<html><head><base href="x-msg://185/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gavin<div><br></div><div>For v60 we have now set the cigar_line field to a VARCHAR with a sensible field length of 50. The current largest cigar_line in human is around 30 characters long.</div><div><br></div><div>This should remove the issue of tmp tables being created on disk.</div><div><br></div><div>Nath</div><div><br></div><div><br></div><div><br><div><div>On 25 Aug 2010, at 10:12, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div lang="EN-US" link="blue" vlink="purple"><div class="Section1" style="page: Section1; "><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Hi all,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">I’ve been running some tests on our server, annotating a test batch of around 50 Affy probesets (25-mer probes, 11 probes per set).<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Running the same batch of probesets has completed in anywhere from 30 mins to just over 2 hours!<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">The load on the server does not seem to be the issue. I have run a number of mysql tuners to optimize things and the only complaint I am seeing is that 50% of our temporary tables are being created on disk rather than in memory. Apparently this is a major cause of inconsistent mySQL performance. I have increased all relevant variables but it does not seem to affect the % of temp tables being created on disk. I know that BLOB and TEXT fields cannot be stored in memory and must be created on disk so I’m beginning to think this may be the problem. Has anyone else experienced similar problems or does anyone have any ideas on how the BLOB and TEXT fields could be redefined to enable in-memory storage?<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Best,<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" face="Arial"><span style="font-size: 10pt; font-family: Arial; ">Gavin</span></font><o:p></o:p></div></div><font face="Tahoma" size="2"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><strong><b><span style="font-size: 12pt; color: blue; "><font face="Times New Roman"> </font></span></b></strong></div><strong><b><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font color="#000000"><span lang="EN-GB" style="font-family: 'Times New Roman'; ">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font color="#0000ff"><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Group (UK) Limited, registered no. NI061368.<span> <span class="Apple-converted-space"> </span></span>Almac Sciences Limited, registered no. NI041550.<span> <span class="Apple-converted-space"> </span></span>Almac Discovery Limited, registered no. NI046249.<span class="Apple-converted-space"> </span><span> </span>Almac Pharma Services Limited, registered no. NI045055.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Services Limited, registered no. NI041905.<span> <span class="Apple-converted-space"> </span></span>Almac Clinical Technologies Limited, registered no. NI061202.<span class="Apple-converted-space"> </span><span> </span>Almac Diagnostics Limited, registered no. NI043067.<span> <span class="Apple-converted-space"> </span></span>All preceding companies are registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on">Northern Ireland</st1:country-region><span class="Apple-converted-space"> </span>with a registered office address of Almac House, 20 Seagoe Industrial Estate,<st1:place w:st="on"><st1:city w:st="on">Craigavon</st1:city>,<span class="Apple-converted-space"> </span><st1:postalcode w:st="on">BT63 5QD</st1:postalcode>,<span class="Apple-converted-space"> </span><st1:country-region w:st="on">UK</st1:country-region></st1:place>.<span class="Apple-converted-space"> </span><span> </span><o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in<span class="Apple-converted-space"> </span><st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region><span class="Apple-converted-space"> </span>no. SC154034.<o:p></o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; "><o:p> </o:p></span></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><span lang="EN-GB" style="color: black; font-family: 'Times New Roman'; ">Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are<span class="Apple-converted-space"> </span><st1:state w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:state><span class="Apple-converted-space"> </span>limited liability companies and Almac Group Incorporated is a Delaware Corporation.<span> <span class="Apple-converted-space"> </span></span>More information on the Almac Group can be found on the Almac website:<a href="http://www.almacgroup.com" style="color: blue; text-decoration: underline; ">www.almacgroup.com</a><o:p></o:p></span></div></b></strong></font>_______________________________________________<br>Dev mailing list<br><a href="mailto:Dev@ensembl.org" style="color: blue; text-decoration: underline; ">Dev@ensembl.org</a><br><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: blue; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TelNo: (+44)1223 492629</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span><br class="Apple-interchange-newline">
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