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
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