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<p class="MsoNormal">We’ve worked with MAKER on Lustre and GPFS w/o significant issues (we’re also in the process of setting up MAKER on cluster using Ceph). I’ve always found the trickiest part in initial MAKER setup and testing is making sure the proper
tempfile space is set (point to local disk or /dev/shm) and wrangling MPI issues.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Carson Holt <carsonhh@gmail.com><br>
<b>Date: </b>Tuesday, July 18, 2017 at 12:06 AM<br>
<b>To: </b>"zhushilin@frasergen.com" <zhushilin@frasergen.com><br>
<b>Cc: </b>maker-devel <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] some suggestion<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The system we commonly use with MAKER is Lustre and we get no issues. We also commonly run MAKER on TACC which uses Lustre for all it’s file systems. So there is no Lustre limitation. MAKER does require that each node also have a local
temporary directory for some operations which can generate high IOPS or require that traditional flock support (cannot be guaranteed on some NFS systems). These operations occur in the location specified by TMP= in the control file. Perhaps you are attempting
to set your TMP value in the control files to a Lustre space which can overload the MDS (metadata server) used by Lustre. Make sure you do not set TMP to a shared location. Your working directory can be a shared Lustre space and result files will be stored
there, but IO operations that are not safe for shared spaces will occur in TMP, and TMP must be set to a local storage location (usually /tmp).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Carson<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Jul 12, 2017, at 12:19 AM, <a href="mailto:zhushilin@frasergen.com">
zhushilin@frasergen.com</a> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif">Dear developer,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif">It seems that MAKER can only run in the general hard disk which support structrued data<span style="background:white">, as SQLite was used.</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif">When running in lustre filesystem, we got <span style="background:white">I/O error and nothing was written to .db file which saves the gff information.</span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif">Maybe the best way is to check the filesystem automatically and give the different strategy to store the information in gff files.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"微软雅黑",serif">Best wishes<o:p></o:p></span></p>
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director</span></b><span style="font-size:10.5pt;font-family:"微软雅黑",serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Times",serif;background:white">DEPT. of Bioinformatics</span><span style="font-size:10.5pt;font-family:"微软雅黑",serif"><o:p></o:p></span></p>
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