A GPU performance estimation model based on micro-benchmarks and black-box kernel profiling

Κατά την τελευταία δεκαετία, οι επεξεργαστές γραφικών (GPUs) έχουν εδραιωθεί στον τομέα των υπολογιστικών συστημάτων υψηλής απόδοσης ως επιταχυντές υπολογισμών. Τα βασικά χαρακτηριστικά που δικαιολογούν αυτή τη σύγχρονη τάση είναι η εξαιρετικά υψηλή υπολογιστική απόδοση τους και η αξιοσημείωτη ενεργειακή αποδοτικότητα τους. Ωστόσο, η απόδοση τους είναι πολύ ευαίσθητη σε πολλούς παράγοντες, όπως π.χ. τον τύπο των μοτίβων πρόσβασης στη μνήμη (memory access patterns), την απόκλιση διακλαδώσεων (branch divergence), τον βαθμό παραλληλισμού και τις δυνητικές καθυστερήσεις (latencies). Συνεπώς, ο χρόνος εκτέλεσης ενός πυρήνα (kernel) σε ένα επεξεργαστή γραφικών είναι ένα δύσκολα προβλέψιμο μέγεθος. Στην περίπτωση που η απόδοση του πυρήνα δεν περιορίζεται από καθυστερήσεις, μπορεί να παρασχεθεί μια χονδρική εκτίμηση του χρόνου εκτέλεσης σε ένα συγκεκριμένο επεξεργαστή εφαρμόζοντας το μοντέλο γραμμής-οροφής (roofline), το οποίο χρησιμοποιείται για να αντιστοιχίσει την ένταση υπολογισμών του προγράμματος στην μέγιστη αναμενόμενη απόδοση για ένα συγκεκριμένο επεξεργαστή. Αν και αυτή η προσέγγιση είναι απλή, δεν μπορεί να παρέχει ακριβή αποτελέσματα πρόβλεψης. Σε αυτή τη διατριβή, μετά την επαλήθευση της αρχής του μοντέλου γραμμής-οροφής σε επεξεργαστές γραφικών με τη χρήση ενός μικρο-μετροπρογράμματος, προτείνεται ένα αναλυτικό μοντέλο απόδοσης. Συγκεκριμένα, βελτιώνεται το μοντέλο γραμμής-οροφής ακολουθώντας μια ποσοτική προσέγγιση και παρουσιάζεται μία πλήρως αυτοματοποιημένη μέθοδος πρόβλεψης απόδοσης σε επεξεργαστή γραφικών. Από αυτή την άποψη, το προτεινόμενο μοντέλο χρησιμοποιεί την αξιολόγηση μέσω μικρο-μετροπρογραμμάτων και την καταγραφή μετρικών με μέθοδο «μαύρου κουτιού», καθώς δεν απαιτείται διερεύνηση του πηγαίου/δυαδικού κώδικα. Το προτεινόμενο μοντέλο συνδυάζει τις παραμέτρους του επεξεργαστή γραφικών και του πυρήνα για να χαρακτηρίσει τον παράγοντα περιορισμού της απόδοσης και να προβλέψει το χρόνο εκτέλεσης στο στοχευόμενο υλικό, λαμβάνοντας υπόψη την αποδοτικότητα των ωφελίμων υπολογιστικών εντολών. Επιπλέον, προτείνεται η οπτική αναπαράσταση «διαμοιρασμού-τεταρτημορίου» (“quadrant-split”), η οποία αποδίδει τα χαρακτηριστικά πολλών επεξεργαστών σε σχέση με έναν συγκεκριμένο πυρήνα. Η πειραματική αξιολόγηση συνδυάζει δοκιμαστικές εκτελέσεις σε υπολογισμούς μορίων (κόκκινο/μαύρο SOR, LMSOR), πολλαπλασιασμό πινάκων (SGEMM) και ένα σύνολο 28 πυρήνων της σουίτας μετροπρογραμμάτων Rodinia, όλα εφαρμοσμένα σε έξι επεξεργαστές γραφικών CUDA. Το παρατηρηθέν απόλυτο σφάλμα στις προβλέψεις ήταν 27,66% στη μέση περίπτωση. Διερευνήθηκαν και αιτιολογήθηκαν ιδιαίτερες περιπτώσεις εσφαλμένων προβλέψεων. Επιπλέον, το προαναφερθέν μικρο-μετροπρόγραμμα χρησιμοποιήθηκε ως αντικείμενο για την πρόβλεψη απόδοσης και τα αποτελέσματα ήταν πολύ ακριβή. Προσθέτως, το μοντέλο απόδοσης εξετάστηκε σε σύνθετο περιβάλλον μεταξύ διαφορετικών κατασκευαστών, εφαρμόζοντας τη μέθοδο πρόβλεψης στους ίδιους πηγαίους κώδικες πυρήνων μέσω του περιβάλλοντος προγραμματισμού HIP που υποστηρίζεται από την πλατφόρμα AMD ROCm. Τα σφάλματα πρόβλεψης ήταν συγκρίσιμα αυτών των πειραμάτων του περιβάλλοντος CUDA, παρά τις σημαντικές διαφορές αρχιτεκτονικής που παρατηρούνται μεταξύ των διαφορετικών κατασκευαστών επεξεργαστών γραφικών.Over the last decade GPUs have been established in the High Performance Computing sector as compute accelerators. The primary characteristics that justify this modern trend are the exceptionally high compute throughput and the remarkable power efficiency of GPUs. However, GPU performance is highly sensitive to many factors, e.g. the type of memory access patterns, branch divergence, the degree of parallelism and potential latencies. Consequently, the execution time of a kernel on a GPU is a difficult to predict measure. Unless the kernel is latency bound, a rough estimate of the execution time on a particular GPU could be provided by applying the roofline model, which is used to map the program’s operation intensity to the peak expected performance on a particular processor. Though this approach is straightforward, it cannot not provide accurate prediction results. In this thesis, after validating the roofline principle on GPUs by employing a micro-benchmark, an analytical throughput oriented performance model is proposed. In particular, this improves on the roofline model following a quantitative approach and a completely automated GPU performance prediction technique is presented. In this respect, the proposed model utilizes micro-benchmarking and profiling in a “black-box” fashion as no inspection of source/binary code is required. The proposed model combines GPU and kernel parameters in order to characterize the performance limiting factor and to predict the execution time on target hardware, by taking into account the efficiency of beneficial computational instructions. In addition, the “quadrant-split” visual representation is proposed, which captures the characteristics of multiple processors in relation to a particular kernel. The experimental evaluation combines test executions on stencil computations (red/black SOR, LMSOR), matrix multiplication (SGEMM) and a total of 28 kernels of the Rodinia benchmark suite, all applied on six CUDA GPUs. The observed absolute error in predictions was 27.66% in the average case. Special cases of mispredicted results were investigated and justified. Moreover, the aforementioned micro-benchmark was used as a subject for performance prediction and the exhibited results were very accurate. Furthermore, the performance model was also examined in a cross vendor configuration by applying the prediction method on the same kernel source codes through the HIP programming environment supported on the AMD ROCm platform. Prediction errors were comparable to CUDA experiments despite the significant architectural differences evident between different vendor GPUs

A Note on Gradient/Fractional One-Dimensional Elasticity and Viscoelasticity

An introductory discussion on a (weakly non-local) gradient generalization of some one-dimensional elastic and viscoelastic models, and their fractional extension is provided. Emphasis is placed on the possible implications of micro-and nano-engineering problems, including small-scale structural mechanics and composite materials, as well as collagen biomechanics and nanomaterials

Non-cooperation by popular vote : expectations, foreign intervention, and the vote in the 2015 Greek bailout referendum

When popular referendums fail to ratify new international agreements or succeed in reversing existing ones, it not only affects domestic voters but also creates negative spillovers for the other parties to such agreements. We explore how voters respond to this strategic environment. We use original survey data from a poll fielded just one day before the 2015 Greek bailout referendum - a referendum in which the stakes for other countries were particularly high - to investigate how expectations about the likely foreign response to a noncooperative referendum outcome influence voting behavior and to what extent foreign policymakers can influence those expectations. Our analysis of the Greek referendum shows that such expectations had a powerful effect on voting behavior: voters expecting that a noncooperative referendum outcome would force Greece to leave the eurozone were substantially more likely to vote cooperatively than those believing that it would result in renewed negotiations with the country's creditors. Leveraging the bank closure that took place right before the vote, we also show that costly signals by foreign actors made voters more pessimistic about the consequences of a noncooperative vote and substantially increased the share of cooperative votes

Tuber pulchrosporum sp. nov., a black truffle of the Aestivum clade (Tuberaceae, Pezizales) from the Balkan peninsula

Knowledge on the diversity of hypogeous sequestrate ascomycetes is still limited in the Balkan Peninsula. A new species of truffle, Tuber pulchrosporum, is described from Greece and Bulgaria. Specimens were collected from habitats dominated by various oak species (i.e. Quercus ilex, Q. coccifera, Q. robur) and other angiosperms. They are morphologically characterised by subglobose, ovoid to irregularly lobed, yellowish-brown to dark brown ascomata, usually with a shallow basal cavity and surface with fissures and small, dense, almost flat, trihedral to polyhedral warts. Ascospores are ellipsoid to subfusiform, uniquely ornamented, crested to incompletely reticulate and are produced in (1–)2–8-spored asci. Hair-like, hyaline to light yellow hyphae protrude from the peridium surface. According to the outcome of ITS rDNA sequence analysis, this species forms a distinct well-supported group in the Aestivum clade, with T. panniferum being the closest phylogenetic taxon

The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions

We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid–rich intestine and manure of herbivores—two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche–adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT–acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements