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Migration from Deimos to Atlas

Warning

This page is deprecated! Atlas is a former system!

Atlas is a different machine than Deimos, please have a look at the table:

Deimos Atlas
number of hosts 584 92
cores per host 2...8 64
memory [GB] per host 8...64 64..512
example benchmark: SciMark (higher is better) 655 584

A single thread on Atlas runs with a very poor performance in comparison with the 6 year old Deimos. The reason for this is that the AMD CPU codenamed "Bulldozer" is designed for multi-threaded use.

Modules

We have grouped the module definitions for a better overview. This is only for displaying the available modules, not for loading a module. All available modules can be made visible with module load ALL; module av.

Batch System

Although we are running LSF as batch system there are certain differences to the older versions known from Deimos and Mars.

The most important changes are:

  • Specify maximum runtime instead of a queue (-W <hh:mm>).
  • Specify needed memory (per process in MByte) with -M <memory per process in MByte>, the default is 300 MB, e.g. -M 2000.
Hosts on Atlas number per process/core user memory limit in MB (-M option)
nodes with 64 GB RAM 48 940
nodes with 128 GB RAM 24 1950
nodes with 256 GB RAM 12 4000
nodes with 512 GB RAM 8 8050
  • Jobs with a job runtime greater than 72 hours (jobs that will run in the queue long) will be collected over the day and scheduled in a time window in accordance with their priority.
  • Interactive Jobs with X11 tunneling need an additional option -XF to work (bsub -Is -XF -n <N> -W <hh:mm> -M <MEM> bash).
  • The load of the system can be seen with lsfview and lsfnodestat.

Atlas is designed as a high-throughput machine. With the large compute nodes you have to be more precise in your resource requests.

  • In ninety nine percent of the cases it is enough when you specify your processor requirements with -n <n> and your memory requirements with -M <memory per process in MByte>.
  • Please use -x ("exclusive use of a hosts") only with care and when you really need it.
  • The option -x in combination with -n 1 leads to an "efficiency" of only 1.5% - in contrast with 50% on the single socket nodes at Deimos.
  • You will be charged for the whole blocked host(s) within your CPU hours budget.
  • Don't use -x for memory reasons, please use -M instead.
  • Please use -M <memory per process in MByte> to specify your memory requirements per process.
  • Please don't use -R "span[hosts=1]" or -R "span[ptile=<n>]" or any other -R "..." option, the batch system is smart enough to select the best hosts in accordance with your processor and memory requirements.
  • Jobs with a processor requirement ‚ȧ 64 will always be scheduled on one node.
  • Larger jobs will use just as many hosts as needed, e.g. 160 processes will be scheduled on three hosts.

For more details, please see the pages on LSF.

Software

Depending on the applications we have seen a broad variety of different performances running binaries from Deimos on Atlas. Some can run without touching, with others we have seen significant degradations so that a re-compile made sense.

Applications

As a default, all applications provided by ZIH should run an atlas without problems. Please tell us if you are missing your application or experience severe performance degradation. Please include "Atlas" in your subject.

Development

From the benchmarking point of view, the best compiler for the AMD Bulldozer processor, the best compiler comes from the Open64 suite. For convenience, other compilers are installed, Intel 12.1 shows good results as well. Please check the best compiler flags at [this overview] developer.amd.com/Assets/CompilerOptQuickRef-62004200.pdf.

MPI parallel applications

Please note the more convenient syntax on Atlas. Therefore, please use a command like

bsub -W 2:00 -M 200 -n 8 mpirun a.out

to submit your MPI parallel applications.