Hi Roland,
The output of "mount" is :
/dev/mapper/grid01-root on / type ext3 (rw)
proc on /proc type proc (rw)
sysfs on /sys type sysfs (rw)
devpts on /dev/pts type devpts (rw,gid=5,mode=620)
/dev/md0 on /boot type ext3 (rw)
tmpfs on /dev/shm type tmpfs (rw)
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
172.30.100.254:/home on /home type nfs
(rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254)
172.30.100.210:/opt on /opt type nfs
(rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210)
172.30.100.210:/var/spool/torque/server_logs on
/var/spool/pbs/server_logs type nfs
(ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210)
none on /ipathfs type ipathfs (rw)
172.31.100....@o2ib,172.30.100....@tcp:172.31.100....@o2ib,172.30.100....@tcp:/lprod
on /lustre/ws1 type lustre (rw,noatime,nodiratime)
172.31.100....@o2ib,172.30.100....@tcp:172.31.100....@o2ib,172.30.100....@tcp:/lbm
on /lustre/lbm type lustre (rw,noatime,nodiratime)
172.30.100.219:/export/necbm on /nfs/nec type nfs
(ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)
172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs
(rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)
On 11/26/2010 05:41 PM, Roland Schulz wrote:
Hi Baofu,
could you provide more information about the file system?
The command "mount" provides the file system used. If it is a
network-file-system than the operating system and file system used on the
file server is also of interest.
Roland
On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao<qia...@gmail.com> wrote:
Hi Roland,
Thanks a lot!
OS: Scientific Linux 5.5. But the system to store data is called as
WORKSPACE, different from the regular hardware system. Maybe this is the
reason.
I'll try what you suggest!
regards,
Baofu Qiao
On 11/26/2010 04:07 PM, Roland Schulz wrote:
Baofu,
what operating system are you using? On what file system do you try to
store
the log file? The error (should) mean that the file system you use
doesn't
support locking of files.
Try to store the log file on some other file system. If you want you can
still store the (large) trajectory files on the same file system.
Roland
On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao<qia...@gmail.com> wrote:
Hi Carsten,
Thanks for your suggestion! But because my simulation will be run for
about 200ns, 10ns per day(24 hours is the maximum duration for one
single job on the Cluster I am using), which will generate about 20
trajectories!
Can anyone find the reason causing such error?
regards,
Baofu Qiao
On 11/26/2010 09:07 AM, Carsten Kutzner wrote:
Hi,
as a workaround you could run with -noappend and later
concatenate the output files. Then you should have no
problems with locking.
Carsten
On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote:
Hi all,
I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is
about
30% slower than 4.5.3. So I really appreciate if anyone can help me with
it!
best regards,
Baofu Qiao
于 2010-11-25 20:17, Baofu Qiao 写道:
Hi all,
I got the error message when I am extending the simulation using the
following command:
mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi
pre.cpt -append
The previous simuluation is succeeded. I wonder why pre.log is
locked,
and the strange warning of "Function not implemented"?
Any suggestion is appreciated!
*********************************************************************
Getting Loaded...
Reading file pre.tpr, VERSION 4.5.3 (single precision)
Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010
-------------------------------------------------------
Program mdrun, VERSION 4.5.3
Source code file: checkpoint.c, line: 1750
Fatal error:
Failed to lock: pre.log. Function not implemented.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"It Doesn't Have to Be Tip Top" (Pulp Fiction)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 64
gcq#147: "It Doesn't Have to Be Tip Top" (Pulp Fiction)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec has exited due to process rank 0 with PID 32758 on
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