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siesta

siesta

Kurzinformation

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.

http://www.icmab.es/siesta/


Detailinformation

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 to
    PZHETRD parameter number   11 had an illegal value 

    please switch to versions compiled with newer Intel compilers, or GCC (with new Intel MKL versions):

    module switch intel intel/19.0
  • Using 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).

zuletzt geändert am 29.01.2021

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