The script charmm_gen.com was designed at NIH for easy maintenance of multiple executables in an active research environment. Multiple versions versions can be derived from the same source code, incorporating different features and maximum atom limits. It is assumed that install.com has already been run, and any porting or compiling issues resolved before charmm_gen.com is used. In fact, charmm_gen.com simply calls install.com after doing a little creative copying and renaming. The script is interactive; it asks a few questions, does a lot of checking, and then proceeds to make up to nine different versions in one operation with no further human intervention required. A "test" or development version can also be prepared, and is in fact the "path of least resistance", i.e. the accepting of all the defaults to each prompt. Since simply starting up a LARGE version of CHARMM with most of the available feature sets can easily require 100 Mbyte of memory, we recognized the need to have multiple executables available. Our choice was to create 3 principal versions: "full", with most major modules included; "lite", a version without most of the high memory usage or rarely used modules; and "am1", which adds the QUNATUM QM/MM code and few other features to the "lite" feature set. Each is available in 3 sizes, small, medium, and large. We also use a "cover" script in /usr/local/bin to run CHARMM, after parsing feature set and size keywords, and stripping them from the command line. An example is included at the end of this description. Currently, ten different sets of object libraries are maintained as well; this does require a bit of disk space, but allows rapid re-building of all versions when bugfixes are made.
To use charmm_gen.com, the following additional files are *required* in build/mach, where mach = hpux in this case: Makefile_hpux.gamess Makefile_hpux.nogamess Makefile_hpux.test Makefile_hpux.test.list pref.dat.large.am1 pref.dat.large.full pref.dat.large.lite pref.dat.medium.am1 pref.dat.medium.full pref.dat.medium.lite pref.dat.small.am1 pref.dat.small.full pref.dat.small.lite pref.dat.test Makefile_hpux.gamess defines additional tools, directories, and libraries needed to compile the GAMESS code for QM/MM calculations, while the .nogamess version is a typical generic version of Makefile_hpux. Makefile_hpux.test is configured for rapid re-compiling of CHARMM during development, while Makefile_hpux.test.list produces cross-referenced source listings by changing the definition of the variable FC at the top of the makefile. The remaining files represent the ten different possible versions; at NIH, the keywords in pref.dat.test are usually the same as pref.dat.medium.full, but that doesn't have to be the case. The following listing shows the pref.dat keywords we chose for the 2 different feature sets at NIH: Feature set "am1" HPUX ! machine type UNIX PARALLEL ! multiple processors/workstations PARAFULL ! req'd for parallel SYNCHRON ! req'd for parallel SOCKET ! req'd for parallel MEDIUM ! size directive = 25120 atom limit SCALAR ! machine characteristics = default for scalar machines VECTOR ! feature directive * = Vectorized routines PARVECT ! Parallel vector code (multi processor vector machines) CRAYVEC ! Fast vector code (standard vector code) SAVEFCM ! Include all SAVE statements PUTFCM FCMDIR=fcm XDISPLAY ASPENER ! feature directive * = Atomic Solvation Parameter energy term MOLVIB ! feature directive = MOLVIB vibrational analysis code NIH ! feature directive * = NIH default specs code OLDDYN ! feature directive = Old dynamics integrator PERT ! feature directive * = NIH free energy code QUANTUM ! feature directiver = include AM1 semi-empirical code REPLICA ! feature directive = Replica code RISM ! feature directive = RISM solvation code RXNCOR ! feature directive * = RXNCOR code TRAVEL ! feature directive * = PATH and TRAVEL code DIMB ! feature directive FMA ! feature directive ZTBL ! feature directive END ! end Feature set "full" HPUX ! machine type UNIX PARALLEL ! multiple processors/workstations PARAFULL ! req'd for parallel SYNCHRON ! req'd for parallel SOCKET ! req'd for parallel MEDIUM ! size directive = 25120 atom limit SCALAR ! machine characteristics = default for scalar machines VECTOR ! feature directive * = Vectorized routines PARVECT ! Parallel vector code (multi processor vector machines) CRAYVEC ! Fast vector code (standard vector code) SAVEFCM ! Include all SAVE statements PUTFCM FCMDIR=fcm XDISPLAY ! X11 graphics display ASPENER ! feature directive * = Atomic Solvation Parameter energy term BLOCK ! feature directive * = Energy partition and free energy code MOLVIB ! feature directive = MOLVIB vibrational analysis code MTS ! feature directive = Multiple time step code NIH ! feature directive * = NIH default specs code OLDDYN ! feature directive = Old dynamics integrator PERT ! feature directive * = NIH free energy code GAMESS ! GAMESS ab initio interface for QM/MM REPLICA ! feature directive = Replica code RISM ! feature directive = RISM solvation code RXNCOR ! feature directive * = RXNCOR code TNPACK ! Truncated Newton TRAVEL ! feature directive * = PATH and TRAVEL code TSM ! feature directive = TSM and ICPERT code DIMB ! feature directive FMA ! feature directive FOURD ! feature directive PRIMSH ! feature directive PBOUND ! simple Periodic BOUNDary (min image) SHAPES ! feature directive = SHAPE descriptor code ZTBL ! feature directive END ! end Feature set "lite" HPUX ! machine type UNIX PARALLEL ! multiple processors/workstations PARAFULL ! req'd for parallel SYNCHRON ! req'd for parallel SOCKET ! req'd for parallel MEDIUM ! size directive = 25120 atom limit SCALAR ! machine characteristics = default for scalar machines VECTOR ! feature directive * = Vectorized routines PARVECT ! Parallel vector code (multi processor vector machines) CRAYVEC ! Fast vector code (standard vector code) SAVEFCM ! Include all SAVE statements PUTFCM FCMDIR=fcm XDISPLAY ASPENER ! feature directive * = Atomic Solvation Parameter energy term MOLVIB ! feature directive = MOLVIB vibrational analysis code NIH ! feature directive * = NIH default specs code PERT ! feature directive * = NIH free energy code REPLICA ! feature directive = Replica code RXNCOR ! feature directive * = RXNCOR code TRAVEL ! feature directive * = PATH and TRAVEL code END ! end
Finally, to make live easy for the end users, we use the following
script to run CHARMM on a routine basis:
#! /bin/csh
# INITIALIZE VARIABLES
set n = $#argv
setenv HOST `hostname | cut -d. -f1`
set chmsiz = small
set i = 1
set cleanup = date
set chmopt = lite
# CHECK FOR OPTIONAL KEYWORDS
while ( $i <= $n )
switch ( $argv[$i] )
case small:
set chmsiz = small
breaksw
case large:
set chmsiz = large
breaksw
case medium:
set chmsiz = medium
breaksw
case test:
set chmopt = test
breaksw
case lite:
set chmopt = lite
breaksw
case full:
set chmopt = full
breaksw
endsw
@ i = $i + 1
end
# STRIP KEYWORDS FROM ARGUMENT STRING
set t = `echo $* | sed -e 's/small//' -e 's/medium//' -e 's/test//' \
-e 's/full//' -e 's/large//' -e 's/lite//' -e 's/am1//'`
# CHECK FOR DESIGNATED PARALLEL HOSTS
switch ( $HOST )
case par0:
set cleanup = 'qpara_clean par0 bypass'
setenv NODE0 par0f
setenv NODE1 par1f
setenv NODE2 par2f
setenv NODE3 par3f
echo "Parallel; $NODE0 $NODE1 $NODE2 $NODE3"
breaksw
case par11:
set cleanup = 'qpara_clean par11 bypass'
setenv NODE0 par11f
setenv NODE1 par12f
setenv NODE2 par13f
setenv NODE3 par14f
echo "Parallel; $NODE0 $NODE1 $NODE2 $NODE3"
breaksw
default:
echo "Single processor; $HOST"
breaksw
endsw
# ECHO WORKING DIRECTORY AND CHARMM VERSION W. TIMESTAMP
if ( $?PWD ) then
echo $PWD
else
echo $cwd
echo "Warning: env var PWD not defined; required for parallel CHARMM"
endif
# SET THE VERSION TO BE RUN
if ( $chmopt == test ) then
set exe = $chmopt
else
set exe = $chmsiz.$chmopt
endif
# VERIFY THE ACTUAL EXECUTABLE; RUN AT REDUCED PRIORITY
ls -o ~charmm/c24n4/exec/hpux/charmm.$exe | cut -c33-
if { /bin/nice -5 ~charmm/c24n4/exec/hpux/charmm.$exe $t } then
echo ''
$cleanup
else
echo '(charmm) ABNORMAL EXIT'
$cleanup
exit(1)
endif
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute