Predefined Software Environment Runtimes As A Measure For Reproducibility

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Bibliographic Details
Main Author:	Kaushik, Aaruni
Format:	Preprint
Published:	2024
Subjects:	Mathematical Software
Online Access:	Acceder al recurso
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author	Kaushik, Aaruni
author_facet	Kaushik, Aaruni
contents	As part of Mathematical Research Data Initiative (MaRDI), we have developed a way to preserve a software package into an easy to deploy and use sandbox environment we call a "runtime", via a program we developed called MaPS : MaRDI Packaging System. The program relies on Linux user namespaces to isolate a library environment from the host system, making the sandboxed software reproducible on other systems, with minimal effort. Moreover an overlay filesystem makes local edits persistent. This project will aid reproducibility efforts of research papers: both mathematical and from other disciplines. As a proof of concept, we provide runtimes for the OSCAR Computer Algebra System, polymake software for research in polyhedral geometry, and VIBRANT Virus Identification By iteRative ANnoTation. The software is in a prerelease state: the interface for creating, deploying, and executing runtimes is final, and an interface for easily publishing runtimes is under active development. We thus propose publishing predefined, distributable software environment runtimes along with research papers in an effort to make research with software based results reproducible.
format	Preprint
id	arxiv_https___arxiv_org_abs_2404_05563
institution	arXiv
publishDate	2024
record_format	arxiv
spellingShingle	Predefined Software Environment Runtimes As A Measure For Reproducibility Kaushik, Aaruni Mathematical Software As part of Mathematical Research Data Initiative (MaRDI), we have developed a way to preserve a software package into an easy to deploy and use sandbox environment we call a "runtime", via a program we developed called MaPS : MaRDI Packaging System. The program relies on Linux user namespaces to isolate a library environment from the host system, making the sandboxed software reproducible on other systems, with minimal effort. Moreover an overlay filesystem makes local edits persistent. This project will aid reproducibility efforts of research papers: both mathematical and from other disciplines. As a proof of concept, we provide runtimes for the OSCAR Computer Algebra System, polymake software for research in polyhedral geometry, and VIBRANT Virus Identification By iteRative ANnoTation. The software is in a prerelease state: the interface for creating, deploying, and executing runtimes is final, and an interface for easily publishing runtimes is under active development. We thus propose publishing predefined, distributable software environment runtimes along with research papers in an effort to make research with software based results reproducible.
title	Predefined Software Environment Runtimes As A Measure For Reproducibility
topic	Mathematical Software
url	https://arxiv.org/abs/2404.05563

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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