[khmer] How to speed up the filter-below-abund script ?
Alexis Groppi
alexis.groppi at u-bordeaux2.fr
Wed Mar 13 07:48:29 PDT 2013
Another clue :
A empty .below file is generated (174r1_prinseq_good_bFr8.fasta.keep.below)
Alexis
Le 13/03/2013 15:13, Alexis Groppi a écrit :
> 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
>>>>> --
>>>
>>> --
>>>
>>> _______________________________________________
>>> khmer mailing list
>>> 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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