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
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