The HECToR Service is now closed and has been superceded by ARCHER.

Compiling NAMD 2.7 on Phase 3

Setup environment

Use the GNU compiler suite and the FFTW 2 library.

unset CFLAGS
module swap PrgEnv-pgi PrgEnv-gnu
module add fftw/

Full module list for the centrally compiled version:

Currently Loaded Modulefiles:
  1) modules/
  2) nodestat/2.2-1.0400.29866.4.3.gem
  3) sdb/1.0-1.0400.30000.6.18.gem
  4) MySQL/5.0.64-1.0000.4667.20.1
  5) lustre-cray_gem_s/1.8.4_2.6.32.45_0.3.2_1.0400.6221.1.1-1.0400.30252.1.29
  6) udreg/2.3.1-1.0400.3911.5.6.gem
  7) ugni/2.3-1.0400.3912.4.29.gem
  8) gni-headers/2.1-1.0400.3906.5.1.gem
  9) dmapp/3.2.1-1.0400.3965.10.12.gem
 10) xpmem/0.1-2.0400.29883.4.6.gem
 11) hss-llm/6.0.0
 12) Base-opts/1.0.2-1.0400.29823.8.1.gem
 13) xtpe-network-gemini
 14) PrgEnv-gnu/4.0.30
 15) xt-mpich2/5.3.4
 16) atp/1.3.0
 17) xt-asyncpe/5.03
 18) pmi/2.1.4-1.0000.8596.8.9.gem
 19) xt-libsci/11.0.03
 20) gcc/4.6.1
 21) pbs/
 22) packages-phase2b
 23) budgets/1.0
 24) xtpe-interlagos
 25) fftw/

Build TCL

Download and unpack the TCL source tarball (you must use TCL 8.4). Go to subdirectory: tcl8.4.19/unix and Configure TCL with:

./configure --enable-gcc --disable-load --disable-shared --disable-threads --prefix=/usr/local/packages/2.7/tcl8.4

Modify the Makefile options to the following:

CC=cc -pipe -m64  -minline-all-stringops -march=native

Build TCL with:

make clean
make install

Install CHARMM++

The version of CHARMM++ bundled with NAMD 2.7 version does not work on HECToR phase 3 so you should download and use CHARM++ version 6.1 instead.

Unzip the charm source

tar -xvf charm.6.1.tar

Modify charm-6.1/src/arch/mpi-crayxt/ to remove all references to -lrca.

Build CHARMM++

cd charm-6.1
./build charm++ mpi-crayxt -O -DCMK_OPTIMIZE=1

Build NAMD

Modify arch/CRAY-XT.fftw to:

FFTLIB=-lsrfftw -lsfftw

Modify arch/CRAY-XT.tcl to point to your TCL installtion. For example:

TCLLIB=-L$(TCLDIR)/lib -ltcl8.4

Make sure that the make.charm file points to the correct charm-6.1 directory for your CHARMM++ installation.

Configure NAMD:

./config CRAY-XT-g++

(If memory optimisation is required you can set this with --with-memopt option to config. See for more information).

Make NAMD:

cd CRAY-XT-g++

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