9 Replies Latest reply on Jul 16, 2011 7:28 AM by

    Decisions for Computational Chemistry

    rvm

      Hello everyone,

       

      I am an undergraduate student learning computational chemistry techniques. In order to continue my projects, I need to build a machine dedicated to my calculations.

       

      The programs that I use to carry out these calculatoins (AMPAC and Gaussian 09) are very resource heavy (especially G09) and I would benefit a lot from having a very high end machine.

       

      I am wondering whether I should build a machine that utilizes two Xeon processors, which would allow me a max of 144 GB of memory down the road, or whether a machine that runs one Core-i7 six-core processor with 48 GB would be more advisable. Do any Core-i7/motherboard combinations allow for something like 64 GB of memory?

       

      Thanks,

       

      RVM

        • 1. Re: Decisions for Computational Chemistry
          mechbob

          Contact Intel sales about their Workstations , They have machines ready built for just what you need . If not look at the Dell workstations.

          • 2. Re: Decisions for Computational Chemistry
            rvm

            Hi Robert. Fantastic name! (It is my name too)

             

            This does not suit me.

             

            I have a limited budget due to grants limitations, and the cost of a dell workstation almost completely finishes off what I have left in my grant. Other sources of funding are available of course, but I do not want to take up a part of someone's budget if there is the alternative that another machine could do the job.

             

            Besides which, the memory included in Dell's workstations is 12 GB -- not nearly enough to do the kinds of calculations I do.

             

            Xeon vs Core i7?

             

            RVM

            • 3. Re: Decisions for Computational Chemistry
              Doc_SilverCreek

              Xeon if you want the max.

              The i7 will do for most jobs, but if you get into some real heavy computational work, cores count.

               

              Dual Xeon hyperthreaded 6 cores processors will get you more raw power than your get from any single processor system.

              (at least till Moore's law kicks in and another generation of processors hit the market.) .

              taskmgr.bmp

              (you can tell surfing the internet is not working this system very hard)

               

              If the budget is of greater concern and space and power consummation is not, you might consider a small computer cluster.

              For the cost of a nicly configured Dual XEON workstation, you could pick up 4 or 6 single CPU desktops to run in a cluster.

              Set-up does require a bit more and you would need to make sure the applications you want to use would be supported in a cluster configuration.

              As one person stated, "I bought the S5520SC workstation because I don't want to be a computer geek,I just want to use the darn thing."

              • 4. Re: Decisions for Computational Chemistry
                Doc_SilverCreek

                Hmm, you may also want to check out http://www.gaussian.com/g_prod/comp_req.htm

                 

                "The multiprocessor version of G09W is limited to 4 processors (or cores). Similarly, any individual node within a cluster/network parallel job can take advantage of at most 4 processors/cores (e.g., a parallel calculation across 2 dual quad-core computer systems will require 4 workers: 2 per system)."

                 

                Which if i am reading correctly, limits this application to 4 Cores, 32bit mode, 2 GB of RAM and 16 GB of disk regardless of how munch you have in the system under windows unless you are clustering. (Most windows laptop's exceeds this now days.) 

                • 5. Re: Decisions for Computational Chemistry
                  rvm

                  Impressive.

                   

                  In any case...

                   

                  Gaussian 09 allows me to have multiple computers running the same calculation through a program they call Linda. However, this will only work well with a very high network throughput between them. Since I might not be able to set this up (due to cost), the benefits of parallel computing might be outweighed by the detriments of slow networking.

                   

                  A single dedicated machine is the best way to go with my budget. I can afford myself a machine with a Core i7 processor, 48 GB of memory, etc. I can muster funding for a Xeon machine. I am just not sure which of the two processors is best.

                   

                  RVM

                  • 6. Re: Decisions for Computational Chemistry
                    rvm

                    That is only true for Windows and G09W. We will be running Red Hat Linux Enterprise for Workstations.

                     

                    I already have a laptop which I use for calculations. It isn't a great machine, and it's done okay with semi-empirical calculations. However, these empirical calculations require much higher stats with, at minumum, a 48 GB memory capacity and 6 cores.

                     

                    I am debating whether it is worth the extra expense --- in terms of processing power/cost ratio --- to go with a machine that runs Xeon, or to go with a machine that runs Core i7.

                     

                    RVM

                    • 7. Re: Decisions for Computational Chemistry
                      mechbob

                      Buy the way , If you don't mind asking what is your budget on this machine ?? that way I could know if it's even posible to build a machine within your budget , you know what you are talking about if you build this it's probable going to be $4grand or more.

                      • 8. Re: Decisions for Computational Chemistry
                        mechbob

                        The SuperMicro 7046A-T would be a good place to start. Barebones at Newegg about $900.00.

                        • 9. Re: Decisions for Computational Chemistry

                          It seems that you are limited to only a quad-core processor and 2 gb max ram if you have the windows version with specs shown below.

                           

                          Gaussian 09W

                          Gaussian 09W is a complete implementation of Gaussian 09 for the Windows environment. Be aware that Gaussian 09W is a 32-bit application. It is accordingly limited to 2 GB of RAM and 16 GB of disk regardless of how much memory is available on the system.

                          Pricing Information

                          Recommended Minimum System Requirements

                          Processor: Intel Pentium 4, Celeron, Xeon, AMD Athlon, AMD Phenom II. AMD Phenom/Barcelona processors with B2 stepping are not currently supported. G09W runs in 32-bit mode on 64-bit processors.
                          Operating System:

                          requirements for G09W alone: Microsoft Windows XP, Server 2003, Vista (Home Basic, Business, Ultimate), Windows 7
                          requirements for G09W Cluster/Network Parallel versions: Microsoft Windows XP or Vista Ultimate
                          Memory (RAM): 1 GB
                          Disk: 200 MB (G09W storage); and 500 MB or more (scratch space)
                          Other: CD-ROM drive; Mouse

                           

                          Multiprocessor and Cluster/Network Parallel Versions

                          The multiprocessor version of G09W is limited to 4 processors (or cores). Similarly, any individual node within a cluster/network parallel job can take advantage of at most 4 processors/cores (e.g., a parallel calculation across 2 dual quad-core computer systems will require 4 workers: 2 per system).