Szeged

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The system is maintained by NIIF.

Specification

Type HP CP4000BL
# of CPUs / node 4
# of cores / CPU 12
Memory / node 132 GB
Memory / core 2.75 GB
CPU AMD Opteron 6174 @ 2.2GHz
Architecture x86_64 / intel64 / em64t little-endian
Scheduler Slurm
MPI Intel (impi)

Logging in

Set up the SSH access from Skynet, and mount its storage on skynet. (log into skynet and type:)

cd ~/shf3/mid/ssh
cp niif/szeged szeged
cd ~/shf3/key/ssh

Then place your private NIIF key here, and rename it as:

mv <YOUR_NIIF_KEY> szeged.sec

You might need to export the private key from putty in OPENSSH format, if you used puttygen to generate the keypair.

Precompiled Environment

From Skynet sync up the precompiled environment:

 cd /share/niif/szeged
 sshput -m szeged -s .

Log into szeged: You can do this with putty, etc if you don't like logging into szeged from Skynet.

 sshto -m szeged

Then add the following into your .profile:

 PATH=$PATH:$HOME/bin
 export NCE_INTEL_MPI=/opt/intel/composer_xe_2013_sp1.1.106/mpirt                                                                    
 export I_MPI_ROOT=/opt/intel/composer_xe_2013_sp1.1.106/mpirt                                                                                                                                                                           
 PATH=$I_MPI_ROOT/bin/intel64:$PATH                                                                                                  
 LD_LIBRARY_PATH=$I_MPI_ROOT/lib/intel64:$LD_LIBRARY_PATH                                                                            
 LD_RUN_PATH=$I_MPI_ROOT/lib/intel64:$LD_RUN_PATH

VASP

We use intel MPI for VASP.

First please transfer the compiled VASP binary and projectors from skynet. Log into "skynet"

 cd /share/niif/
 sshput -t 2 -m szeged -s vasp/5.4.1.03082016.impi
 sshput -t 2 -m szeged -s vasp/proj
 echo -e "\nexport VASP_PROJ_HOME=$HOME/vasp/proj" >> $HOME/.profile
 

Log into "szeged" You can find a sample job of an ozone molecule in $HOME/jobsamples

 cd $HOME/jobsamples/ozone

Please fill your email in the szeged jobfile,

 mcedit szeged_impi

then submit it:

 sbatch szegedt_impi

You can easily increase the number of nodes:

 #SBATCH --nodes=4

Job Monitoring