Budapest

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The system is maintained by NIIF.

Specification

Type HP CP4000BL
# of CPUs / node 2
# of cores / CPU 12
Memory / node 66 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/budapest budapest
cd ~/shf3/key/ssh

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

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

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

 sshto -m budapest

Then add the following into your .profile:

 PATH=$PATH:$HOME/bin                                                                                                              
                                                                                                                                   
 export PATH                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                   
 module unload openmpi/1.6.3-intel                                                                                                   
                                                                                                                                   
 export VASP_PROJ=$HOME/vasp/proj                                                                                                    
 export VASP_PROJ_HOME=$HOME/vasp/proj                                                                                               
                                                                                                                                                                                                                                
 export NCE_INTEL_MPI=intel/mpi/5.1.1.109                                                                                            
 export I_MPI_ROOT=/opt/intel/impi/4.1.0.027                                                                                         
                                                                                                                                   
 PATH=$I_MPI_ROOT/bin64:$PATH                                                                                                        
 MANPATH=$I_MPI_ROOT/man:$MANPATH                                                                                                    
 LD_LIBRARY_PATH=$I_MPI_ROOT/intel64/lib:$LD_LIBRARY_PATH                                                                            
 LD_RUN_PATH=$I_MPI_ROOT/intel64/lib:$LD_RUN_PATH                                                                                
 #NCE_CFLAGS -I$I_MPI_ROOT/include                                                                                                   
 #NCE_FFLAGS -I$I_MPI_ROOT/include                                                                                                   
 #NCE_LDFLAGS -L$I_MPI_ROOT/intel64/lib

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

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

 cd $HOME/jobsamples/ozone

Please fill your email in the debrecen jobfile,

 mcedit budapest_impi

then submit it:

 sbatch budapest_impi

You can easily increase the number of nodes:

 #SBATCH --nodes=4

Job Monitoring