[maker-devel] NFSLock problem

[Carson Holt]

Stop the job and restart it.  No need to delete anything.  Just restart it.

Thanks,
Carson


On 10/3/13 2:44 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

>I have a MAKER job running that seems to be stalled on a failed scaffold.
> It's running via MPI (MAKER v2.28, openMPI 1.6.3), that appears to have
>worked successfully for the most part.  This is a run that only uses
>transcriptome and protein information in order to get a decent dseat of
>
>The failed scaffold seems to be holding the job from completion.  There
>does seem to be changes, but mainly they are on the NFSLock files:
>
>./.NFSLock.gi_lock.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
>./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLo
>ck.KB913038%2E1.281.end.blastn.holdover.NFSLock.STACK
>
>Everything else seems to have completed.
>
>I have seen a few issues re: NFS locking problems, would this be related?
> Should I stop the job?
>
>We're running GPFS for our NFS.  Here's 'mount':
>
>-system-specific-4.1$ mount
>/dev/sda5 on / type ext4 (rw)
>proc on /proc type proc (rw)
>sysfs on /sys type sysfs (rw)
>devpts on /dev/pts type devpts (rw,gid=5,mode=620)
>tmpfs on /dev/shm type tmpfs (rw)
>/dev/sda1 on /boot type ext4 (rw)
>/dev/sdb1 on /export type ext4 (rw)
>/dev/sda2 on /var type ext4 (rw)
>tmpfs on /var/lib/ganglia/rrds type tmpfs
>(rw,size=6180842000,gid=99,uid=99)
>none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
>sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
>nfsd on /proc/fs/nfsd type nfsd (rw)
>/dev/IGBHOME0 on /home type gpfs (rw,mtime,dev=IGBHOME0)
>128.174.124.79:/shares/group on /archive/group type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>128.174.124.79:/shares/CBC on /archive/CBC type nfs
>(rw,sync,hard,intr,retrans=10,timeo=300,rsize=65536,wsize=1048576,vers=3,p
>roto=tcp,mountproto=tcp,addr=128.174.124.79)
>
>chris
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