[EMAIL PROTECTED] wrote: >Send Mpiblast-users mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/mpiblast-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Mpiblast-users digest..." > > >Today's Topics: > > 1. Re: mpisub needs --removedb ? (Lucas Carey) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 16 Aug 2006 18:02:35 -0400 >From: Lucas Carey <[EMAIL PROTECTED]> >Subject: Re: [Mpiblast-users] mpisub needs --removedb ? >To: [email protected] >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=us-ascii > >On Monday, August 14, 2006 at 17:53 +0100, Ann Jee Lee wrote: > > > >>Error opening Error opening Error opening /tmp/swissprot.mbf >>open: Permission denied >>Error/tmp/swissprot.mbf >>open: Permission denied >> >> > > > >>In this case, no output is returned. One thing I notice is that the >>headnode is trying to access the db segments from its own /tmp (which >>doesn't exist but in compute nodes' /tmp). >> >> >Do you really mean that the head node does not contain a directory called >'/tmp' ? >If so, then of course the head node can't write to a directory which doesn't >exist. > > > > The '/tmp' directory exists in both head node and compute nodes. My understanding is that when running the mpiblast job,the db segments will be copied to each compute node's '/tmp' directory (not head node's '/tmp'). My suspicion is that the mpiblast is trying to access the segments copied to head node's '/tmp' instead of compute node's '/tmp' in which I think why I got the above errors.
>>However when I change the 'Local' variable in .ncbirc from '/tmp' to >>some other directory which appear unique to both head node and backend >>nodes, it works fine. Or else, I need to use '--removedb' option when >> >> >This is expected behavior. 'Local' is often, but doesn't have to be, unique to >each node. It does, however, have to be writable by user. >submiting the job to be able to get the output after the job run, this >is peculiar. Also, I notice even with '--removedb' used, the database is >not removed at all. Can someone point out anything I miss? The .ncbirc > > The permission of the directory seems correct and so does the standard '/tmp' directory which is definitely writable. What confuses me is why the mpiblast program looks for the the '/tmp' in head node and not the compute nodes. Also, I even checked that the copied segments do exist in the compute node's '/tmp' directory. >This also sounds like a possible issue with permisions. >Try assigning 'Local' to a directory you've created. It should be the fastest >disk availible to the node, often this is /tmp. > > If I change the 'Local' variable back to '/tmp' (not appeared unique to both head and compute nodes) and not using --removedb, I will definitely get the same error. Thus, I have to use a uniquer directory, for instance '/home/ann/scratch/mpiblast/data/local' for 'Local', which it returns the result correctly. But then again supposedly even if '--removedb' is used in this case, the db segments should be removed in the end of the job run but I didn't. May be I am confused with what 'Shared' and 'Local' really mean and used when an MPIBlast job is run? Could you please re-explain again what is being done behind the scene, for instance where the segmented db will be copied to and if '--removedb' is used, from where the db segments will be removed? You help is very much appreciated. >-Lucas > > > > >------------------------------ > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > >------------------------------ > >_______________________________________________ >Mpiblast-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/mpiblast-users > > >End of Mpiblast-users Digest, Vol 3, Issue 4 >******************************************** > > Ann ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
