[Bioclusters] requesting help for computational server setup

[karthik viswanathan]

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/)
2. GENESEQER  (http://bioinformatics.iastate.edu/bioinformatics2go/gs/help.html)

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

This output i have run two days back. I have installed bonnie++, but a client is
running a program for the past two days so i couldnt run bonnie++ since i fear
the output wont be correct.

We dont have a software raid, but we have hardware raid. I am not sure about the
chunk size though. Will i be able to see this while system reboot or can i check
on linux ? 

Yes we are running NFS. The network speed is 100Mbs but the usage of the file
system is not often since the no of clients is 4.


Aaron:

 There are two hard SCSI hard disks of 146 GB each set on a RAID 0


Thanks
Karthik




Hi Karthik:
 
On Wed, 2003-09-17 at 15:04, karthik viswanathan wrote:
> We have a PowerEdge 4600 server running RedHat 9. The system spec is given 
> below. 
> [...]
> 
> The main usage of this server is for bioinformatics computational work.
Clients
> > run search/match C or C++ programs on this server through protocols like ssh.
> > The no of clients will be not more than 4. This server is also acting as a
file
> > server for the same clients. T Get 3 newhe performance is not satisfactory so
we
> 
> I can't parse this "T Get 3 newhe performance is not satisfactory".  I
> assume that you meant something like 
> 
> 	"To get 3 new ..." 
> 
> and then I lost the meaning.  Could you elaborate a bit more?
> 
> > are planning to do some modification in the configuration. One of our plan is
> > promote a client workstation(dell precision-340, 1.5 GHz & 1GB ram) to a file
> > server and switch the two SCSI hard disk from the PowerEdge server to this
> > workstation. Add 3 new SCSI hard disk (37 GB) to the PowerEdge server and set
a
> > RAID 0, if possible also add a second identical processor to the server.
> > 
> > We are interested to know if this will improve the performance of the
> > computational server. Also it would be helpful if you could suggest any other
> > alternatives for improving the computational performance for bioinformatics
> > work. If any of you have poweredge 4600 please share your experience and ur
> 
> Most important questions:
> 
> 1) what software are you running, what type of inputs, what size data
> sets
> 
> 2) have you run any of the standard system performance viewing tools?  
> 
> 3) what are the contents of your /etc/raidtab if you are using a
> software RAID0, and if not, what is the chunk size on the hardware
> RAID0?
> 
> 4) are you running NFS?  What is your network speed?  What are the
> chipsets?
> 
> Initial observations:
> 
> 1) ext3 is not as good as some of the other file systems for specific
> work loads.  It might be worth looking into XFS
> 
> 2) many bioinformatics tools are great with a divide and conquer
> approach.  If we understood what tools you are running this might help
> facilitate this discussion.
> 
> > system configuration. Suggestions on disk partitioning, kernel and file system

> > to use will also be helpful
> 
> Lots of tuning possibilities, but we don't know where your systems hot
> spots are yet.
> 
> > 
> > Thanks for your time and help
> > Karthik
> > 
> > 
> > PS: We are more interested to improve the computational power than file
handling!
> 
> Sometimes the two are very much related.
> 
> 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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