siesta
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
1. How to access the software
$ module load CHEMISTRY $ module load siesta |
Available binaries:
- Serial version: siesta, transiesta
- MPI version: siesta_mpi, transiesta_mpi
- Tools: 2dplot.py Eig2DOS build_all.sh ccViz cdf2dm cdf2grid cdf2xsf cdf_laplacian countJobs denchar dm2cdf dm_creator driver eig2bxsf eigfat2plot fat fcbuild fmpdos fractional g2c_ng gen-basis getResults get_chem_labels grid2cdf grid2cube grid2val grid_rotate horizontal hs2hsx hsx2hs info_wfsx ioncat ionplot.sh lwf2cdf macroave md2axsf mixps mprop new.gnubands orbmol_proj para pdosxml plstm protoNEB queue.sh readwf readwfx rho2xsf runJobs siesta simple simple_pipes_parallel simple_pipes_serial simplex sockets.sh stm surf.py swarm tbtrans test.sh vib2xsf vibra wfs2wfsx wfsnc2wfsx wfsx2wfs xv2xsf
2. Further Information
$ okular $SIESTA_ROOT/Docs/siesta.pdf |
3. Example batch script (MPI)
#!/usr/local_rwth/bin/zsh ### Job name, %J is the job ID #SBATCH --job-name=siesta.%J ### Request the time you need for execution. The full format is D-HH:MM:SS ### You must at least specify minutes or days and hours and may add or ### leave out any other parameters #SBATCH --time=60 #### Request the memory you need for your job. You can specify this ### in either MB (1024M) or GB (4G). #SBATCH --mem-per-cpu=1850M # Request 12 processes, all on a single node #SBATCH --nodes=1 #SBATCH --ntasks-per-node=12 # Load the required modulefiles module load CHEMISTRY module load siesta # execute the SIESTA binary $MPIEXEC $FLAGS_MPI_BATCH siesta_mpi < in.fdf > [name_of_outputfile] |
4. FAQ / Known Issues
- We strongly recommend to use the Intel MPI version.
- versions compiled using the GCC compiler need also Intel MKL module to be loaded:
module switch intel gcc module load CHEMISTRY module load siesta module load LIBRARIES module load intelmkl |
version compiled using the Intel compiler v.16, could produce errors like this:
{ 1, 1}: On entry toPZHETRD parameter number 11 had an illegal valueplease switch to versions compiled with newer Intel compilers, or GCC (with new Intel MKL versions):
module switch intel intel/19.0Using OpenMPI, you could suffer a failure with below error message. In this case, swith to the Intel MPI.
[linuxbmc0008:8435] *** An error occurred in MPI_Bcast[linuxbmc0008:8435] *** reported by process [2972647425,4][linuxbmc0008:8435] *** on communicator MPI COMMUNICATOR 12 SPLIT FROM 9[linuxbmc0008:8435] *** MPI_ERR_TRUNCATE: message truncated[linuxbmc0008:8435] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,[linuxbmc0008:8435] *** and potentially your MPI job)If in doubt about correctness of the results, try out a version compiled with another compiler (e.g. gcc instead of intel).