Siesta
2.0
Siesta 2.0 has been compiled and installed on the cluster To use siesta
$ module load jnc/siestaThen create a script file (say runscript.sh) with the following lines in it
#!/bin/bash mpirun -srun siesta < input.file > output.fileMake the script file executable
$ chmod +x runscript.shSubmit the job with
$ bsub -n<cores> -q<queue> ./runscript.shTop...
LAMMPS
22Jun07
To use lammps first
$ module load jnc/lammpsthen to make a parallel run
$ bsub -q <queue> -n <no of cores> mpirun -srun lmp_linux -in <input_file>Top...
NAMD
2.6
to use NAMD first
$ module load jnc/namdthen to make a parallel run
$ bsub -q <queue> -n <no of cores> namd2Top...
Espresso
4.0.2
To use espresso. first.
$ module load jnc/espressoexecute the parallel pwscf with
$ bsub -n <no of cores> mpirun -srun pw.xTop...
Espresso
3.2
To use espresso (v 3.0). first.
$ module load jnc/espresso_all/espresso-3.2execute the parallel pwscf with
$ bsub -n <no of cores> mpirun -srun pw.xTop...
VASP
5.2
to load the VASP environment
$ module load jnc/vasp
to execute parallel code for vasp
$ bsub -n <no of cores> -q < queue> mpirun -srun vasp
If you have any problem with running non collinear calculations by the above method, please use the following executable:
$ bsub -n <no of cores> -q < queue> mpirun -srun vasp-noncolTop...
VASP
4.6
to load the VASP environment
$ module load jnc/vasp_all/4.6/vasp
to execute parallel code for vasp
$ bsub -n <no of cores> -q < queue> mpirun -srun vaspTop...
Intel Software
All Versions
$ module load jnc/intel/compilers $ module load jnc/intel/cmkl
The above modules are links to the latest versions of the Intel Compiler Suite and Math Kernel Libraries (MKL). They will always load the latest version of the compilers and MKL. Load these modules before compiling any new package to ensure that you are using the latest installed compilers and libraries.
After compilation, you will need to load the same modules that you had loaded during compilation. To ensure that you are loading the correct version despite future upgrades, use the permanent module names for the different versions installed instead of the link to the latest version. Also, use the permanent module names if you intend to put the module load lines in your login scripts (.bashrc).
Compilers Ver. 11.0, MKL 10.1.0.015 (Latest)
$ module load jnc/intel_all/112008/compilers $ module load jnc/intel_all/112008/cmkl
Compilers Ver. 10.1, MKL 10.0.011
$ module load jnc/intel_all/012008/compilers $ module load jnc/intel_all/012008/cmkl
Compilers Ver. 10.0, MKL 9.1
$ module load jnc/intel_all/072007/compilers $ module load jnc/intel_all/072007/cmklTop...