QUESTION: what about the speed and size of the scratch filesystem? NFS ok? global/parallel/clustered filesystem? current thinking is to have one massive scratch space and another for home directories served from SAN underneath all nodes. basically we fiber mount under one work node, the I/O node, and NFS mount from there to all others.
Generic responses of similar users.
|What applications do you plan to run on the Cluster? Is it home grown or third party. Please list some typical application names.||Accelrys InsightII||Matlab $$$||Matlab and homegrown applications.||AMBER, NAMD||C code. Also Gromacs, CHARMM, AMBER||“Gaussian”|
|For each application, is the application written in C, C++, or f90? Any particular compiler or packages you would need to use?||mex,mcc||C, C++ or Fortran $$$||C||Fortran + Linda $$$|
|Is your code parallel?||no||yes||10%||yes|
|Does the application require high interprocessor communication (i.e. Does your code benefit from using low latency interconnect or are these independent calculations that need to run on many processors)?||yes, low latency required||low latency, yes||4 8-core nodes + SMP|
|Does the application use MPI ?||yes||yes||no (Linda)|
|If MPI, how many nodes can the code can take advantage of, and with what interconnects (IB, myrinet or GE), and what is the memory requirement per core?||typical 16 to 32 nodes (scales to 100's), myrinet, 1 GB per node||<200MB||4 nodes with 2 quad-core processors and 16 - 32 GB ram per node|
|Does the Application use OPENMP, if yes how many CPU's does the application scale to? Does it use large amounts of shared memory? How large?||no||up to 32 cpus (6 nodes), up to 128 gb ram|
|Is the application data intensive or CPU intensive?||both||some data, some cpu||cpu||cpu||cpu, some arrays > 100 gb|
|Is the application 64-bit?||yes||no||32 or 64||32 or 64||64|
|Is the application integer or FP intensive?||some, FP yes||FP||FP||FP|
|RAM needed per processor? Amount of storage space required?||1GB (storage or ram?)||512 MB/cpu, 2 GB storage/run||Usually <200 MB, some 4 GB (ram?)||min 2 gb/core (?), scratch files 1,000 GB|
|Which Scheduling software does user prefer - LSF, PBS or SGE?||any||lsf or pbs, no pref|