<div>Hi,</div><div><br></div><div>we use Lustre too and it doesn't cause any problem. I found this message on the Lustre list:</div><div><a href="http://lists.lustre.org/pipermail/lustre-discuss/2008-May/007366.html" target="_blank">http://lists.lustre.org/pipermail/lustre-discuss/2008-May/007366.html</a></div>
<div><br></div><div>And according to your mount output, lustre on your machine is not mounted with the flock or localflock option. This seems to be the reason for the problem. Thus if you would like to run the simulation directly on lustre you have to ask the sysadmin to mount it with flock or localflock ( I don't recommend localflock. It doesn't guarantee the correct locking). </div>
<div><br></div><div>If you would like to have an option to disable the locking than please file a bug report on bugzilla. The reason we lock the logfile is: We want to make sure that only one simulation is appending to the same files. Otherwise the files could get corrupted. This is why the locking is on by default and currently can't be disabled. </div>
<div><br></div><div>Roland</div><div><br></div><br><div class="gmail_quote">On Fri, Nov 26, 2010 at 3:17 PM, Baofu Qiao <span dir="ltr"><<a href="mailto:qiaobf@gmail.com" target="_blank">qiaobf@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
What Roland said is right! the lustre system causes the problem of "lock". Now I copy all the files to a folder of /tmp, then run the continuation. It works!<br>
<br>
Thanks!<br>
<br>
regards,<br>
<br>
<br>
$于 2010-11-26 22:53, Florian Dommert 写道:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-----BEGIN PGP SIGNED MESSAGE-----<br>
Hash: SHA1<br>
<br>
To make things short. The used file system is lustre.<br>
<br>
/Flo<br>
<br>
On 11/26/2010 05:49 PM, Baofu Qiao wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Roland,<br>
<br>
The output of "mount" is :<br>
/dev/mapper/grid01-root on / type ext3 (rw)<br>
proc on /proc type proc (rw)<br>
sysfs on /sys type sysfs (rw)<br>
devpts on /dev/pts type devpts (rw,gid=5,mode=620)<br>
/dev/md0 on /boot type ext3 (rw)<br>
tmpfs on /dev/shm type tmpfs (rw)<br>
none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw)<br>
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)<br>
172.30.100.254:/home on /home type nfs<br>
(rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.254)<br>
172.30.100.210:/opt on /opt type nfs<br>
(rw,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210)<br>
172.30.100.210:/var/spool/torque/server_logs on<br>
/var/spool/pbs/server_logs type nfs<br>
(ro,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.210)<br>
none on /ipathfs type ipathfs (rw)<br>
172.31.100.222@o2ib,172.30.100.222@tcp:172.31.100.221@o2ib,172.30.100.221@tcp:/lprod<br>
on /lustre/ws1 type lustre (rw,noatime,nodiratime)<br>
172.31.100.222@o2ib,172.30.100.222@tcp:172.31.100.221@o2ib,172.30.100.221@tcp:/lbm<br>
on /lustre/lbm type lustre (rw,noatime,nodiratime)<br>
172.30.100.219:/export/necbm on /nfs/nec type nfs<br>
(ro,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)<br>
172.30.100.219:/export/necbm-home on /nfs/nec/home type nfs<br>
(rw,bg,tcp,nfsvers=3,actimeo=10,hard,rsize=65536,wsize=65536,timeo=600,addr=172.30.100.219)<br>
<br>
<br>
On 11/26/2010 05:41 PM, Roland Schulz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Baofu,<br>
<br>
could you provide more information about the file system?<br>
The command "mount" provides the file system used. If it is a<br>
network-file-system than the operating system and file system used on the<br>
file server is also of interest.<br>
<br>
Roland<br>
<br>
On Fri, Nov 26, 2010 at 11:00 AM, Baofu Qiao<<a href="mailto:qiaobf@gmail.com" target="_blank">qiaobf@gmail.com</a>> wrote:<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Roland,<br>
<br>
Thanks a lot!<br>
<br>
OS: Scientific Linux 5.5. But the system to store data is called as<br>
WORKSPACE, different from the regular hardware system. Maybe this is the<br>
reason.<br>
<br>
I'll try what you suggest!<br>
<br>
regards,<br>
Baofu Qiao<br>
<br>
<br>
On 11/26/2010 04:07 PM, Roland Schulz wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Baofu,<br>
<br>
what operating system are you using? On what file system do you try to<br>
<br>
</blockquote>
store<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
the log file? The error (should) mean that the file system you use<br>
<br>
</blockquote>
doesn't<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
support locking of files.<br>
Try to store the log file on some other file system. If you want you can<br>
still store the (large) trajectory files on the same file system.<br>
<br>
Roland<br>
<br>
On Fri, Nov 26, 2010 at 4:55 AM, Baofu Qiao<<a href="mailto:qiaobf@gmail.com" target="_blank">qiaobf@gmail.com</a>> wrote:<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Carsten,<br>
<br>
Thanks for your suggestion! But because my simulation will be run for<br>
about 200ns, 10ns per day(24 hours is the maximum duration for one<br>
single job on the Cluster I am using), which will generate about 20<br>
trajectories!<br>
<br>
Can anyone find the reason causing such error?<br>
<br>
regards,<br>
Baofu Qiao<br>
<br>
<br>
On 11/26/2010 09:07 AM, Carsten Kutzner wrote:<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
as a workaround you could run with -noappend and later<br>
concatenate the output files. Then you should have no<br>
problems with locking.<br>
<br>
Carsten<br>
<br>
<br>
On Nov 25, 2010, at 9:43 PM, Baofu Qiao wrote:<br>
<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I just recompiled GMX4.0.7. Such error doesn't occur. But 4.0.7 is<br>
<br>
</blockquote></blockquote></blockquote></blockquote>
about<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote></blockquote>
30% slower than 4.5.3. So I really appreciate if anyone can help me with<br>
<br>
</blockquote></blockquote>
it!<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
best regards,<br>
Baofu Qiao<br>
<br>
<br>
于 2010-11-25 20:17, Baofu Qiao 写道:<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I got the error message when I am extending the simulation using the<br>
<br>
<br>
</blockquote></blockquote></blockquote>
following command:<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
mpiexec -np 64 mdrun -deffnm pre -npme 32 -maxh 2 -table table -cpi<br>
<br>
<br>
</blockquote></blockquote></blockquote>
pre.cpt -append<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The previous simuluation is succeeded. I wonder why pre.log is<br>
<br>
</blockquote></blockquote></blockquote></blockquote></blockquote>
locked,<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote></blockquote></blockquote>
and the strange warning of "Function not implemented"?<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Any suggestion is appreciated!<br>
<br>
*********************************************************************<br>
Getting Loaded...<br>
Reading file pre.tpr, VERSION 4.5.3 (single precision)<br>
<br>
Reading checkpoint file pre.cpt generated: Thu Nov 25 19:43:25 2010<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.3<br>
Source code file: checkpoint.c, line: 1750<br>
<br>
Fatal error:<br>
Failed to lock: pre.log. Function not implemented.<br>
For more information and tips for troubleshooting, please check the<br>
<br>
<br>
</blockquote></blockquote></blockquote>
GROMACS<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"It Doesn't Have to Be Tip Top" (Pulp Fiction)<br>
<br>
Error on node 0, will try to stop all the nodes<br>
Halting parallel program mdrun on CPU 0 out of 64<br>
<br>
gcq#147: "It Doesn't Have to Be Tip Top" (Pulp Fiction)<br>
<br>
<br>
<br>
<br>
</blockquote></blockquote></blockquote>
<br>
</blockquote></blockquote>
--------------------------------------------------------------------------<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD<br>
with errorcode -1.<br>
<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
You may or may not see output from other processes, depending on<br>
exactly when Open MPI kills them.<br>
<br>
<br>
<br>
</blockquote></blockquote></blockquote>
<br>
</blockquote></blockquote>
--------------------------------------------------------------------------<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote></blockquote></blockquote>
<br>
</blockquote></blockquote>
--------------------------------------------------------------------------<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
mpiexec has exited due to process rank 0 with PID 32758 on<br>
<br>
<br>
<br>
<br>
</blockquote>
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<br>
</blockquote>
<br>
- -- Florian Dommert<br>
Dipl.-Phys.<br>
<br>
Institute for Computational Physics<br>
<br>
University Stuttgart<br>
<br>
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<br>
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iEYEARECAAYFAkzwHkkACgkQLpNNBb9GiPkTDACfYqLGXTdRuyg5cZB82pEdF1L4<br>
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</blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>