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Acknowledging Zen Astrophysics If your work is astrophysics then please include the following sentence in the acknowledgements of your publications which have used ...
Setting up a new user account 1 The script newuser is used to set up a new user account. To run the script use: newuser username1 username2 ... The numeric ...
SPH SPH is a particle based compressible fluid dynamics code used to model star and planet formation. It is written in FORTRAN 77 and parallelized in both !OpenMP ...
MPI Correctness checking using Intel MPI version 4. The Intel MPI has the ability to perform correctness checking of MPI codes, which can detect errors and resource ...
To reopen any issue use the instructions at StayOrganised to reparent it to OpenIssues. JohnRowe 27 Jun 2007
JohnRowe 28 Jan 2008
Combining !OpenMP and MPI Some jobs will run efficiently using a combination of !OpenMP and MPI, but care needs to be taken to make sure that !OpenMP threads are correctly ...
Intel compilers and MPI library Compilers are available as part of the Intel Cluster Studio which can be enabled by loading ics2012 , ics2013 or ics2013sp1 modules ...
The mail SMTP agent is postfix, setting are changed in /etc/sysconfig/postfix Then run: SuSEconfig verbose /etc/init.d/postfix restart JohnRowe 31 ...
File Systems on Zen There are two file systems ( /home and /data ) on Zen where you can store files. All file systems are RAID, which offers some protection against ...
The University has a new HPC system called Isca. For more information please see the Isca Wiki (https://wiki.exeter.ac.uk/display/ISCA/Isca Wiki) or http://www.exeter ...
Job arrays When running a number of similar jobs on different nodes they can be collated into a job array (to run multiple jobs on the same node see MultipleSerialJobs ...
Linux and UNIX Resources Unix Tutorial from the University of Surrey Configuring your account You can configure your account by putting a file called .cshrc ...
Met Office Unified Model Background The UM (Met Office Unified Model) is a Global Circulation Model (GCM) we are adapting in collaboration with the UK Met Office ...
MKL version : 10.0.1.014 If when linking with libmkl lapack.so you get the error message: undefined reference to `mkl serv load dll' try adding lmkl core ...
MPInside Detailed MPI performance information is available from SGI's MPInside tool. To enable MPInside run module load MPInside on a compute node. If you are using ...
If you have a number of serial jobs to run you can run them simultaneously on one node. Each compute node has 12 cores so can run up to 12 copies of a serial program ...
Open a new issue JohnRowe 27 Jun 2007
OpenMP is a parallelisation method for processors and cores that share the same memory, i.e. in our case the twelve cores that live on a single node. The most common ...
Compiler Flags The Intel compilers have several flags which can help with detecting errors (e.g. out of bounds array access). ifort has a check all option which ...
Performance profiling If you want to make your application faster then you will probably need to profile it to find out where it spends most of its time. Profiling ...
This page describes problems encountered when porting code to Zen and when setting up codes to run using MPI. Multiple processes simultaneously writing to the same ...
post zen is an astrophysics group server which is separate from zen. If you need an account on post zen please contact Martyn Brake. This table shows the mapping ...
If you have a problem with a job on Zen first check the output from your job for errors, warnings or signs of unusual behaviour. If the problem seems to be a system ...
JohnRowe 09 Jan 2008
Profiling MPI This page describes how to use the Intel Trace Analyzer and Collector (ITAC) to profile MPI code which uses Intel MPI. ITAC is part of the Intel Cluster ...
Espresso version : 3.2.3 To compile espresso 3.2.3, load the modules mkl and fftw (make sure you also load these in your run file) and set the following environmental ...
About Zen Zen consists of diskless compute nodes each with twelve cores and 24GiB of RAM. The compute nodes communicate over a high speed infiniband network, with ...
Running Abinit This page describes how to build and run Abinit on Zen. How to build Abinit These instructions apply to version 5.8.4. First you will need to set ...
Running Jobs Work is submitted to Zen by putting it into a queuing system which allocates compute nodes to run your job. The qstat command is used to show what is ...
SGI's Message Passing Toolkit The Message Passing Toolkit (MPT) from SGI provides an alternative implementation of MPI. More information is available in the user ...
To display Greek letters in splash plot titles you will need to set the GIZA FONT environment variable e.g. setenv GIZA FONT helv This is required because the default ...
Command Name Description Notes ds9 FITS file viewer emacs Text editor eog Image viewer fcm Met Office configuration ...
Modules Much of our software is installed using the GNU module system. This allows us to have several versions of each package installed and the specific version ...
Astrophysics Wiki's Zen web
Never used a wiki before? WebHome is an on line wiki reference manual and WebHome is a scratch area you can use to practice in. Please help this wiki StayOrganised ...
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Zen Web Preferences The following settings are web preferences of the Zen web. These preferences overwrite the site level preferences in and , and can be ...
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