Sam: Randy will have to answer that question for you, since he is the one who actually ran the command. I'll get with him in the morning and find out.
Becky > > 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 > > -- Becky Ligon PVFS Developer Clemson University 864-656-3865 _______________________________________________ Pvfs2-users mailing list [email protected] http://www.beowulf-underground.org/mailman/listinfo/pvfs2-users
