[Pvfs2-users] help with pvfs2 and formatdb (used with BLAST)

Randall Martin wolf at clemson.edu
Tue Jun 16 09:10:42 EDT 2009


We download the source from http://www.mpiblast.org/Downloads/Stable.  The
mmap() call with MAP_SHARED is in mpiblast-1.5.0-pio/ncbi/corelib/ncbimem.c.

-Randy

> From: Becky Ligon <ligon at clemson.edu>
> Reply-To: Becky Ligon <ligon at clemson.edu>
> Date: Mon, 15 Jun 2009 17:49:46 -0400 (EDT)
> To: Sam Lang <slang at mcs.anl.gov>
> Cc: Becky Ligon <ligon at clemson.edu>, Phil Carns <carns at mcs.anl.gov>, Randall
> Martin <wolf at clemson.edu>, <pvfs2-users at beowulf-underground.org>
> Subject: Re: [Pvfs2-users] help with pvfs2 and formatdb (used with BLAST)
> 
> Sam:
> 
> Randy will have to answer that question for you, since he is the one who
> actually ran the command.  I'll get with him in the morning and find out.
> 
> Becky
> 
>> 
>> Hi Becky,
>> 
>> Does clemson build formatdb (and blast) from the source code tarball
>> ncbi?  The reason I ask is that we might be able to make a small
>> modification (switching from MAP_SHARED to MAP_PRIVATE) to allow blast
>> to work on PVFS deployments.  I can give further info if that's
>> something you all are willing to try.
>> 
>> Thanks,
>> -sam
>> 
>> 
>> On Jun 11, 2009, at 9:18 AM, Becky Ligon wrote:
>> 
>>> Phil:
>>> 
>>> We have a 4Gb input file for the formatdb command.  The problem
>>> doesn't
>>> seem to occur until after the command has crunched for several hours.
>>> 
>>> I'll be happy to share the file with you (and the formatdb command
>>> that
>>> Randy is using).  Just let me know the best way to get the file to
>>> you...I
>>> can ftp it to you or put it on a machine that you still have access
>>> to....just let me know!
>>> 
>>> Becky
>>> 
>>> 
>>>> Hi Becky,
>>>> 
>>>> Is there an example input file (either for public download or that
>>>> you
>>>> could send to us) that triggers the problem?  I tried this trivial
>>>> example:
>>>> 
>>>> http://en.wikipedia.org/wiki/Fasta_format#Header_line
>>>> 
>>>> ... by just pasting it into a text file and running "formatdb -i
>>>> <file>".  I also tried just concatenating the same input together
>>>> many
>>>> times to get a bigger file, but I didn't have any luck triggering the
>>>> problem.
>>>> 
>>>> -Phil
>>>> 
>>>> Sam Lang wrote:
>>>>> 
>>>>> Hi Becky,
>>>>> 
>>>>> pvfs2_file_write is a kernel module function, so I think that
>>>>> message
>>>>> must have come from the kernel log.  There may not be any messages
>>>>> in
>>>>> the client log (/tmp/pvfs2-client.log), but I was hoping there
>>>>> would be
>>>>> something that might point us at the problem (the client daemon got
>>>>> restarted, for example).  Also, the server logs might have
>>>>> something.
>>>>> As a last resort, you could try to enable debugging in the kernel
>>>>> module
>>>>> to see what happens around the time of another error.
>>>>> 
>>>>> -sam
>>>>> 
>>>>> On Jun 9, 2009, at 3:19 PM, Becky Ligon wrote:
>>>>> 
>>>>>> The second message (pvfs2_file_write) came out of the client log
>>>>>> (/tmp/pvfs2-client.log).
>>>>>> 
>>>>>> We are thinking that either the client or server processes are
>>>>>> running
>>>>>> out
>>>>>> of system resources.....maybe file descriptors, for example.
>>>>>> 
>>>>>> We have now put PVFS on our Palmetto cluster as the primary
>>>>>> parallel
>>>>>> file
>>>>>> system .... no more lustre!  So, now we are trying to iron some of
>>>>>> these
>>>>>> problems, which is why I think the problem is really system-
>>>>>> resource
>>>>>> related.
>>>>>> 
>>>>>> I found an old thread from Dec of 2007 where a guy in Beijing had
>>>>>> the
>>>>>> same
>>>>>> problem; unfortunately, there was no response to his problem.
>>>>>> 
>>>>>> Becky
>>>>>> 
>>>>>>> 
>>>>>>> Hi Becky,
>>>>>>> What about the client log?  Anything in there?
>>>>>>> -sam
>>>>>>> 
>>>>>>> On Jun 9, 2009, at 10:42 AM, Becky Ligon wrote:
>>>>>>> 
>>>>>>>> PVFS-USERS:
>>>>>>>> 
>>>>>>>> When I use formatdb to create a BLAST-usable database, I get the
>>>>>>>> error:
>>>>>>>> 
>>>>>>>> [formatdb] ERROR:  Failed to create index:  ISAMErrorCode -5.
>>>>>>>> 
>>>>>>>> The PVFS kernel log shows the following error:
>>>>>>>> 
>>>>>>>> pvfs2_file_write: error in vectored write to handle xxxx, FILE:
>>>>>>>> xxxx.
>>>>>>>> 
>>>>>>>> (the x's have values but are just specific to my database).
>>>>>>>> 
>>>>>>>> I saw a thread in the pvfs2-users archive where someone else has
>>>>>>>> this same
>>>>>>>> problem, but there were no responses to it.  Am I just having a
>>>>>>>> setup
>>>>>>>> issue with PVFS?
>>>>>>>> 
>>>>>>>> We are running PVFS 2.8.
>>>>>>>> 
>>>>>>>> Any help would be apprecited.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> Becky Ligon
>>>>>>>> --
>>>>>>>> Becky Ligon
>>>>>>>> Clemson University
>>>>>>>> 864-656-3865
>>>>>>>> _______________________________________________
>>>> 
>>> 
>>> 
>>> --
>>> Becky Ligon
>>> PVFS Developer
>>> Clemson University
>>> 864-656-3865
>> 
>> 
> 
> 
> -- 
> Becky Ligon
> PVFS Developer
> Clemson University
> 864-656-3865



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