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

[Phil Carns]

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
>>>> _______________________________________________