<div dir="ltr">Hi Alexis,<div><br></div><div style>What does:</div><div style> qstat -f <job-id></div><div style>where <job-id> is the ID of your job tell you for the following fields:</div><div style> resources_used.cput</div>
<div style> resources_used.vmem</div><div style><br></div><div style>And how do those values compare to actual amount of elapsed time for the job, the amount of physical memory on the node, and the total memory (RAM + swap space) on the node?</div>
<div style>Just checking to make sure that everything is running as it should be and that your process is not heavily into swap or something like that.</div><div style><br></div><div style>Thanks,</div><div style> Eric</div>
<div style><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Mar 19, 2013 at 11:23 AM, Alexis Groppi <span dir="ltr"><<a href="mailto:alexis.groppi@u-bordeaux2.fr" target="_blank">alexis.groppi@u-bordeaux2.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Adina,<br>
<br>
First of all thanks for your answer and your advices :)<br>
The script extract-partitions.py works !<br>
For the do-partition.py on my second set, it runs since 32 hours.
Should it not have produced at least one temporary .pmap file ?<br>
<br>
Thanks again<br>
<br>
Alexis<br>
<br>
<div>Le 19/03/2013 12:58, Adina Chuang Howe
a écrit :<br>
</div>
<blockquote type="cite"><div><div class="h5"><br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Message: 1<br>
Date: Tue, 19 Mar 2013 10:41:45 +0100<br>
From: Alexis Groppi <<a href="mailto:alexis.groppi@u-bordeaux2.fr" target="_blank">alexis.groppi@u-bordeaux2.fr</a>><br>
Subject: [khmer] Duration of do-partition.py (very long !)<br>
To: <a href="mailto:khmer@lists.idyll.org" target="_blank">khmer@lists.idyll.org</a><br>
Message-ID: <<a href="mailto:514832D9.7090207@u-bordeaux2.fr" target="_blank">514832D9.7090207@u-bordeaux2.fr</a>><br>
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Format="flowed"<br>
<br>
Hi Titus,<br>
<br>
After digital normalization and filter-below-abund, upon your
advice I<br>
performed <a href="http://do.partition.py" target="_blank">do.partition.py</a>
on 2 sets of data (approx 2.5 millions of<br>
reads (75 nt)) :<br>
<br>
/khmer-BETA/scripts/do-partition.py -k 20 -x 1e9<br>
/ag/khmer/Sample_174/174r1_prinseq_good_bFr8.fasta.keep.below.graphbase<br>
/ag/khmer/Sample_174/174r1_prinseq_good_bFr8.fasta.keep.below<br>
and<br>
/khmer-BETA/scripts/do-partition.py -k 20 -x 1e9<br>
/ag/khmer/Sample_174/174r2_prinseq_good_1lIQ.fasta.keep.below.graphbase<br>
/ag/khmer/Sample_174/174r2_prinseq_good_1lIQ.fasta.keep.below<br>
<br>
For the first one I got a<br>
<a href="http://174r1_prinseq_good_bFr8.fasta.keep.below.graphbase.info" target="_blank">174r1_prinseq_good_bFr8.fasta.keep.below.graphbase.info</a>
with the<br>
information : 33 subsets total<br>
Thereafter 33 files .pmap from 0.pmap to 32.pmap regurlarly
were created<br>
and finally I got unique file<br>
174r1_prinseq_good_bFr8.fasta.keep.below.part (all the .pmap
files were<br>
deleted)<br>
This treatment lasted approx 56 hours.<br>
<br>
For the second set (174r2), do-partition.py is started since
32 hours<br>
but I only got the<br>
<a href="http://174r2_prinseq_good_1lIQ.fasta.keep.below.graphbase.info" target="_blank">174r2_prinseq_good_1lIQ.fasta.keep.below.graphbase.info</a>
with the<br>
information : 35 subsets total<br>
And nothing more...<br>
<br>
Is this duration "normal" ?<br>
</blockquote>
<div><br>
</div>
<div>Yes, this is typical. The longest I've had it run is 3
weeks for very large (billions of reads). In general,
partitioning is the most time consuming of all the steps.
Once its finished, you'll have much smaller files which can
be assembled very quickly. Since I run assembly on multiple
assembler and with multiple K lengths, this gain is often
significant for me. </div>
<div><br>
</div>
<div>To get the actual partitioned files, you can use the
following script:</div>
<div><br>
</div>
<div><a href="https://github.com/ged-lab/khmer/blob/master/scripts/extract-partitions.py" target="_blank">https://github.com/ged-lab/khmer/blob/master/scripts/extract-partitions.py</a></div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
(The parameters for the threads are by default (4 threads))<br>
33 subsets and only one file at the end ?<br>
Should I stop do-partition.py on the second set and re run it
with more<br>
threads ?<br>
<br>
</blockquote>
<div><br>
</div>
<div>I'd suggest letting it run.</div>
<div><br>
</div>
<div>Best,</div>
<div>Adina</div>
</div>
<br>
<fieldset></fieldset>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Eric McDonald</div><div>HPC/Cloud Software Engineer</div><div> for the Institute for Cyber-Enabled Research (iCER)</div><div> and the Laboratory for Genomics, Evolution, and Development (GED)</div>
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