<div dir="ltr">Forwarding my earlier reply to the list, since I didn't reply-to-all earlier.<div><br></div><div>Also, Alexis, you may wish to change the following in your job script:</div><div> #PBS -l nodes=1:ppn=1</div>
<div>to</div><div> #PBS -l nodes=1:ppn=8</div><div>assuming that you have 8-core nodes available. 'filter-below-abund.py' uses 8 threads by default; if a 'khmer' job runs on the same node as another job, it may try using more CPU cores than it was allocated and that could create problems with your systems administrators. And, if a job's threads are restricted to the requested number of cores, then you will also not be getting optimal performance by using more threads (8) than available cores (1).<br>
<br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Eric McDonald</b> <span dir="ltr"><<a href="mailto:emcd.msu@gmail.com">emcd.msu@gmail.com</a>></span><br>Date: Wed, Mar 13, 2013 at 3:12 PM<br>
Subject: Re: [khmer] How to speed up the filter-below-abund script ?<br>To: <a href="mailto:alexis.groppi@u-bordeaux2.fr">alexis.groppi@u-bordeaux2.fr</a><br><br><br><div dir="ltr">Alexis,<div><br></div><div>I just realized that the floating-point exception is from inside the Python interpreter itself. If the floating-point exception had appeared from within the 'filter-below-abund.py' script, then we shoul have seen a traceback from the exception, ending with:</div>
<div> ZeroDivisionError: float division by zero</div><div>Instead, we are seeing:</div><div class="im"><div> <span style="font-family:monospace">line 49: 54757 Floating point exception(core dumped)</span></div></div><div>
from your job shell. (I should've noticed that earlier.)</div>
<div><br><div class="gmail_extra">Would you please add the following lines to your job script somewhere before you invoke 'filter-below-abund.py':</div><div class="gmail_extra"> python --version</div><div class="gmail_extra">
which python</div><div class="gmail_extra"><br></div><div class="gmail_extra">And would you please add the following line _immediately after_ you invoke 'filter-below-abund.py':</div><div class="gmail_extra"> echo "Exit Code: $?"</div>
<div class="gmail_extra"><br></div><div class="gmail_extra">Also, would you remove the 'time' command from in front of your invocation of 'filter-below-abund.py'?</div><div class="gmail_extra"><br></div><div class="gmail_extra">
And, one more action before trying again... please run:</div><div class="gmail_extra"> git pull</div><div class="gmail_extra">in your 'khmer-BETA' directory. (I added another possible fix to the 'bleeding-edge' branch. This command will pull that fix into your clone.)</div>
<div class="gmail_extra"><br></div><div class="gmail_extra">Thank you,</div><div class="gmail_extra"> Eric<div><div class="h5"><br><br><div class="gmail_quote">On Wed, Mar 13, 2013 at 10:13 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi,<br>
<br>
<div>Le 13/03/2013 14:12, Eric McDonald a
écrit :<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Alexis,
<div><br>
</div><div>
<div>First, let me say thank you for being patient and
working with us in spite of all the problems you are
encountering.</div>
</div></div>
</blockquote>
<br>
That's bioinformatician life ;)<div><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<div><br>
</div>
<div>With regards to the floating point exception, I
see several opportunities for a division-by-zero condition in
the threading utilities used by the script. These
opportunities exist if an input file is empty. (The problem
may be coming from another place, but this would be my first
guess.) What does the following command say:</div>
<div><br>
</div>
<div> ls -lh <span style="font-family:monospace;font-size:10px">/scratch/ag/khmer/</span><a href="http://174r1_table.kh/" style="font-family:monospace;font-size:10px" target="_blank">174r1_table.kh</a> <span style="font-family:monospace;font-size:10px">/mnt/var/home/ag/174r1_</span><span style="font-family:monospace;font-size:10px">prinseq_good_bFr8.fasta.keep</span></div>
</div>
</blockquote>
<br></div>
The result : (the files are not empty)<br>
<tt>-rw-r--r-- 1 ag users 299M 12 mars 20:54
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep</tt><tt><br>
</tt><tt>-rw-r--r-- 1 ag users 141G 12 mars 21:05
/scratch/ag/khmer/<a href="http://174r1_table.kh" target="_blank">174r1_table.kh</a></tt><div><br>
<br>
<blockquote type="cite">
<div dir="ltr"><br>
<div>Also, since you appear to be using TORQUE as your
resource manager/batch system, could you please attach the
complete output and error files for the job? (These files
should be of the form <job_name>.o2693 and
<job_name>.e2693, where <job_name> is the name of
your job. There may only be one or the other of these files,
depending on site defaults and whether you specified "-j oe"
or "-j eo" in your job submission.)<br>
</div>
</div>
</blockquote>
<br></div>
I re run the job since I have deleted previous (2693) err/out files.<br>
Here is the new file (merged with the option -j oe in the bash
script) :<br>
<br>
<tt>#############################</tt><tt><br>
</tt><tt>User: ag</tt><tt><br>
</tt><tt>Date: Wed Mar 13 14:59:21 CET 2013</tt><tt><br>
</tt><tt>Host: <a href="http://rainman.cbib.u-bordeaux2.fr" target="_blank">rainman.cbib.u-bordeaux2.fr</a></tt><tt><br>
</tt><tt>Directory: /mnt/var/home/ag</tt><tt><br>
</tt><tt>PBS_JOBID: 2695.rainman</tt><tt><br>
</tt><tt>PBS_O_WORKDIR: /mnt/var/home/ag</tt><tt><br>
</tt><tt>PBS_NODEFILE: rainman</tt><tt><br>
</tt><tt>#############################</tt><tt><br>
</tt><tt>#############################</tt><tt><br>
</tt><tt>Debut filter-below-abund: Wed Mar 13 14:59:21 CET 2013</tt><div><tt><br>
</tt><tt>starting threads</tt><tt><br>
</tt><tt>starting writer</tt><tt><br>
</tt><tt>loading...</tt><tt><br>
</tt><tt>... filtering 0</tt><tt><br>
</tt></div><tt>/var/lib/torque/mom_priv/jobs/<a href="http://2695.rainman.SC" target="_blank">2695.rainman.SC</a>: line 49:
54757 Floating point exception(core dumped)
./khmer-BETA/sandbox/fi</tt><tt><br>
</tt><tt>lter-below-abund.py /scratch/ag/khmer/<a href="http://174r1_table.kh" target="_blank">174r1_table.kh</a>
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep</tt><tt><br>
</tt><tt><br>
</tt><tt>real 3m54.873s</tt><tt><br>
</tt><tt>user 0m0.085s</tt><tt><br>
</tt><tt>sys 2m2.180s</tt><tt><br>
</tt><tt>Date fin: Wed Mar 13 15:03:15 CET 2013</tt><tt><br>
</tt><tt>Job finished</tt><br>
<br>
Thanks again for your help :)<br>
<br>
Alexis<div><div><br>
<br>
<blockquote type="cite">
<div dir="ltr">
<div>
</div>
<div><br>
</div>
<div>Thanks,</div>
<div> Eric</div>
<div><span style="font-family:monospace;font-size:10px"><br>
</span></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 13, 2013 at 5:38 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> Hi Eric,<br>
<br>
Thanks for your answer.<br>
But unfortunately, after many attempts I'm getting this
error :<tt><br>
<br>
</tt><tt>starting threads</tt><tt><br>
</tt><tt>starting writer</tt><tt><br>
</tt><tt>loading...</tt><tt><br>
</tt><tt>... filtering 0</tt><tt><br>
</tt><tt>/var/lib/torque/mom_priv/jobs/<a href="http://2693.rainman.SC" target="_blank">2693.rainman.SC</a>: line 46: 63657
Floating point exception(core dumped)
./khmer-BETA/sandbox/filter-below-abund.py
/scratch/ag/khmer/<a href="http://174r1_table.kh" target="_blank">174r1_table.kh</a>
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep</tt><tt><br>
</tt><tt><br>
</tt><tt>real 3m30.163s</tt><tt><br>
</tt><tt>user 0m0.088s</tt><br>
<br>
Your opinion ?<br>
<br>
Thanks<br>
<br>
Alexis<br>
<br>
<br>
<div>Le 13/03/2013 00:55, Eric McDonald a écrit :<br>
</div>
<div>
<div>
<blockquote type="cite">
<div dir="ltr">Hi Alexis,
<div><br>
</div>
<div>One way to get the 'bleeding-edge' branch is
to clone it into a fresh directory; for example:</div>
<div> git clone <a href="http://github.com/ged-lab/khmer.git" target="_blank">http://github.com/ged-lab/khmer.git</a>
-b bleeding-edge khmer-BETA</div>
<div><br>
</div>
<div>Assuming you already have a clone of the
'ged-lab/khmer' repo, then you should also be
able to do:</div>
<div> git fetch origin</div>
<div> git checkout bleeding-edge</div>
<div>Depending on how old your Git client is and
what its defaults are, you may have to do the
following instead:</div>
<div> git checkout --track -b bleeding-edge
origin/bleeding-edge</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div> Eric</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Mar 12, 2013 at
11:32 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"> <br>
<div>Le 12/03/2013 16:16, C. Titus Brown a
écrit :<br>
</div>
<div>
<blockquote type="cite">
<pre>On Tue, Mar 12, 2013 at 04:15:05PM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre>Hi Titus,
Thanks for your answer
Actually it's my second attempt with filter-below-abund.
The first time, I thought the problem was coming from the location of my
<a href="http://table.kh" target="_blank">table.kh</a> file : in a storage element with poor level performance of I/O
I killed the job after 24h, moved the file in a best place and re run it
But with the same result : no completion after 24h
Any Idea ?
Thanks
Cheers From Bordeaux :)
Alexis
PS : The command line was the following :
./filter-below-abund.py <a href="http://174r1_table.kh" target="_blank">174r1_table.kh</a> 174r1_prinseq_good_bFr8.fasta.keep
Is this correct ?
</pre>
</blockquote>
<pre>Yes, looks right... Can you try with the bleeding-edge branch, which now
incorporates a potential fix for this issue?</pre>
</blockquote>
</div>
From here : <a href="https://github.com/ged-lab/khmer/tree/bleeding-edge" target="_blank">https://github.com/ged-lab/khmer/tree/bleeding-edge</a>
?<br>
or <br>
here : <a href="https://github.com/ctb/khmer/tree/bleeding-edge" target="_blank">https://github.com/ctb/khmer/tree/bleeding-edge</a>
?<br>
<br>
Do I have to make a fresh install ? and How
?<br>
Or just replace all the files and folders ?<br>
<br>
Thanks :)<br>
<br>
Alexis
<div>
<div><br>
<br>
<blockquote type="cite">
<pre>thanks,
--titus
</pre>
<blockquote type="cite">
<pre>Le 12/03/2013 14:41, C. Titus Brown a ?crit :
</pre>
<blockquote type="cite">
<pre>On Tue, Mar 12, 2013 at 10:48:03AM +0100, Alexis Groppi wrote:
</pre>
<blockquote type="cite">
<pre>Metagenome assembly :
My data :
- original (quality filtered) data : 4463243 reads (75 nt) (Illumina)
1/ Single pass digital normalization with normalize-by-median (C=20)
==> file .keep of 2560557 reads
2/ generated a hash table by load-into-counting on the .keep file
==> file .kh of ~16Go (huge file ?!)
3/ filter-below-abund with C=100 from the two previous file (<a href="http://table.kh" target="_blank">table.kh</a>
and reads.keep)
Still running after 24 hours :(
Any advice to speed up this step ? ... and the others (partitionning ...) ?
I can have an access to a HPC : ~3000 cores.
</pre>
</blockquote>
<pre>Hi Alexis,
filter-below-abund and filter-abund have occasional bugs that prevent them
from completing. I would kill and restart. For that few reads it should
take no more than a few hours to do everything.
Most of what khmer does cannot easily be distributed across multiple chassis,
note.
best,
--titus
</pre>
</blockquote>
<pre>--
</pre>
</blockquote>
</blockquote>
<br>
</div>
</div>
<span><font color="#888888">
<div>-- <br>
<img src="cid:part12.04040604.04000609@u-bordeaux2.fr" border="0"></div>
</font></span></div>
<br>
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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>
<div>Michigan State University</div>
<div>P: <a href="tel:517-355-8733" value="+15173558733" target="_blank">517-355-8733</a></div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
<span><font color="#888888">
<div>-- <br>
<img src="cid:part16.01060504.07000405@u-bordeaux2.fr" border="0"></div>
</font></span></div>
</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>
<div>Michigan State University</div>
<div>P: <a href="tel:517-355-8733" value="+15173558733" target="_blank">517-355-8733</a></div>
</div>
</div>
</blockquote>
<br>
</div></div><span><font color="#888888"><div>-- <br>
<img src="cid:part17.09020606.02060503@u-bordeaux2.fr" border="0"></div>
</font></span></div>
</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>
<div>Michigan State University</div><div>P: <a href="tel:517-355-8733" value="+15173558733" target="_blank">517-355-8733</a></div></div>
</div></div></div></div></div>
</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>
<div>Michigan State University</div><div>P: 517-355-8733</div></div>
</div></div>