{{{ #!access #allow(DOWNLOADS_VIEW) = idefix user documentation = [[Image(idefix.png,nolink,400px,right)]] == System overview == || hostname ||idefix || || CPU architecture ||Intel Xeon Haswell || || CPU model ||E7-4850 v4 || || # CPU ||4 || || Processor cores / CPU ||16 || || Threads / CPU ||32 || || Total processor cores ||64 || || CPU clock ||2.1GHz || || CPU peak ||2150 GFlop/s || || L1d/L1i/L2/L3 cache ||32K/32K/256K/40960K || || RAM ||256GB DDR4 || || Harddisk ||1.6 TB SSD PCIe3 (/work) || || ||0.5 TB SSD SATA (/) || || ||2.0 TB SAS 7.2K (/data) || == Access and user environment == '''idefix''' can be accessed via: {{{ ssh -X replace_by_your_idefix_username@idefix.muk.uni-hannover.de or ssh -X replace_by_your_idefix_username@130.75.105.239 }}} Create an ssh key on your local PC, and copy it to idefix using the command:\\\\ {{{ ssh-copy-id -i replace_by_your_local_path_to/.ssh/id_dsa.pub replace_by_your_idefix_username@130.75.105.239 }}} Add this user login script file [attachment:.myprofile .myprofile] to your $HOME directory on '''idefix'''. The file contains the following lines: {{{ #Required software modules for running PALM module load intel-compiler/2017.1.132 module load mvapich2/2.2/intel module load fftw/3.3.6-pl1/mvapich2-intel module load hdf5-parallel/1.10.0-patch1/intel module load netcdf4_hdf5parallel/4411c_443f/intel #To use the PALM scripts, the PATH variable has to be extended and the environment variable PALM_BIN has to be set export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS #Increase stack size to unlimited, otherwise large runs may abort ulimit -s unlimited }}} You may have to login again in order to activate these settings. \\ == Installation of PALM == To download and install the latest PALM version, follow the first steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Packageinstallation advanced installation procedure] as described on the PALM website. The [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/automatic automatic installer] will be available soon. Following steps also need to be carried out and are slightly different to those described on the PALM website. With the automatic installer, the following steps will be carried out automatically. (1) Copy '''idefix'''-specific palmbuild/palmrun configuration file (available from r2523) to your working directory: {{{ cp $HOME/palm/current_version/trunk/SCRIPTS/.palm.config.idefix $HOME/palm/current_version/. }}} Besides many other things, this file contains typical installation parameters like compiler name, compiler options, etc. In this file, enter your '''idefix''' user name at locations ''''.\\\\ '''Warning: When editing the configuration file, please NEVER use the TAB key. Otherwise, very confusing errors may occur when palmrun is executing.'''\\\\ (2) Compilation of utilities and source code: After modifying the configuration file, helper programs and PALM code are compiled by executing {{{ palmbuild -c idefix }}} (3) Installation verification: Follow the steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Installationverification verification procedure] as described on the PALM website.\\ (4) Start a simulation ---- '''NOTE: Jobs must be started using the batch system (see below), otherwise users might block each others simulation''' ---- To start a PALM run in batch mode (palmrun option -b), use this command and replace the <..>: {{{ palmrun -r -c idefix -a "d3#" -X -T -m -t -b }}} * -X | max. 64 * -T | =X, since idefix has only one node * -t | max. 43200 (s) The graphical user interface [https://palm.muk.uni-hannover.de/trac/wiki/doc/app/palmrungui palmrungui] can be used to create a palmrun command line for starting a selected PALM simulation. == Batch system == The Portable Batch System (PBS, version PBSPro14) is designed to manage the distribution of batch jobs and interactive sessions across the available nodes in the cluster. This is necessary to ensure an efficient use of the available computing resources among the users. PBS is available on '''idefix'''. The required settings for using the PBS are already included in the configuration file {{{.palm.config.idefix}}}.\\\\ The status of a queued job can be obtained via the command '''qstat'''. Further relevant commands are: || '''Command''' || '''Description''' || || pbsnodes || List the status and attributes of all nodes in the cluster || || qsub || Submit a job || || qdel || Delete a batch job || || qsig || Send a signal to batch job || || qhold || Hold a batch job || || qrls || Release held jobs || || qrerun || Rerun a batch job || || qmove || Move a batch job to another queue || || qstat || Show status of batch jobs || || qselect || Select a specific subset of jobs || || qalter || Alter a batch job || || qmsg || Send a message to a batch job || Attached to this page is a [attachment:pbs_quickguide.pdf quickstart guide], as well as an extended [attachment:PBSRefGuide14.2.pdf reference guide] for PBS and the available options. == File systems and data management == == Software == (1) Compiler, MPI, NetCDF, ... * Intel Fortran * mvapich2 * fftw * netcdf4 * hdf5-parallel \\\\ (2) Data processing and visualization * ncl * nco/cdo * ncview * udunits \\\\ }}}