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.