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Autori principali:	Simon, William Andrew, Yavits, Leonid, Koliogeorgi, Konstantina, Falevoz, Yann, Shibuya, Yoshihiro, Lavenier, Dominique, Boybat, Irem, Zambaku, Klea, Şahin, Berkan, Sadrosadati, Mohammad, Mutlu, Onur, Sebastian, Abu, Chikhi, Rayan, Consortium, The BioPIM, Alkan, Can
Natura:	Preprint
Pubblicazione:	2025
Soggetti:	Genomics Hardware Architecture
Accesso online:	https://arxiv.org/abs/2506.00597
Tags:	Aggiungi Tag Nessun Tag, puoi essere il primo ad aggiungerne!!

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author	Simon, William Andrew Yavits, Leonid Koliogeorgi, Konstantina Falevoz, Yann Shibuya, Yoshihiro Lavenier, Dominique Boybat, Irem Zambaku, Klea Şahin, Berkan Sadrosadati, Mohammad Mutlu, Onur Sebastian, Abu Chikhi, Rayan Consortium, The BioPIM Alkan, Can
author_facet	Simon, William Andrew Yavits, Leonid Koliogeorgi, Konstantina Falevoz, Yann Shibuya, Yoshihiro Lavenier, Dominique Boybat, Irem Zambaku, Klea Şahin, Berkan Sadrosadati, Mohammad Mutlu, Onur Sebastian, Abu Chikhi, Rayan Consortium, The BioPIM Alkan, Can
contents	Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.
format	Preprint
id	arxiv_https___arxiv_org_abs_2506_00597
institution	arXiv
publishDate	2025
record_format	arxiv
spellingShingle	Processing-in-memory for genomics workloads Simon, William Andrew Yavits, Leonid Koliogeorgi, Konstantina Falevoz, Yann Shibuya, Yoshihiro Lavenier, Dominique Boybat, Irem Zambaku, Klea Şahin, Berkan Sadrosadati, Mohammad Mutlu, Onur Sebastian, Abu Chikhi, Rayan Consortium, The BioPIM Alkan, Can Genomics Hardware Architecture Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.
title	Processing-in-memory for genomics workloads
topic	Genomics Hardware Architecture
url	https://arxiv.org/abs/2506.00597

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

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