Delete NAMD_Run_README.txt

namd/NAMD_Run_README.txt

-Run instructions for NAMD.
-ntell@grnet.gr
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-After build of NAMD you have an executable called namd2.
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-The best performance and scaling of namd is achieved using
-hybrid MPI/MT version. On a system with nodes of NC cores per node
-use 1 MPI task per node and NC threads per task,
-for example on a 20 cores/node system use 1 MPI process,
-set OMP_NUM_THREADS or any batch system related variable to 20. 
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-Set a  variable, for example MYPPN to NC-1, 
-for example to 19 for a 20 cores/node system.
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-You can also try other combinations of TASKSPERNODE/THREADSPERTASK to check.
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-The control file is stmv.8M.memopt.namd for tier-1 and stmv.28M.memopt.namd
-for tier-0 systems.
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-The general way to run is :
-WRAPPER WRAPPER_OPTIONS PATH_TO_namd2 +ppn $MYPPN stmv.8M.memopt.namd > logfile
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-WRAPPER and WRAPPER_OPTIONS  depend on system, batch system etc.
-Few common pairs are :
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-CRAY     : aprun -n TASKS -N NODES -d THREADSPERTASK
-Curie    : ccc_mrun with no options - obtained from batch system
-Juqueen  : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
-Slurm    : srun  with no options, obtained from slurm if the variables below are set.
-#SBATCH --nodes=NODES
-#SBATCH --ntasks-per-node=TASKSPERNODE
-#SBATCH --cpus-per-task=THREADSPERTASK
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-The run walltime is reported at the end of logfile : grep WallClock: logfile  | awk -F ' ' '{print $2}'
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