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A precision : <br>
<br>
The file submitted to the script do-partition.py contains 2576771
reads (file.below)<br>
The job was launched with the following options : <br>
khmer-BETA/scripts/do-partition.py -k 20 -x 1e9 -T 20 file.graphbase
file.below<br>
<br>
Alexis<br>
<br>
<br>
<div class="moz-cite-prefix">Le 21/03/2013 10:13, Alexis Groppi a
écrit :<br>
</div>
<blockquote cite="mid:514ACF3A.9020006@u-bordeaux2.fr" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
Hi Eric,<br>
<br>
The script do-partition.py is now running since 22 hours.<br>
Only the file.info has been generated. No .pmap file were created.<br>
<br>
qstat -f gives :<br>
resources_used.cput = 441:04:21<br>
resources_used.mem = 12764228kb<br>
resources_used.vmem = 13926732kb<br>
resources_used.walltime = 22:05:56<br>
<br>
The amount of RAM on the server is 256 Go and the swap space is
also 256 Go<br>
<br>
Your opinion ?<br>
<br>
Thanks<br>
<br>
Alexis<br>
<br>
<div class="moz-cite-prefix">Le 20/03/2013 16:43, Alexis Groppi a
écrit :<br>
</div>
<blockquote cite="mid:5149D918.8080602@u-bordeaux2.fr" type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
Hi Eric,<br>
<br>
Actually the previous job was terminated by the limit of the
walltime.<br>
I relaunched the script.<br>
qstat -fr gives : <br>
resources_used.cput = 93:23:08<br>
resources_used.mem = 12341932kb<br>
resources_used.vmem = 13271372kb<br>
resources_used.walltime = 04:42:39<br>
<br>
At this moment only the file.info has been generated.<br>
<br>
Let's wait and see ...<br>
<br>
Thanks again<br>
<br>
Alexis<br>
<br>
<br>
<div class="moz-cite-prefix">Le 19/03/2013 21:50, Eric McDonald
a écrit :<br>
</div>
<blockquote
cite="mid:CAGhFaV3U77wRhRZ5dfZ1xrqjdbnS51pWcBR+cDnZ8phsXy-Sxw@mail.gmail.com"
type="cite">
<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
moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:khmer@lists.idyll.org"
target="_blank">khmer@lists.idyll.org</a><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:514832D9.7090207@u-bordeaux2.fr"
target="_blank">514832D9.7090207@u-bordeaux2.fr</a>><br>
Content-Type: text/plain;
charset="iso-8859-1"; Format="flowed"<br>
<br>
Hi Titus,<br>
<br>
After digital normalization and
filter-below-abund, upon your advice I<br>
performed <a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<br>
</div>
</div>
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<br>
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<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>
<div>Michigan State University</div>
<div>P: 517-355-8733</div>
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