Budapest2

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This system maintained by NIIF.

Specification

Type HP SL205s
# of CPUs / node 2
# of cores / CPU 10
Memory / node 60 GB
Memory / core 3 GB
CPU Intel Xeon E5-2680v2 @ 2.80GHz
Architecture x86_64 / intel64 / em64t little-endian
Scheduler Slurm
MPI Intel MPI (impi), Open MPI (ompi)

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/budapest2 budapest2
cd ~/shf3/key/ssh

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

mv <YOUR_NIIF_KEY> budapest2.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/budapest2
 sshput -m budapest2 -s .

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

 sshto -m budapest2

Then add the following into your .bash_profile:

 PATH=$PATH:$HOME/bin

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 budapest2 -s vasp/5.4.1.03082016.impi
 sshput -t 2 -m budapest2 -s vasp/proj
 echo -e "\nexport VASP_PROJ_HOME=$HOME/vasp/proj" >> $HOME/.bash_profile
 echo -e "\nmodule load intel/mpi/5.1.1.109" >> $HOME/.bash_profile


Log into "budapest2" You can find a sample job of an ozone molecule in $HOME/jobsamples

 cd $HOME/jobsamples/ozone

Please fill your email in the budapest2 jobfile,

 mcedit budapest2_impi

then submit it:

 sbatch budapest2_impi

You can easily increase the number of nodes:

 #SBATCH --nodes=4

Job Monitoring