[maker-devel] NFSLock problem

[Fields, Christopher J]

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/.NFSLock.KB913038%2E1.281.282.junction.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.281.end.blastn.holdover.NFSLock
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.KB913038%2E1.282.start.blastn.holdover.NFSLock.STACK
./Zalbi.unplaced.scaf_datastore/2C/0F/KB913038.1/theVoid.KB913038.1/.NFSLock.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,proto=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,proto=tcp,mountproto=tcp,addr=128.174.124.79)

chris