[Bioclusters] Taking a poll

[Glen Otero]

Hi Anand-

Thanks for responding to my bioclusters poll! You should be receiving  
your ThinkGeek gift certificate via email soon.

Thanks again!

Glen

On Jun 22, 2005, at 8:14 PM, Anand S Bisen wrote:

>
>
> Glen Otero wrote:
>
>> Greetings biocluster intelligentsia!
>> I have some new BioBrew (biobrew.org) feature ideas that I'd like  
>> to  scrutinize against the collective intelligence and experience  
>> of this  community. I've written a few information gathering  
>> questions that,  if answered, ought to help me judge the  
>> feasibility of my ideas.  What's in it for those of you who take a  
>> few minutes to respond?  Well, the first 20 folks to email me  
>> (offline at  gotero at linuxprophet.com) with sufficient answers to  
>> *all* 20  questions will receive a $10 ThinkGeek gift certificate.  
>> The next 10  people with answers to all the questions will receive  
>> a $5 ThinkGeek  gift certificate. The questions are below with  
>> example answers in  parentheses (sometimes). Be as detailed as you  
>> like, because more  detailed answers will win in the event of a  
>> tie breaker : )
>> Thanks for your help!!-- Glen
>> 1) What is the size of your Linux cluster? (e.g. 128 nodes)
>>
> 48 nodes
>
>
>> 2) What is the compute node architecture? (e.g. dual 3GHz Xeon,  
>> dual  Opteron)
>>
> dual 3.2GHz Xeon
>
>
>> 3) Do your compute nodes have local hard drives or are they diskless?
>>
> Local hard disk
>
>
>> 4) What is the cluster interconnect? (e.g. GigE)
>>
> GigE
>
>
>> 5) What application(s) primarily run on your cluster (e.g. BLAST,  
>> HMMER)
>>
> sequest, tandem, statistical/mathematical ad-hoc scripts
>
>
>> 6) If BLAST is running on your cluster, describe the type of  
>> BLAST  jobs (e.g. blastn- genome vs. genome, blastn-genome  
>> annotation with  ESTs)
>>
> NA
>
>
>> 7) What type of cluster filesystem is in use on your cluster?  
>> (e.g.  NFS, GFS, proprietary)
>>
> NFS
>
>
>> 8) If you use NFS, is your NFS server the same as the cluster  
>> head  node or is it a separate server?
>>
> Seperate
>
>
>> 9) If you use NFS, what type of machine is your NFS server? (e.g.   
>> dual Xeon Linux Box w/ x number of yGB hard drives)
>>
> Quad Intel Xeon 3.0 GHz with Dual Path Fiber Connect IBM  
> TotalStorage FAStT600 Turbo
>
>
>
>> 10) What is the ratio of NFS servers to compute nodes in your  
>> cluster?
>>
> 8:48
>
>
>> 11) How do you benchmark the throughput of your NFS server, i.e.  
>> what  application(s) do you use to stress the NFS server and what  
>> tool(s)  do you use to measure throughput?
>>
> bonnie++
>
>
>> 12) If you have a NAS/SAN, what type of machine(s) are they?  
>> (e.g.  NetApp w/ x number of yGB hard drives)
>>
> In all i have around 3TB of storage attached with this cluster  
> consisting of 36 Fiber Channel Hard Disks
>
>
>> 13) What is the ratio of NAS servers to compute nodes in your  
>> cluster?
>>
> 1:48
>
>
>> 14) What is the throughput of your NAS server(s)/SAN?
>>
> around 35-39 MB/s
>
>
>> 15) How do you benchmark the throughput of your NAS server/SAN,  
>> i.e.  what application(s) do you use to stress the servers and  
>> what tool(s)  do you use to measure throughput?
>>
>
>
>> 16) Are you satisfied overall with your cluster filesystem solution?
>>
> Yes/No
>
>
>> 17) What are the two biggest problems you have with your cluster   
>> filesystem solution?
>>
> Bottleneck is NFS due to excessive amount of file I/O over NFS
>
>
>> 18) With regard to cluster filesystems, what would you do  
>> differently  when building your next cluster? (e.g. increase NFS  
>> servers/compute  node ratio, different filesystem)
>>
> Try different file systems
>
>
>> 19) What NFS server/compute node or NAS-SAN/compute node ratio  
>> will  you aim for with the next cluster you build or upgrade?
>>
> Still evaluating
>
>
>> 20) If necessary, do you mind if Glen emails you offline to seek   
>> clarification on some of your answers? (Answering "Yes" is not   
>> necessary to be eligible for a gift certificate).
>>
> Feel free
>
>
>
> thanks
>
> Anand
>
>
>
> ---
> Anand Singh Bisen
> http://www.abisen.com
>
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>