Hi,
yes that helps a lot. One more question. What filesystem on hopper 2 are you
using for this test (home, scratch or proj, to see if it is Lustre or GPFS)
? And are you running the test on the login node or on the compute node?
Thanks
Roland
On Wed, Jun 8, 2011 at 1:17 PM, Dimitar Pachov
Hi,
On Thu, Jun 9, 2011 at 2:55 AM, Roland Schulz rol...@utk.edu wrote:
Hi,
yes that helps a lot. One more question. What filesystem on hopper 2 are
you using for this test (home, scratch or proj, to see if it is Lustre or
GPFS) ?
I used home.
And are you running the test on the login
Hi Dimitar,Thanks for the bug report. Would you mind trying the test program I attached on the same file system that you get the truncated files on?compile it with gcc testje.c -o testioSander
testje.c
Description: Binary data
On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:Hello,Just a quick
Hello,
On Wed, Jun 8, 2011 at 4:21 AM, Sander Pronk pr...@cbr.su.se wrote:
Hi Dimitar,
Thanks for the bug report. Would you mind trying the test program I
attached on the same file system that you get the truncated files on?
compile it with gcc testje.c -o testio
Yes, but no problem:
Hello,
Just a quick update after a few shorts tests we (my colleague and I) quickly
did. First, using
*You can emulate this yourself by calling sleep 10s before mdrun and see
if that's long enough to solve the latency issue in your case.*
doesn't work for a few reasons, mainly because it
Dimitar Pachov wrote:
Hello,
Just a quick update after a few shorts tests we (my colleague and I)
quickly did. First, using
/You can emulate this yourself by calling sleep 10s before mdrun and
see if that's long enough to solve the latency issue in your case./
doesn't work for a few
On 5/06/2011 12:31 PM, Dimitar Pachov wrote:
This script is not using mdrun -append.
-append is the default, it doesn't need to be explicitly listed.
Ah yes, very true.
Your original post suggested the use of -append was a problem. Why
aren't we seeing a script with mdrun
On Sun, Jun 5, 2011 at 2:14 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 5/06/2011 12:31 PM, Dimitar Pachov wrote:
As I said, the queue is like this: you submit the job, it finds an empty
node, it goes there, however seconds later another user with
higher privileges on that particular
On 5/06/2011 5:42 PM, Dimitar Pachov wrote:
On Sun, Jun 5, 2011 at 2:14 AM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 5/06/2011 12:31 PM, Dimitar Pachov wrote:
As I said, the queue is like this: you submit the job, it finds
an empty node, it
Dear Dimitar,
I'm following the debate regarding:
The point was not why I was getting the restarts, but the fact
itself that I was getting restarts close in time, as I stated in my
first post. I actually also don't know whether jobs are deleted or
suspended. I've thought that a job returned
On 5/06/2011 11:08 PM, Francesco Oteri wrote:
Dear Dimitar,
I'm following the debate regarding:
The point was not why I was getting the restarts, but the fact
itself that I was getting restarts close in time, as I stated in my
first post. I actually also don't know whether jobs are deleted
Two comments about the discussion:
1) I agree that buffered output (Kernel buffers - not application buffers)
should not affect I/O. If it does it should be filed as bug to the OS. Maybe
someone can write a short test application which tries to reproduce this
idea. Thus writing to a file from one
By the way, is this ever reviewed:
Your mail to 'gmx-users' with the subject
Re: [gmx-users] Why does the -append option exist?
Is being held until the list moderator can review it for approval.
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 4/06/2011 8
Hi,
On Jun 4, 2011, at 19:11, Dimitar Pachov dpac...@brandeis.edu wrote:
By the way, is this ever reviewed:
Your mail to 'gmx-users' with the subject
Re: [gmx-users] Why does the -append option exist?
Is being held until the list moderator can review it for approval
On Fri, 3 Jun 2011 18:26:17 -0400
Dimitar Pachov dpac...@brandeis.edu wrote:
If one uses that option and the run is restarted and is again
restarted before reaching the point of attempting to write a file,
then things are lost, and most importantly, the most important piece
of data, that being
On 5/06/2011 3:11 AM, Dimitar Pachov wrote:
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 4/06/2011 8:26 AM, Dimitar Pachov wrote
If this is true, then it wants fixing, and fast, and will get it
:-) However, it
On Sat, Jun 4, 2011 at 9:09 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 5/06/2011 3:11 AM, Dimitar Pachov wrote:
On Fri, Jun 3, 2011 at 9:24 PM, Mark Abraham mark.abra...@anu.edu.au
wrote:
On 4/06/2011 8:26 AM, Dimitar Pachov wrote
Here is an example:
Dear Dimitar:
to me, your posts have indeed appeared very aggressive. So much so
that there are probably many people who can help who have decided not
to bother due to what they perceive your tone to be.
On to the problem at hand: I agree with the previous suggestion that
you may have
At first, I thought the -append option of the mdrun command was great.
However, I don't think it is anymore and have actually started questioning
myself why it exists at the first place, and second, why has it become the
default option in the newest versions?
It is useless unless you run your
Well sometimes i run out of walltime when doing long simulations and append
helps me not to do any file management after restarting simulations from the
previous checkpoint.
On Fri, Jun 3, 2011 at 3:26 PM, Dimitar Pachov dpac...@brandeis.edu wrote:
At first, I thought the -append option of the
On 4/06/2011 8:26 AM, Dimitar Pachov wrote:
At first, I thought the -append option of the mdrun command was great.
However, I don't think it is anymore and have actually started
questioning myself why it exists at the first place, and second, why
has it become the default option in the
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