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General hints for using the NEC SX-Aurora TSUBASA A300-8 system at IMUK
The system is part of the LUIS-cluster at LUH.
You need a user-account for the cluster-system to access the NEC-system. The login procesure is as follows:
- Login to the LUIS cluster-system from a workstation at IMUK:
ssh -X <your LUIS username>@login.luis.uni-hannover.de
- From the LUIS system, you need to start an interactive job on the NEC-machine:
qsub -I -l nodes=1:ppn=1,mem=20gb -W x=PARTITION:muk
By default, the interactive job sessions runs for 24h. Your $HOME-filesystem of the LUIS cluster is mounted on the NEC-System. For storing large output files, use the NEC-local filesystem /scratch/<your LUIS username>
On the NEC-machine only specific software to compile and run PALM is available (NEC Fortran compiler, NetCDF-,
Furthermore, edit file $HOME/.bash_profile and add the following lines:
# User specific environment and startup programs PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS export PALM_BIN PATH=$PALM_BIN:$PATH export PATH LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/netcdf/4.1.1/lib export LD_LIBRARY_PATH
tatara-system http://www2.cc.kyushu-u.ac.jp/scp/system/general/CX/how_to_use
The system is supported starting from revision r1097. You can find a configuration file adjusted for this system in the svn-repository under /palm/trunk/SCRIPTS/.mrun.config.tatara. Just copy this file to your working directory
cd ~/palm/current_version cp trunk/SCRIPTS/.mrun.config.tatara .mrun.config
Don't forget to edit the file in order to replace the string <replace by your tatara username> with your respective username.
For the rest of the installation procedure just follow the instructions given on the installation page.
hayaka-system http://www2.cc.kyushu-u.ac.jp/scp/system/general/FX10/how_to_use
This system is supported starting from r1103 The configuration file adjusted for this system can be found under /palm/trunk/SCRIPTS/.mrun.config.hayaka. Copy this file to your working directory
cd ~/palm/current_version cp trunk/SCRIPTS/.mrun.config.hayaka .mrun.config
Don't forget to edit the file in order to replace the string <replace by your hayaka username> with your respective username.
Restrictions on hayaka
The hayaka login node only provides a cross compiler (frtpx) for the compute nodes. Therefore, the utility programs like interpret_config and check_parameter_files can be compiled, but they cannot be run. This requires to set appropriate mrun options
mrun ... -z -S ...
in order to switch off the parameter check (-z) and to interpret the configuration file directly from the script (-S).
For compiling some parts of the PALM code, the Fujitsu compiler (frtpx) requires more memory than given by default. Please increase the maximum virtual memory size by command
ulimit -v 8097152
For convenience, you should add this command to the file $HOME/.bash_profile.
No automatic restarts are possible on the hayaka system. You have to submit restart runs manually after the previous job has finished. In the job protocol file (see ~/job_queue) of the previous run information is given about which mrun options are to be used for the restart.
