software:namd2

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software:namd2 [2013/02/14 11:43]
ulges
software:namd2 [2014/03/13 14:59]
schlarbm
Line 14: Line 14:
 ===== Available Versions and Combinations ===== ===== Available Versions and Combinations =====
  
-^ Version ^ Compiler                   ^ MPI                                        ^ FFT Library                         ^ Path      ^  +^ Version ^ Compiler                   ^ MPI                                            ^ Path                                        ^ Environment
-| 2.9   | [[software:gcc|GCC]] 4.7.0 | [[software:intelmpi|intelmpi]] 4.0.3.008 |                                     | ''/cluster/Apps/NAMD/gcc_4.7.0/impi_4.0.3.008/'' |  +| 2.9   | [[software:gcc|GCC]] 4.7.0 | [[software:intelmpi|intelmpi]] 4.0.3.008 |''/cluster/Apps/NAMD/gcc_4.7.0/impi_4.0.3.008/'' 
-| :::   | :::                        | [[software:openmpi|OpenMPI]] 1.6.1       |                                     | ''/cluster/Apps/NAMD/gcc_4.7.0/openmpi_1.6.1/'' +| :::   | :::                        | [[software:openmpi|OpenMPI]] 1.6.1       |''/cluster/Apps/NAMD/gcc_4.7.0/openmpi_1.6.1/''  
-| :::   | :::                        |                                          |                                     | ''/cluster/Apps/NAMD/gcc_4.7.0/ibverbs/'' +| :::   | :::                        |                                          |''/cluster/Apps/NAMD/gcc_4.7.0/ibverbs/''  
-| :::   | [[software:icc|Intel Composer]] 2011 SP1 10.319 | [[software:intelmpi|intelmpi]] 4.0.3.008 | FFTW_3.3.3     | ''/cluster/Apps/NAMD/intel-studio-2011-sp1-10/impi_4.0.3.008/''| +| :::   | [[software:icc|Intel Composer]] 2011 SP1 10.319 | [[software:intelmpi|intelmpi]] 4.0.3.008 |''/cluster/Apps/NAMD/intel-studio-2011-sp1-10/impi_4.0.3.008/''I_MPI_FABRICS=shm:ofa((This version of NAMD will be faster, if you set the Intel-MPI runtime environment variable I_MPI_FABRICS to shm:ofa. Just type ''export I_MPI_FABRICS=shm:ofa'' in your console and then run Namd)) |
 ===== Usage ===== ===== Usage =====
-To use NAMD you need to load the corresponding modulefiles and then +To use NAMDyou first need to load the corresponding modulefiles.\\ 
 + 
 +For single-cpu usage: 
 <code bash>$ $PATH/namd2 <configfile></code> <code bash>$ $PATH/namd2 <configfile></code>
  
-For parallel usage with LSF +For parallel usage with LSF: 
-<code bash>$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun.lsf $PATH/namd2 <configfile></code>+<code bash>$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun $PATH/namd2 <configfile></code> 
 + 
 +===== Notes ===== 
 +For computations with up to around 256 cores the version ''gcc_4.7.0/impi_4.0.3.008/'' will be faster than ''intel-studio-2011-sp1-10/impi_4.0.3.008/''
 +With a higher number of cores it will be reversed.