software:namd2

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software:namd2 [2013/02/14 11:33]
ulges 		software:namd2 [2021/09/14 15:07]
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 ====== NAMD ====== ====== NAMD ======
-[[http://www.ks.uiuc.edu/Research/namd/]]\\ \\+[[http://www.ks.uiuc.edu/Research/namd/]]\\ 
 + 
 +NAMD (**N**ot (just) **A**nother **M**olecular **D**ynamics program) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
 +Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations.\\
  
 ^  NAMD  ^^ ^  NAMD  ^^
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 |**Lizenz:**|[[http://en.wikipedia.org/wiki/University_of_Illinois_license|University of Illinois license]]| |**Lizenz:**|[[http://en.wikipedia.org/wiki/University_of_Illinois_license|University of Illinois license]]|
 |**Developer**:|Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)| |**Developer**:|Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL)|
-|http://www.ks.uiuc.edu/Research/namd/|| 
  
-NAMD (**N**ot (just) **A**nother **M**olecular **D**ynamics program) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. 
-Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. 
  
 ===== 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/''  | | 
-| :::   | [[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/''|+| :::   | :::                        |                                          |''/cluster/Apps/NAMD/gcc_4.7.0/ibverbs/''  | | 
 +| :::   | [[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 ===== 
 +To use NAMD, you first need to load the corresponding modulefiles.\\ 
 + 
 +For single-cpu usage:  
 +<code bash>$ $PATH/namd2 <configfile></code> 
 + 
 +For parallel usage with LSF: 
 +<code bash>$ bsub -a <mpi> -q <queuename> -o <outputfile> -e <errorfile> -n <amount of cores> -app Reserve1900M -R 'span[ptile=32]' mpirun $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.