Differences

This shows you the differences between two versions of the page.

--- software:namd2 [2013/02/14 11:35]
ulges [Available Versions and Combinations]
+++ software:namd2 [2021/09/14 15:07]
jrutte02 removed
@@ Line 14: / Line 14: @@
 ===== 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 =====
+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.