[Bioclusters] requesting help for computational server setup - bonnie output !

[karthik viswanathan]

Hi Joe:

I got a chance to run bonnie when the server was free. the output is

Version  1.03       ------Sequential Output------ --Sequential Input- --Random-
                    -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
Machine        Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
xxxxxxxx-xxxx 7440M  6352  91 27899   7 14508   4  6005  82 38493   5 336.1   0
                    ------Sequential Create------ --------Random Create--------
                    -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
              files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
                 16  2774  90 +++++ +++ +++++ +++  3231  98 +++++ +++  9226  91
xxxxxxxx-xxxx.xxx,7440M,6352,91,27899,7,14508,4,6005,82,38493,5,336.1,0,16,2774,90,+++++,+++,+++++,+++,3231,98,+++++,+++,9226,91

When Lucy and bonnie were running together the output was

Version  1.03       ------Sequential Output------ --Sequential Input- --Random-
                    -Per Chr- --Block-- -Rewrite- -Per Chr- --Block-- --Seeks--
Machine        Size K/sec %CP K/sec %CP K/sec %CP K/sec %CP K/sec %CP  /sec %CP
xxxxxxxx-xxxx 7440M  2779  39 28787   7 14079   5  1020   9 27275   6 330.7   2
                    ------Sequential Create------ --------Random Create--------
                    -Create-- --Read--- -Delete-- -Create-- --Read--- -Delete--
              files  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP  /sec %CP
                 16  1676  52 +++++ +++ +++++ +++  1143  36 +++++ +++  2983  35
xxxxxxxx-xxxx.xxx,7440M,2779,39,28787,7,14079,5,1020,9,27275,6,33
0.7,2,16,1676,52,+++++,+++,+++++,+++,1143,36,+++++,+++,2983,35

I am not sure how to interpret the result, but was expecting some values in Read
instead of ++++
Could you help me in interpreting this result.

Thanks for your help
karthik



> On Wed, 2003-09-17 at 16:41, karthik viswanathan wrote:
> > Hi Joe:
> > 
> > Thanks for ur reply. 
> > 
> > " T Get 3 newhe performance ..." 
> > this is a typo error, sorry about that. I am surprised how this got appended!
it
> > should have been
> > "The performance is not satisfactory ..."
> 
> :)
> 
> > The programs the client run mostly are
> > 
> > 1. LUCY  (http://www.tigr.org/software/)
> 
> Somewhat disk intensive.
> 
> > 2. GENESEQER 
(http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html)
> 
> More CPU intensive.
> 
> > I had ran hdparm
> > 
> > # /sbin/hdparm -tT /dev/sda2
> >  
> >  /dev/sda2: 
> > Timing buffer-cache reads: 128 MB in 0.25  seconds =512.00 MB/sec 
> > Timing buffered disk reads: 64 MB in 1.75 seconds = 36.57 MB/sec
> 
> Egad!  Thats low....
> 
> [root@squash landman]# hdparm -tT /dev/md0
>  
> /dev/md0:
>  Timing buffer-cache reads:   128 MB in  0.30 seconds =426.67 MB/sec
>  Timing buffered disk reads:  64 MB in  0.68 seconds = 94.12 MB/sec
> 
> These are two IDE drives in a software RAID0.
> 
> See if you can adjust the stripe unit on the hardware raid.  It would
> require rebuilding the raided file system though.  Also, look at using
> XFS rather than ext3.
> 
> One thing to do, while others are running, is to use vmstat.  Run
> 
> 	vmstat 1
> 
> in a window, and watch the state of the machine.  Read the man page for
> details on the fields.  
> 
> Joe
> -- 
> Joseph Landman, Ph.D
> Scalable Informatics LLC,
> email: landman@scalableinformatics.com
> web  : http://scalableinformatics.com
> phone: +1 734 612 4615
> 
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