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  • #16
    Originally posted by What_Da_Seq View Post
    Our 2 Xeon quad core, 32GB, 1.5TB Raid5 cost less than 3grand. You have to shop around for the memory and hard drives. And don't forget if you order a tower server the FANs are seriously loud.
    The question is what computations are you running with this hardware?
    How are the hdds? SAS? SATA? rpms?

    That machine can probably compute the alignments of a full illumina FC or
    full SOLiD slide (Fragments -- illumina:75bp/SoLiD:50bp -- human data -- bfast recommended indexes/parameters) in 3 or 4 days?

    Now if you add faster Cpus, faster FSB and _specially_ faster hdds you can reduce that to one day. Is it worth it 3k more to get your computation
    done in 1 day instead of 3 or 4? It depends.

    P.S: of course computing this in your cluster is the way to go. But we are talking here about single machine performance.
    -drd

    Comment


    • #17
      Originally posted by drio View Post
      The question is what computations are you running with this hardware?
      How are the hdds? SAS? SATA? rpms?

      That machine can probably compute the alignments of a full illumina FC or
      full SOLiD slide (Fragments -- illumina:75bp/SoLiD:50bp -- human data -- bfast recommended indexes/parameters) in 3 or 4 days?

      Now if you add faster Cpus, faster FSB and _specially_ faster hdds you can reduce that to one day. Is it worth it 3k more to get your computation
      done in 1 day instead of 3 or 4? It depends.

      P.S: of course computing this in your cluster is the way to go. But we are talking here about single machine performance.
      @drio: to give you an idea about performance on our setup, please see http://www.clcmachine.com/benchmarks.php Note, that the benchmarks are on our SIMD accelerated softwares, so it may not be immediately comparable to e.g. other assemblers.

      Because of the heavy IO fast discs for temporary storage help a lot.

      Regarding your PS, we can comfortably handle all our computational needs by just using single machines with specs as discussed in this thread. To us there has been no need for large clusters or clouds yet.

      Cheers

      Roald

      ********* Disclaimer: I work for CLC bio ************

      Comment


      • #18
        Originally posted by Roald View Post
        Hi Najim,

        Due to the large file sizes there is a lot of IO going on in NGS bioinformatics analysis. For this reason it is a good idea to purchase a machine with fast discs.

        For inspiration, you can have a look at the specs of the machine we have put together:


        Cheers

        Roald Forsberg

        ************Disclaimer: I work at CLC bio*************
        I find that you can configure a similar box at dell.com. I think the cost is abt US$10,000+

        Comment


        • #19
          Originally posted by nilshomer View Post
          Get your systems administrator to give you some space on one of their racks (another reason to be nice to sys-admins). You should be able to get such a system (depending on how many Us and vendor) for $2,500 - $5,000.
          I would like you to sell that to me for $5,000

          I am in the process of shopping around, too. 48GB of RAM alone is at least $3,500.

          Comment


          • #20
            Originally posted by ymc View Post
            I would like you to sell that to me for $5,000

            I am in the process of shopping around, too. 48GB of RAM alone is at least $3,500.
            Feel free to PM me. I just looked at the website of a vendor (the ram is <$2500). I would make ~$500 dollars selling you that (intel 5550 and 48GB of RAM)) for $5,000

            Comment


            • #21
              Originally posted by nilshomer View Post
              Feel free to PM me. I just looked at the website of a vendor (the ram is <$2500). I would make ~$500 dollars selling you that (intel 5550 and 48GB of RAM)) for $5,000
              Hmm... I was talking about the whole system for $5,000. Not just CPUs and RAMs.

              But is your $2,500 RAM 6 x 8GB DDR3-1333 ECC Regsitered???

              Maybe I can pm you what I want and you tell me how much you can get it.

              Comment


              • #22
                Originally posted by ymc View Post
                Hmm... I was talking about the whole system for $5,000. Not just CPUs and RAMs.

                But is your $2,500 RAM 6 x 8GB DDR3-1333 ECC Regsitered???

                Maybe I can pm you what I want and you tell me how much you can get it.
                Note: I do not work for a vendor etc. I am just a happy customer .

                Go to http://www.siliconmechanics.com/
                Click "Products"
                Click "Rackform Rackmount Servers"
                Under "Chipset", click "Intel 5550 & 5520".
                Under "Max Memory", click "48GB".
                Now click the computer you want, say the "Rackform iServ R304.v2".
                Under "RAM", select "48GB".
                All for under $5K USD.

                Comment


                • #23
                  Originally posted by nilshomer View Post
                  Note: I do not work for a vendor etc. I am just a happy customer .

                  Go to http://www.siliconmechanics.com/
                  Click "Products"
                  Click "Rackform Rackmount Servers"
                  Under "Chipset", click "Intel 5550 & 5520".
                  Under "Max Memory", click "48GB".
                  Now click the computer you want, say the "Rackform iServ R304.v2".
                  Under "RAM", select "48GB".
                  All for under $5K USD.
                  Thanks for the link. But after I selected 2 x X5550 and 48GB. Then it becomes $5,834. But this system doesn't allow me to add RAID card, so I can't build the SAS RAID like the CLC machine.

                  It does seem to me it is true that 6 x 8GB ECC Registered of an unknown brand there is about $2,500 though.

                  Comment


                  • #24
                    Originally posted by nilshomer View Post
                    Note: I do not work for a vendor etc. I am just a happy customer .

                    Go to http://www.siliconmechanics.com/
                    Click "Products"
                    Click "Rackform Rackmount Servers"
                    Under "Chipset", click "Intel 5550 & 5520".
                    Under "Max Memory", click "48GB".
                    Now click the computer you want, say the "Rackform iServ R304.v2".
                    Under "RAM", select "48GB".
                    All for under $5K USD.
                    I choose R346.v2 and now I able to replicate most of that CLC machine except for the graphics card. It gave me a quote of $9,885

                    Comment


                    • #25
                      Still, I find that hardware at that site is about 10% lower than the market price. I think it is worth looking into.

                      Comment


                      • #26
                        Originally posted by ymc View Post
                        I choose R346.v2 and now I able to replicate most of that CLC machine except for the graphics card. It gave me a quote of $9,885
                        Originally posted by ymc View Post
                        Still, I find that hardware at that site is about 10% lower than the market price. I think it is worth looking into.
                        If it is about the price of the CLC machine, does the CLC machine come with any value added? If so, get the CLC machine.

                        Comment

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