More Like this

1. RDMA is Turing complete, we just did not know it yet!

   Reda, Waleed ; Kostić, Dejan ; Canini, Marco ; Peter, Simon ( January 2022 , 19th USENIX Symposium on Networked Systems Design and Implementation (NSDI))

   It is becoming increasingly popular for distributed systems to exploit offload to reduce load on the CPU. Remote Direct Memory Access (RDMA) offload, in particular, has become popular. However, RDMA still requires CPU intervention for complex offloads that go beyond simple remote memory access. As such, the offload potential is limited and RDMA-based systems usually have to work around such limitations. We present RedN, a principled, practical approach to implementing complex RDMA offloads, without requiring any hardware modifications. Using self-modifying RDMA chains, we lift the existing RDMA verbs interface to a Turing complete set of programming abstractions. We explore what is possible in terms of offload complexity and performance with a commodity RDMA NIC. We show how to integrate these RDMA chains into applications, such as the Memcached key-value store, allowing us to offload complex tasks such as key lookups. RedN can reduce the latency of key-value get operations by up to 2.6× compared to state-of-the-art KV designs that use one-sided RDMA primitives (e.g., FaRM-KV), as well as traditional RPC-over-RDMA approaches. Moreover, compared to these baselines, RedN provides performance isolation and, in the presence of contention, can reduce latency by up to 35× while providing applications with failure resiliency to OS and process crashes. 

   more » « less
2. OpenSHMEM Checker - A Clang Based Static Checker for OpenSHMEM

   Bari, Md Abdullah ; Arora, Ujjwal ; Hegde, Varun ; Curtis, Tony ; Chapman, Barbara ( January 2021 , 20th International Symposium on Parallel and Distributed Computing (ISPDC’2020))

   null (Ed.)

   Compilers are generally not aware of the semantics of library-based parallel programming models such as MPI and OpenSHMEM, and hence are unable to detect programming errors related to their use. To alleviate this issue, we developed a custom static checker for OpenSHMEM programs based on LLVM’s Clang Static Analyzer framework (CSA). We leverage the Symbolic Execution engine of the core Static Analyzer framework and its path-sensitive analysis to check for bugs on all OpenSHMEM program paths. We have identified common programming mistakes in OpenSHMEM programs that are detectable at compile-time and provided checks for them in the analyzer. They cover: utilization of the right type of mem- ory (private vs. symmetric memory); safe/synchronized access to program data in the presence of asynchronous, one-sided communication; and double-free of memories allocated using OpenSHMEM memory allocation routines. Our experimental analysis showed that the static checker successfully detects bugs in OpenSHMEM code. 

   more » « less
3. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

   more » « less
4. Task-graph scheduling extensions for efficient synchronization and communication

   https://doi.org/10.1145/3447818.3461616  

   Bak, Seonmyeong ; Hernandez, Oscar ; Gates, Mark ; Luszczek, Piotr ; Sarkar, Vivek ( June 2021 , 35th ACM International Conference on Supercomputing (ICS))

   Task graphs have been studied for decades as a foundation for scheduling irregular parallel applications and incorporated in many programming models including OpenMP. While many high-performance parallel libraries are based on task graphs, they also have additional scheduling requirements, such as synchronization within inner levels of data parallelism and internal blocking communications. In this paper, we extend task-graph scheduling to support efficient synchronization and communication within tasks. Compared to past work, our scheduler avoids deadlock and oversubscription of worker threads, and refines victim selection to increase the overlap of sibling tasks. To the best of our knowledge, our approach is the first to combine gang-scheduling and work-stealing in a single runtime. Our approach has been evaluated on the SLATE high-performance linear algebra library. Relative to the LLVM OMP runtime, our runtime demonstrates performance improvements of up to 13.82%, 15.2%, and 36.94% for LU, QR, and Cholesky, respectively, evaluated across different configurations related to matrix size, number of nodes, and use of CPUs vs GPUs. 

   more » « less
5. Task-graph scheduling extensions for efficient synchronization and communication.

   Bak, S. ; Hernandez, O. ; Gates, M. ; Luszczek, P. ; Sarkar, V. ( June 2021 , Proceedings of the ACM International Conference on Supercomputing.)

   Task graphs have been studied for decades as a foundation for scheduling irregular parallel applications and incorporated in many programming models including OpenMP. While many high-performance parallel libraries are based on task graphs, they also have additional scheduling requirements, such as synchronization within inner levels of data parallelism and internal blocking communications. In this paper, we extend task-graph scheduling to support efficient synchronization and communication within tasks. Compared to past work, our scheduler avoids deadlock and oversubscription of worker threads, and refines victim selection to increase the overlap of sibling tasks. To the best of our knowledge, our approach is the first to combine gang-scheduling and work-stealing in a single runtime. Our approach has been evaluated on the SLATE high-performance linear algebra library. Relative to the LLVM OMP runtime, our runtime demonstrates performance improvements of up to 13.82%, 15.2%, and 36.94% for LU, QR, and Cholesky, respectively, evaluated across different configurations related to matrix size, number of nodes, and use of CPUs vs GPUs 

   more » « less