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

[Sam Lang]

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
>>> _______________________________________________
>>> Pvfs2-users mailing list
>>> Pvfs2-users at beowulf-underground.org
>>> http://www.beowulf-underground.org/mailman/listinfo/pvfs2-users
>>
>>
>
>
> -- 
> Becky Ligon
> PVFS Developer
> Clemson University
> 864-656-3865