Delete NAMD_Build_README.txt

namd/NAMD_Build_README.txt

-Build instructions for namd.
-In order to run benchmarks the memopt build with SMP support is mandatory.
- 
-NAMD may be compiled in an experimental memory-optimized mode that utilizes a compressed version of the molecular structure and also supports parallel I/O. 
-In addition to reducing per-node memory requirements, the compressed structure greatly reduces startup times compared to reading a psf file. 
-
-In order to build this version, your MPI need to have level of thread support: MPI_THREAD_FUNNELED
-You need a NAMD 2.11 version or newer.
-
-1. 	Uncompress/tar the source. 
-2. 	cd NAMD_Source_BASE (the directory name depends on how the source obtained,
-	typically : namd2 or NAMD_2.11_Source )
-3.	untar the charm-VERSION.tar that exists. If you obtained the namd source via
-	cvs, you need to download separately charm.
-4.      cd to charm-VERSION directory
-5.      configure and compile charm :
-        This step is system dependent. Some examples are :
-
-CRAY XE6  : ./build charm++ mpi-crayxe        smp                         --with-production -O -DCMK_OPTIMIZE
-CURIE     : ./build charm++ mpi-linux-x86_64  smp  mpicxx  ifort          --with-production -O -DCMK_OPTIMIZE
-JUQUEEN   : ./build charm++ mpi-bluegeneq     smp  xlc                    --with-production -O -DCMK_OPTIMIZE
-Help      : ./build --help to see all available options.
-For special notes on various systems, you should look in http://www.ks.uiuc.edu/Research/namd/2.11/notes.html.
-
-The syntax is : ./build charm++ ARCHITECTURE  smp (compilers, optional)   --with-production -O -DCMK_OPTIMIZE
-You can find a list of supported architectures/compilers in charm-VERSION/src/arch
-The smp option is mandatory to build the Hybrid version of namd.
-This builds charm++.
-
-6.	cd ..
-7.	Configure NAMD.
-        This step is system dependent. Some examples are :
-CRAY-XE6    	./config CRAY-XT-g++ --charm-base ./charm-6.7.0 --charm-arch mpi-crayxe-smp --with-fftw3 --fftw-prefix $CRAY_FFTW_DIR --without-tcl --with-memopt --charm-opts -verbose
-
-CURIE		./config Linux-x86_64-icc --charm-base ./charm-6.7.0  --charm-arch mpi-linux-x86_64-ifort-smp-mpicxx --with-fftw3 --fftw-prefix PATH_TO_FFTW3_INSTALLATION --without-tcl --with-memopt --charm-opts -verbose --cxx-opts "-O3 -xAVX "  --cc-opts "-O3 -xAVX" --cxx icpc --cc icc --cxx-noalias-opts "-fno-alias -ip -fno-rtti -no-vec  "
-
-Juqueen: 	./config BlueGeneQ-MPI-xlC --charm-base ./charm-6.7.0 --charm-arch mpi-bluegeneq-smp-xlc --with-fftw3 --with-fftw-prefix PATH_TO_FFTW3_INSTALLATION  --without-tcl --charm-opts -verbose --with-memopt
-Help      : ./config --help to see all available options.
-See in http://www.ks.uiuc.edu/Research/namd/2.11/notes.html for special notes on various systems.
-
-What is absolutely necessary is the option : --with-memopt and an SMP enabled charm++ build.
-It is suggested to disable tcl support as it is indicated by the --without-tcl flags, since tcl is not necessary
-to run the benchmarks.
-
-	You need to specify the fftw3 installation directory. On systems that
-	use environment modules you need to load the existing fftw3 module
-	and probably use the provided environment variables - like in CRAY-XE6
-	example above. 
-	If fftw3 libraries are not installed on your system,
-	download and install fftw-3.3.5.tar.gz from http://www.fftw.org/.
-
-	You may adjust the compilers and compiler flags as the CURIE example. 
-        A typical use of compilers/flags adjustement is for example
-        to add -xAVX in the CURIE case and keep all the other compiler flags of the architecture the same.
-        Take care or even just avoid using the --cxx option for NAMD config with no reason, 
-        as this will override the compilation flags from the arch file.
-
-	When config ends prompts to change to a directory and run make. 
-
-8.	cd to the reported directory and run make 
-	If everything is ok you'll find the executable with name namd2 in this
-	directory.
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