CHARMM c30b1 charmm_gen.doc



File: charmm_gen ]-[ Node: Top
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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.



File: charmm_gen ]-[ Node: Configuration
Previous: Top -=- Next: Cover script\n

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





File: charmm_gen ]-[ Node: Cover script
Up: Top -=- Previous: Configuration\n

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



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