Getting started with the "Emmy" cluster at RRZE

1. Login to the HPC machines at RRZE

Course logins for the HPC systems at RRZE are provided during the first exercise. You will get a password for your course account.

You will perform all of the benchmark work on the IvyBridge-EP Cluster "Emmy". Detailed information about login, file systems etc. can be found on the website:

Log into the cluster front-end machine of Emmy using

$ ssh -Y
$ ssh emmy

(substitute the "X...X" with the appropriate  account). Logging in is a two-step process because our clusters all have private IP addresses; our "dialog server" cshpc is the only machine that is visible from the internet. If you need visualization tools (LibreOffice, xmgrace, gnuplot), these are available on cshpc as well but not on the cluster frontends. 

Please do not perform memory-intensive test runs on the frontends or dialog servers as this will disturb user operations. Moreover, many users are active on the frontends and you will not get sensible performance data anyway.
Example code for the hands-on exercises can be found in the directory ~f35y0000. E.g., for copying the directory DIV to your home you can type: 

$ cp -a ~f35y0000/DIV ~
The descriptions of the exercises contain the names of the respective folders.

2. Compilers

On the Emmy cluster we use the Intel compiler suite. Usually the Intel compilers deliver higher performance than the GCC and we are quite familiar with their characteristics. To access the Intel compilers you first have to set up your environment correctly. Execute once per shell:
$ module load intel64
(you can also specify a version number; this will be required from time to time). This will set up the necessary PATH and other variables that you need to work with the Intel compilers. The compilers are called ifort (Fortran77/90), icc(C) and icpc (C++).

2.1 Recommended compiler switches

The Intel compilers have loads of command line options. We recommend to use -O3 -xHost -fno-alias. The option -help will give you a complete list. The standard options (-c, -g, -o etc.) are identical to GCC

3. Batch processing

Short test runs can be started directly on the Emmy frontends. However, for producing reliable benchmark results it is preferable to submit the jobs to the batch queue. The batch system accepts requests for resources (e.g., "6 nodes for 24 hours") and queues them according to some priority scheme. A job gets run, i.e. a previously specified shell script gets executed, when the resources are available and the batch system has chosen the job to be started. Some nodes of the Emmy cluster will be reserved for your exclusive use during tutorial hours. During the rest of the time, no CPUs are reserved, but you have a high priority. Apart from running a batch script (see below) and interactive testing on the frontends you can submit an interactive batch job which gives you, e.g., a shell on a compute node for some time. You can do this by typing:
$ qsub -l nodes=1:ppn=40,walltime=02:00:00 -I
This command will allocate a complete node (40 CPUs) for 2 hours. You should always request complete nodes so that you can do your benchmarks on a quiet machine. There will be no need to request more than one node for this course.

Clock frequency settings

If you want to get accurate timings in terms of processor cycles, you have to know the exact clock speed of the CPU. The Emmy processors have a nominal clock speed of 2.2 GHz, but "Turbo Mode" is enabled by default. This means that the CPU can "overclock" to some degree, depending on the number of active cores and the temperature. The highest possible clock speed is 3.0 GHz. In order to set the clock frequency to a specific (fixed) value you can specify a parameter at job submit time:
$ qsub -I -l nodes=1:ppn=40:f2.2,walltime=01:00:00 ...
In this example, the clock speed for all cores in this job would be set to 2.2 GHz. You can select from the following options: f2.2,f2.1,f2.0,f1.9,f1.8,f1.7,f1.6,f1.5,f1.4,f1.3,f1.2. The likwid-setFrequencies tool, as shown in the lecture, cannot be used on this production cluster.

3. LIKWID Tools

Use the command

$ module load likwid/4.3.2

to set up your shell environment for using the LIKWID tools. If you want to use likwid-perfctr you have to subnmit your job in a special way as to not interfere with system monitoring:

qsub -I -l nodes=1:ppn=40:f2.2:likwid,walltime=01:00:00 ...

Last modified: Wednesday, 7 November 2018, 9:51 PM