configure

config.h

# Compatibility config.h generated by the CMake build system

###############################################################################

# (1)  Location of the installation

BASEDIR=/usr/local/amber20_src/build
AMBER_PREFIX=/usr/local/amber20//
BINDIR=$(AMBER_PREFIX)/bin
LIBDIR=$(AMBER_PREFIX)/lib
INCDIR=$(AMBER_PREFIX)/include
DATDIR=$(AMBER_PREFIX)/dat
LOGDIR=$(AMBER_PREFIX)/logs
AMBER_SOURCE=$(AMBERHOME)

###############################################################################

FLIBS=-L/usr/lib/x86_64-linux-gnu -lsff -lpbsa -lrism -lfftw3 -lblas -llapack -larpack -lm -lnetcdf
FLIBSF=-L/usr/lib/x86_64-linux-gnu -lblas -llapack -larpack -lm -l/usr/local/amber20_src/build/AmberTools/src/xblas/build/libxblas-amb.a
FLIBS_MPI=

###############################################################################

BUILDAMBER=
SHELL=/bin/bash

CC=/usr/bin/gcc
CFLAGS= -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable
CNOOPTFLAGS=
COPTFLAGS=-O3 -mtune=native

CXX=/usr/bin/g++
CXXFLAGS= -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable
CXXNOOPTFLAGS=
CXXOPTFLAGS=-O3 -mtune=native

MV=mv
RM=rm
CP=cp

FC=/usr/bin/gfortran
FFLAGS= -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable
FNOOPTFLAGS=
FOPTFLAGS=-O3 -mtune=native

# pmemd.gem is always enabled in NetCDF builds
PMEMD_GEM=yes

LDFLAGS=

# NetCDF is always enabled in CMake builds
NETCDF=yes

EMIL=EMIL

FEP_MODE=gti

COMPILER=GNU
MKL=

PYTHON=/usr/local/amber20//miniconda/bin/python
SKIP_PYTHON=no

# OS-specific rules for making shared objects
SHARED_SUFFIX=.so

# used by tests
INSTALLTYPE=serial
TESTRISMSFF=testrism
FEP_MODE=gti

configure.sh

#!/bin/sh

error() {
   echo "Configure failed due to the errors above!"
   exit 1
}

check_amberhome() {
   if [ -z "$AMBERHOME" ]; then
      echo ""
      echo "Your AMBERHOME environment variable is not set! Auto set it to: "
      echo "$1"
      export AMBERHOME=$1
   elif [ ! -d $AMBERHOME ]; then
      echo ""
      echo "Your AMBERHOME environment variable is set to $AMBERHOME -- this does"
      echo "not appear to be a directory. It should be set to $1"
      echo "NOT doing so may cause errors when you compile"
      exit 1
   elif [ ! "$AMBERHOME" = "$1" -a ! "$AMBERHOME" = "${1}/" ]; then
      if [ "`uname -s|awk '{print $1}'`" = 'Darwin' ] ; then
        statcmd='stat -f'
      else
        statcmd='stat -c'
      fi
      #try checking the inode incase there is a problem with symlinks
       if [ `$statcmd "%i" $AMBERHOME` != `$statcmd "%i" ${1}` ]; then
           echo ""
           echo "Error: AMBERHOME is expected to be $amberhome but it is currently"
           echo "       $AMBERHOME    This will cause problems!"
           exit 1
       fi
   fi
}

amberhome="`pwd`"
check_amberhome "$amberhome"

# Check for --no-updates in any position
updates="yes"
requested_help="no"
for var in "$@"; do
    case "$var" in
        --no-updates)
            echo "Skipping check for Amber updates"; updates="no";;
        -h|-H|--h|--he|--hel|--help|-help)
            updates="no"; requested_help="yes";;
        -fullhelp|--full|--fullhelp|--full-h|--full-he|--full-hel|--full-help) 
            updates="no"; requested_help="yes";;
    esac
done

# No arguments means we ask for help
if [ $# -eq 0 ]; then
    requested_help="yes"
    updates="no"
fi

python=`which python 2>/dev/null`
if [ -z "$python" ]; then
   python=`which python3 2>/dev/null`
   if [ -z "$python" ]; then
      echo "There is no python or python3 in your PATH; skipping test for updates"
      updates="no"
   fi
fi

if [ "$updates" = "yes" ]; then

   # Tell people we're checking for updates, since this could take a
   # couple seconds, especially if ambermd.org is down
   echo "Checking for updates..."
   
   # Check to see if there are any updates available. This will print a message
   # giving how many patches are available for Amber and AmberTools
   "$python" ./update_amber --check-updates

   # The return code of the above command tells us what happened. Return 1 for
   # an error, and return 2 if there are patches available
   ret_code=$?

   if [ $ret_code -eq 2 ]; then
      printf "There are patches available. Do you want to apply them now? [y/N]"
      echo " (Recommended Y) "
      read answer
      ans=`echo $answer | awk '{print substr($1,1,1)}'`

      if [ "$ans" = "y" -o "$ans" = "Y" ]; then
         # Since patch_amber may patch itself and quit before applying all patches,
         # continue to check for updates and update the tree until they have all
         # been applied.
         while [ $ret_code -eq 2 ]
         do
            "$python" ./update_amber --update
            if [ $? -ne 0 ]; then
               echo "Automatic patching failed! Check the errors before re-configuring"
               exit 1
            fi
            "$python" ./update_amber --check-updates 2>&1 > /dev/null
            ret_code=$?
         done
      else
         echo "NOT updating your tree and continuing anyway."
      fi
   elif [ $ret_code -eq 1 ]; then
      echo "Check for updates failed."
   fi
fi

# Simple redirection to carry out the configure script inside AmberTools/src
echo ""

(cd AmberTools/src && ./configure2 $@) || error

# Bail out if we just got the usage statement
if [ "$requested_help" = "yes" ]; then
    exit 0
fi

ln -sf AmberTools/src/config.h .

# Make clean here

echo "Cleaning the src directories. This may take a few moments."
make clean > /dev/null 2>&1
echo "Configure complete."