Prerequisites

QXMD parallel version requires Fortran compiler, FFT and MPI libraries. There are no other library requirement for the QXMD

Installation

Download QXMD

To get started, clone this repository to your computer.

~$ git clone https://github.com/USCCACS/QXMD.git

Set Working Directory

First, change the working directory to qxmd/

~$ cd qxmd

You will see following files and directories when you use the ‘ls’ command:

qxmd $ ls
Include/  docs/  Makefile    Qxmd/    Sources/     util/

Include/ contains necessary libraries for compilation, Makefile will be used to build the program, Qxmd contains default variables for many input parameters, Sources/ contains all QXMD source codes, docs/ contains the documentation for QXMDand util/ contains helpful codes for post-processing output data from QXMD.

Configure Makefiles

You have to choose makefile based on the configuration of your machine. For most of the facility supercomputers makefile is already configured. Complete list of the preconfigured makefile can be obtain by typing make help.

$make help

make dec        : DEC Alpha Degital Fortran
make gnu        : GNU Fortran (only for classical MD)
make ffc        : PC LINUX (Fujitsu Fortran&C)
make ffc-v64    : PC LINUX (Fujitsu Fortran&C) on VT-64
make ifc        : PC LINUX (Intel Fortran)
make ifc-x86    : PC LINUX (Intel Fortran) on x86-64
make ifc-v64    : PC LINUX (Intel Fortran) on VT-64
make hpc        : PC LINUX (Intel Fortran) on x86-64 at USC-HPC
make hp         : HP FORTRAN 90
make sp         : IBM SP
make origin     : SGI ORIGIN 2000
make origin26   : SGI ORIGIN 2600
make t3e        : CRAY T3E
make sr2201     : HITACHI SR2201
make sr8000     : HITACHI SR8000
make sr11000    : HITACHI SR11000 at ISSP
make ha8000     : HITACHI HA8000-tc/HT210
make vpp        : Fujitsu VPP5000
make sx7        : NEC SX-7
make altix      : SGI Altix3700/1280 at ISSP
make p5         : IBM eServer model p5
make primequest : FUJITSU PRIMEQUEST 580
make primergy   : FUJITSU PRIMERGY RX200S3
make cx400      : FUJITSU PRIMERGY CX400
make primehpc   : FUJITSU PRIMEHPC FX10
make sekirei    : Intel Fortran on SGI ICE XA/UV (systemB) at ISSP

If you are not using aforementioned machine, you might need to modify the Makefile according to your computing environment.

Precompiler variables

Precompiler flags are defined in CPPDEFS as:

CPPDEFS= -DFLAG1 -DFLAG2

Following flags are defined in QXMD

-LIBFFTW = link FFTW library
-LIBFFTW3 = link FFTW3 library
-DPOINTER64 = used for 64-bit machines
-DSSL2VP = used on Fujitsu machine
-DVECTOR = special implementation. It may result in faster computation on some machine.

There are several flags are defined for future development. Currently, they are not used. Several flags are specific to compiler. Please check compiler manual for further details.

Adding New Machine configuration in Makefile

Makefile defines which compiler you will use to build the QXMD executable.There are several predefined compiler setting which must be set. First, open Makefile available in QXMD directory and define the machine name. For example, theta machine at Argonne National Lab

theta: $(WDIR) $(DDIR) $(SOURCEFILE)
        sed "s/^#THETA#//" $(SOURCEFILE) > $(WORKFILE)

This process will ensure that make will understand the target. Next, we need to define the macro such as LINKER, LDFLAGS and FFTLIB in the makefile included in Source directory. For example, theta machine definition are as follow

#THETA#     LINKER        = ftn
#THETA#     FFLAGS        = -c -fast -warn none
#THETA#     LDFLAGS       = -O3 -ipo -no-prec-div
#THETA#     FFLAGS        = -c -O3 -ipo -no-prec-div  -warn none
#THETA#     CPPDEFS       = -traditional $(CPPDEF) -DLIBFFTW3 -DIFC -DVECTOR
#THETA#     MKLPATH       = $(MKLROOT)/intel/lib64
#THETA#     FFTLIB        = -L$(MKLPATH) -Wl,--start-group -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -Wl,--end-group

Definition of each macro is as follow:

LINKER= MPI Fortran compiler
FFLAGS= Compiler flags
LDFLAGS= linking libraries
CPPDEFS= Preprocessing MACROS
MKLPATH= Variable defined for MKL libraries
FFTLIB= FFT library

It is up to the user to define a new macro for better readability. Once you have defined all the macros you are ready to build code for new architecture

Build QXMD

After tailoring the Makefile for your computing environment, type the command below to build the QXMD executable.

qxmd $ make $(MACHINE_NAME)
qxmd $ make qxmd

To create a parallel version of QXMD, please use the following steps

qxmd $ make $(MACHINE_NAME)
qxmd $ make qxmdmpi

Check to see if you the QXMD executable has been created, and if so, you are ready to start a simulation.

qxmd $ ls
Include/    Makefile    docs/   Qxmd/    qxmdmpi*  Sources/     util/

Parallel build is activated by default. The program will use all available core on the machine to build the program efficiently.