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Building NAMD 2.6 From Source Code on Blue Gene/L

Important Note

This sample NAMD 2.6 build is only intended as a guide. Build instructions may vary from one site's Blue Gene to the next.

A. Download the Source Files to Blue Gene

NAMD uses Charm++, Tcl, and FFTW, so you will need those as well as NAMD.
The exact location of the source codes will vary over time, what follows was the status on 3-19-07 and is only offered as a guide.

Download the tar.gz files below to for example /home/johndoe/namd where you should replace johndoe with the name of your home directory on the Blue Gene machine. gunzip each file and then extract the contents from the resulting tar file.

  1. Charm++ download: You cannot use the Charm++ in the NAMD distribution on Blue Gene. Instead, go to the Charm++ source code link, to download charm_src.tar.gz . Notice that this is CHARM++, not CHARMM, which is an altogether different software product.

  2. FFTW download: Use the PowerPC 440 FP2 port of FFTW-GEL (for IBM's BlueGene/L supercomputer) link, to download bglfftwgel-2.1.5.tar.gz

  3. TCL download: Use the tcl8.4.14-src.tar.gz link , to download that file. Note that you don't also want tk8.4.14-src.tar.gz .

  4. NAMD download:At the NAMD download link, under the section titled "Version 2.6 (2006-08-31) Platforms:", select the "Source" hyperlink. At this point you'll need to provide your NAMD username and password, or choose one to register. Then download NAMD_2.6_Source.tar.gz .

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Next, do the TCL, FFTW, CHARMM++, and finally NAMD builds.

B. Build TCL:

  1. Set IBM C Compiler Variables
    Example for Bash shell:
    export CC=/opt/ibmcmp/vacpp/bg/8.0/bin/blrts_xlc
    export CFLAGS="-qarch=440 -lc -lnss_files -lnss_dns -lresolv"
  2. cd /home/johndoe/namd/tcl8.4.14/unix
  3. ./configure --prefix=/home/johndoe/namd --disable-shared --disable-threads --disable-load
  4. Declare undeclared variables
    In /home/johndoe/namd/tcl8.4.14/generic/
    tclStubInit.c and tclIOSock.c,
    some variables are undeclared on Blue Gene, so compilation will stop. Declare them as local ints.
  5. Declare additional undeclared variables
    Similarly, declare as local ints undeclared variables that stop compilation in the following routine:
    /home/johndoe/namd/tcl8.4.14/unix/tclUnixChan.c
  6. Modify the target tclsh in the Makefile
  7. make
  8. make install
  9. TCL library files will be created in /home/johndoe/namd/tcl8.4.14/unix

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C. Build FFTW:

  1. cd /home/johndoe/namd/bglfftwgel-2.1.5/raw/bglfftwgel-2.1.5
  2. ./configure CC=blrts_xlc CFLAGS="-O3 -qarch=440 -qalias=allp" -enable-float --enable-type-prefix -build=i686-linux-gnu --prefix=${HOME}/namd/bglfftwgel-2.1.5 --disable-fortran --host=powerpc
  3. make
  4. make install
  5. FFTW library files will be created in /home/johndoe/namd/bglfftwgel-2.1.5/lib

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D. Build CHARM++:

  1. cd /home/johndoe/namd/charm
  2. ./build charm++ mpi-bluegenel xlc -O3 -DCMK_OPTIMIZE=1 -Q -qarch=440
  3. Library files will be created in /home/johndoe/namd/charm/lib

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E. Build NAMD:

  1. Modify BlueGeneL.fftw
  2. Modify BlueGeneL.tcl
  3. Modify Make.charm
  4. cd /home/johndoe/namd/NAMD_2.6_Source
  5. ./config tcl fftw BlueGeneL-MPI-xlC
  6. Modify the psfgen and namd2 targets in Makefile
  7. cd /home/johndoe/namd/NAMD_2.6_Source/BlueGeneL-MPI-xlC
  8. make
  9. NAMD 2.6 executables
    namd2,psfgen,charmrun,flipdcd,flipbinpdbnamd
    will be created in
    /home/johndoe/namdNAMD_2.6_Source/BlueGeneL-MPI-xlC

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Acknowledgements:

A tip o' the hat and many thanks to the Argonne National Laboratory Mathematics and Computer Science Blue Gene Support team for their help in building NAMD on their Blue Gene. Thanks especially to Ray Loy, Satish Balay, and Dinesh Kaushik. Many special thanks also to Amanda Peters, Carlos Sosa, and Sameer Kumar of IBM!

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