Hi,
we use Lustre too and it doesn't cause any problem. I found this message on
the Lustre list:
http://lists.lustre.org/pipermail/lustre-discuss/2008-May/007366.html
And according to your mount output, lustre on your machine is not mounted
with the flock or localflock option. This seems to be th
Hi all,
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!
Thanks!
regards,
$于 2010-11-26 22:53, Florian Dommert 写道:
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To make things sho
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To make things short. The used file system is lustre.
/Flo
On 11/26/2010 05:49 PM, Baofu Qiao wrote:
> 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
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 b
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 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
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
Hi all,
I just made some tests by using gmx 4.5.1, 4.5.2 and 4.5.3. Neither of
them works on the continuation.
---
Program mdrun, VERSION 4.5.1
Source code file: checkpoint.c, line: 1727
Fatal error:
Failed to lock: pre.log. Already running simu
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 Qia
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 t
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 usin
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