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

[Sam Lang]

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