patterns.We have implemented ResilientStore for HDFS and three different data formats: SequenceFile, Parquet and Avro. Experimental results show that our solution gives 18% better performance than any solution based on a single fixed format.Peer ReviewedPostprint (author's final draft