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 _______________________________________________ Pvfs2-users mailing list [email protected] http://www.beowulf-underground.org/mailman/listinfo/pvfs2-users
