[Pvfs2-users] help with pvfs2 and formatdb (used with BLAST)
ligon at clemson.edu
Tue Jun 9 16:19:49 EDT 2009
The second message (pvfs2_file_write) came out of the 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
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.
> Hi Becky,
> What about the client log? Anything in there?
> On Jun 9, 2009, at 10:42 AM, Becky Ligon wrote:
>> When I use formatdb to create a BLAST-usable database, I get the
>> [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.
>> Becky Ligon
>> Becky Ligon
>> Clemson University
>> Pvfs2-users mailing list
>> Pvfs2-users at beowulf-underground.org
More information about the Pvfs2-users