Miskolc

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This system maintained by NIIF.

Detailed info about miskolc uv2000 is at here

Type SGI UV2000
# of nodes 1 (40 NUMA nodes)
# of CPUs / node 40 (1 per NUMA node)
# of cores / CPU 8 (320 total)
Memory / node 1280 GB (32 GB per NUMA node)
Memory / core 4 GB
CPU Intel Xeon E5-4627 v2 @ 3.33 GHz
Architecture x86_64 / intel64 / em64t little-endian
Interconnect between nodes/blades NUMAlink 6 (~50Gb/sec, ~0.5μs latency)
MPI SGI MPT 2.08


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/miskolc miskolc
cd ~/shf3/key/ssh

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

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

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

 sshto -m miskolc

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 miskolc -s vasp/5.4.1.03082016.impi
 sshput -t 2 -m miskolc -s vasp/proj

Then add the following into your .bash_profile:

 export PATH=$PATH:$HOME/bin
 export VASP_PROJ=$HOME/vasp/proj.
 export VASP_PROJ_HOME=$HOME/vasp/proj
 module unload sgi/mpt/2.12
 module load intel/mpi/5.1.1.109

miskolc with CPU's only

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

 cd $HOME/jobsamples/ozone

Please fill your email in the miskolc jobfile,

 mcedit miskolc_impi

then submit it:

 sbatch miskolc_impi