We download the source from http://www.mpiblast.org/Downloads/Stable. The mmap() call with MAP_SHARED is in mpiblast-1.5.0-pio/ncbi/corelib/ncbimem.c.
-Randy > From: Becky Ligon <[email protected]> > Reply-To: Becky Ligon <[email protected]> > Date: Mon, 15 Jun 2009 17:49:46 -0400 (EDT) > To: Sam Lang <[email protected]> > Cc: Becky Ligon <[email protected]>, Phil Carns <[email protected]>, Randall > Martin <[email protected]>, <[email protected]> > Subject: Re: [Pvfs2-users] help with pvfs2 and formatdb (used with BLAST) > > 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
