[khmer] How to speed up the filter-below-abund script ?
Alexis Groppi
alexis.groppi at u-bordeaux2.fr
Wed Mar 13 07:13:32 PDT 2013
Hi,
Le 13/03/2013 14:12, Eric McDonald a écrit :
> Hi Alexis,
>
> First, let me say thank you for being patient and working with us in
> spite of all the problems you are encountering.
That's bioinformatician life ;)
>
> 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:
>
> ls -lh /scratch/ag/khmer/174r1_table.kh <http://174r1_table.kh/>
> /mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep
The result : (the files are not empty)
-rw-r--r-- 1 ag users 299M 12 mars 20:54
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep
-rw-r--r-- 1 ag users 141G 12 mars 21:05 /scratch/ag/khmer/174r1_table.kh
>
> 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.)
I re run the job since I have deleted previous (2693) err/out files.
Here is the new file (merged with the option -j oe in the bash script) :
#############################
User: ag
Date: Wed Mar 13 14:59:21 CET 2013
Host: rainman.cbib.u-bordeaux2.fr
Directory: /mnt/var/home/ag
PBS_JOBID: 2695.rainman
PBS_O_WORKDIR: /mnt/var/home/ag
PBS_NODEFILE: rainman
#############################
#############################
Debut filter-below-abund: Wed Mar 13 14:59:21 CET 2013
starting threads
starting writer
loading...
... filtering 0
/var/lib/torque/mom_priv/jobs/2695.rainman.SC: line 49: 54757 Floating
point exception(core dumped) ./khmer-BETA/sandbox/fi
lter-below-abund.py /scratch/ag/khmer/174r1_table.kh
/mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep
real 3m54.873s
user 0m0.085s
sys 2m2.180s
Date fin: Wed Mar 13 15:03:15 CET 2013
Job finished
Thanks again for your help :)
Alexis
>
> Thanks,
> Eric
>
>
>
> On Wed, Mar 13, 2013 at 5:38 AM, Alexis Groppi
> <alexis.groppi at u-bordeaux2.fr <mailto:alexis.groppi at u-bordeaux2.fr>>
> wrote:
>
> Hi Eric,
>
> Thanks for your answer.
> But unfortunately, after many attempts I'm getting this error :
>
> starting threads
> starting writer
> loading...
> ... filtering 0
> /var/lib/torque/mom_priv/jobs/2693.rainman.SC
> <http://2693.rainman.SC>: line 46: 63657 Floating point
> exception(core dumped) ./khmer-BETA/sandbox/filter-below-abund.py
> /scratch/ag/khmer/174r1_table.kh <http://174r1_table.kh>
> /mnt/var/home/ag/174r1_prinseq_good_bFr8.fasta.keep
>
> real 3m30.163s
> user 0m0.088s
>
> Your opinion ?
>
> Thanks
>
> Alexis
>
>
> Le 13/03/2013 00:55, Eric McDonald a écrit :
>> Hi Alexis,
>>
>> One way to get the 'bleeding-edge' branch is to clone it into a
>> fresh directory; for example:
>> git clone http://github.com/ged-lab/khmer.git -b bleeding-edge
>> khmer-BETA
>>
>> Assuming you already have a clone of the 'ged-lab/khmer' repo,
>> then you should also be able to do:
>> git fetch origin
>> git checkout bleeding-edge
>> Depending on how old your Git client is and what its defaults
>> are, you may have to do the following instead:
>> git checkout --track -b bleeding-edge origin/bleeding-edge
>>
>> Hope this helps,
>> Eric
>>
>>
>> On Tue, Mar 12, 2013 at 11:32 AM, Alexis Groppi
>> <alexis.groppi at u-bordeaux2.fr
>> <mailto:alexis.groppi at u-bordeaux2.fr>> wrote:
>>
>>
>> Le 12/03/2013 16:16, C. Titus Brown a écrit :
>>> On Tue, Mar 12, 2013 at 04:15:05PM +0100, Alexis Groppi wrote:
>>>> 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
>>>> table.kh <http://table.kh> 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.py174r1_table.kh <http://174r1_table.kh> 174r1_prinseq_good_bFr8.fasta.keep
>>>>
>>>> Is this correct ?
>>> Yes, looks right... Can you try with the bleeding-edge branch, which now
>>> incorporates a potential fix for this issue?
>> From here : https://github.com/ged-lab/khmer/tree/bleeding-edge ?
>> or
>> here : https://github.com/ctb/khmer/tree/bleeding-edge ?
>>
>> Do I have to make a fresh install ? and How ?
>> Or just replace all the files and folders ?
>>
>> Thanks :)
>>
>> Alexis
>>
>>
>>> thanks,
>>> --titus
>>>
>>>> Le 12/03/2013 14:41, C. Titus Brown a ?crit :
>>>>> On Tue, Mar 12, 2013 at 10:48:03AM +0100, Alexis Groppi wrote:
>>>>>> 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 (table.kh <http://table.kh>
>>>>>> 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.
>>>>> 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
>>>> --
>>
>> --
>>
>> _______________________________________________
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>> khmer at lists.idyll.org <mailto:khmer at lists.idyll.org>
>> http://lists.idyll.org/listinfo/khmer
>>
>>
>>
>>
>> --
>> Eric McDonald
>> HPC/Cloud Software Engineer
>> for the Institute for Cyber-Enabled Research (iCER)
>> and the Laboratory for Genomics, Evolution, and Development (GED)
>> Michigan State University
>> P: 517-355-8733 <tel:517-355-8733>
>
> --
>
>
>
>
> --
> Eric McDonald
> HPC/Cloud Software Engineer
> for the Institute for Cyber-Enabled Research (iCER)
> and the Laboratory for Genomics, Evolution, and Development (GED)
> Michigan State University
> P: 517-355-8733
--
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