https://teaching.healthtech.dtu.dk:443/22112/index.php?action=history&feed=atom&title=What_affects_performance 2026-04-11T11:48:11Z Revision history for this page on the wiki MediaWiki 1.41.0 https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=100&oldid=prev 2025-08-05T09:51:53Z

<p><span dir="auto"><span class="autocomment">Exercises</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:51, 5 August 2025</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l32">Line 32:</td> <td colspan="2" class="diff-lineno">Line 32:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Consider that some fasta files have small entries, others have large entries. What impact does that have on your method?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Consider that some fasta files have small entries, others have large entries. What impact does that have on your method?</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>For the record, I could do the indexing in 2.5 seconds on <del style="font-weight: bold; text-decoration: none;">computerome</del>, and 6.5 seconds on my laptop for human.fsa. I would have expected <del style="font-weight: bold; text-decoration: none;">computerome </del>to be slower.&lt;br&gt;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>For the record, I could do the indexing in 2.5 seconds on <ins style="font-weight: bold; text-decoration: none;">a server</ins>, and 6.5 seconds on my laptop for human.fsa. I would have expected <ins style="font-weight: bold; text-decoration: none;">the server </ins>to be slower.&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There can be many reasons for the speed difference, but the main one here is <del style="font-weight: bold; text-decoration: none;">computerome </del>has more memory - more file buffers. It has simply stored the file in memory,</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There can be many reasons for the speed difference, but the main one here is <ins style="font-weight: bold; text-decoration: none;">the server </ins>has more memory - more file buffers. It has simply stored the file in memory,</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>and when I repeatedly test it does not need to go to the disk except the first time. &lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>and when I repeatedly test it does not need to go to the disk except the first time. &lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Another test on <del style="font-weight: bold; text-decoration: none;">computerome </del>gave me 34,6 seconds for indexing when the file was not in the file buffers and 1.6 sec when the file was in the file buffers.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Another test on <ins style="font-weight: bold; text-decoration: none;">the server </ins>gave me 34,6 seconds for indexing when the file was not in the file buffers and 1.6 sec when the file was in the file buffers.</div></td></tr> </table>

WikiSysop https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=94&oldid=prev 2025-01-20T15:47:40Z

<p><span dir="auto"><span class="autocomment">Material for the lesson</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:47, 20 January 2025</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l9">Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/22112_07-Efficiency.ppt Efficiency]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/22112_07-Efficiency.ppt Efficiency]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Resource: [[Example code - memoization]]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Resource: [[Example code - memoization]]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]<ins style="font-weight: bold; text-decoration: none;">&lt;br&gt;</ins></div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Youtube: [https://www.youtube.com/watch?v=tKbV6BpH-C8 Premature optimization] Many good points, but for large projects.</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Exercises ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Exercises ==</div></td></tr> </table>

WikiSysop https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=58&oldid=prev 2024-06-17T09:41:04Z

<p><span dir="auto"><span class="autocomment">Material for the lesson</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:41, 17 June 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l8">Line 8:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/22112_07-Efficiency.ppt Efficiency]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/22112_07-Efficiency.ppt Efficiency]&lt;br&gt;</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Resource: [[Example code - memoization]]&lt;br&gt;</ins></div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> </table>

WikiSysop https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=48&oldid=prev 2024-06-17T09:25:51Z

<p><span dir="auto"><span class="autocomment">Material for the lesson</span></span></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:25, 17 June 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/<del style="font-weight: bold; text-decoration: none;">HPCLife04</del>-Efficiency.ppt Efficiency]&lt;br&gt;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/22112/<ins style="font-weight: bold; text-decoration: none;">22112_07</ins>-Efficiency.ppt Efficiency]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> </table>

WikiSysop https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=20&oldid=prev 2024-03-06T10:53:28Z

<p></p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:53, 6 March 2024</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td> <td colspan="2" class="diff-lineno">Line 7:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/<del style="font-weight: bold; text-decoration: none;">36612</del>/HPCLife04-Efficiency.ppt Efficiency]&lt;br&gt;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Powerpoint: [https://teaching.healthtech.dtu.dk/material/<ins style="font-weight: bold; text-decoration: none;">22112</ins>/HPCLife04-Efficiency.ppt Efficiency]&lt;br&gt;</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br></td></tr> </table>

WikiSysop https://teaching.healthtech.dtu.dk:443/22112/index.php?title=What_affects_performance&diff=19&oldid=prev 2024-03-06T10:53:18Z

<p>Created page with &quot;{| width=500 style=&quot;float:right; margin-left: 10px; margin-top: -56px;&quot; |Previous: <a href="/22112/index.php/Distributed_computing" title="Distributed computing">Distributed computing</a> |Next: <a href="/22112/index.php/Algorithms" title="Algorithms">Algorithms</a> |} == Material for the lesson == Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=27882197-f5e0-4528-bea1-af27012415bd File Systems]&lt;br&gt; Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt; Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307...&quot;</p> <p><b>New page</b></p><div>{| width=500 style=&quot;float:right; margin-left: 10px; margin-top: -56px;&quot;<br /> |Previous: [[Distributed computing]]<br /> |Next: [[Algorithms]]<br /> |}<br /> == Material for the lesson ==<br /> Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=27882197-f5e0-4528-bea1-af27012415bd File Systems]&lt;br&gt;<br /> Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=495a9551-22b7-4253-8857-af270123ef1b Improve performance]&lt;br&gt;<br /> Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=1f931856-2307-4e26-8ada-af270123c811 Random access in Python]&lt;br&gt;<br /> Powerpoint: [https://teaching.healthtech.dtu.dk/material/36612/HPCLife04-Efficiency.ppt Efficiency]&lt;br&gt;<br /> Video: [https://panopto.dtu.dk/Panopto/Pages/Viewer.aspx?id=4d74bc2b-93ec-4aab-aadd-af270123a092 What is expected in exercises]<br /> <br /> == Exercises ==<br /> &#039;&#039;&#039;1)&#039;&#039;&#039;&lt;br&gt;<br /> Make a program that can index a fasta file, that is find all the positions in the file where a header starts and ends where a sequence starts and ends, so 4 numbers per entry.&lt;br&gt;<br /> The result (first numbers from human.fsa shown) should be printed like :<br /> 0 71 72 253105767<br /> 253105768 253105839 253105840 499335927<br /> 499335928 499335999 499336000 700936484<br /> 700936485 700936556 700936557 894321354<br /> 894321355 894321426 894321427 1078885323<br /> Use the *.fsa files for practice.<br /> <br /> &#039;&#039;&#039;2)&#039;&#039;&#039;&lt;br&gt;<br /> Make a program that can be given a fasta file and the 4 numbers from above on command line, and read and print a single entry.<br /> <br /> &#039;&#039;&#039;3)&#039;&#039;&#039;&lt;br&gt;<br /> Think about speed. Insert ways to measure the performance. Don&#039;t use real profiling from lecture 3, but time the code using the python &#039;&#039;&#039;time&#039;&#039;&#039; module.&lt;br&gt;<br /> Make the programs in 1 and 2 work faster. 1 can be tricky, since the way to read data fast does not give precise information about the file pointer.&lt;br&gt;<br /> Perhaps chunk reading is good.&lt;br&gt;<br /> Consider that some fasta files have small entries, others have large entries. What impact does that have on your method?<br /> <br /> For the record, I could do the indexing in 2.5 seconds on computerome, and 6.5 seconds on my laptop for human.fsa. I would have expected computerome to be slower.&lt;br&gt;<br /> There can be many reasons for the speed difference, but the main one here is computerome has more memory - more file buffers. It has simply stored the file in memory,<br /> and when I repeatedly test it does not need to go to the disk except the first time. &lt;br&gt;<br /> Another test on computerome gave me 34,6 seconds for indexing when the file was not in the file buffers and 1.6 sec when the file was in the file buffers.</div>

WikiSysop