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Merge branch 'master' into jblanco/include-mpi
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@alexsavulescu
alexsavulescu authored Apr 28, 2022
2 parents d9d368b + 0dda020 commit 0031a01
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Showing 15 changed files with 109 additions and 194 deletions.
282 changes: 100 additions & 182 deletions bin/nrnivmodl.in
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ set -e

ARCH=@host_cpu@
MODSUBDIR=@modsubdir@
USER_PWD="`pwd`"
USER_PWD="$PWD"

if test "x${NRNHOME}" = x ; then
if [ -z "$NRNHOME" ] ; then
prefix=@prefix@
exec_prefix=@exec_prefix@
bindir=@bindir@
Expand All @@ -17,32 +17,25 @@ else
libdir="${prefix}/lib"
fi

if [ -z ${CORENRNHOME+x} ]; then
if [ -z ${CORENRNHOME+x} ] ; then
# CORENRNHOME wasn't set, use the install prefix
cnrn_prefix=@cnrn_prefix@
else
cnrn_prefix="${CORENRNHOME}"
fi

if test "${NRNHOME_EXEC}" != "" ; then
if [ "${NRNHOME_EXEC}" ] ; then
exec_prefix="${NRNHOME_EXEC}"
bindir="${exec_prefix}/bin"
libdir="${exec_prefix}/lib"
fi

# Besides NRNHOME, one may set NRNBIN to override the default location of user binaries
if test "x$NRNBIN" = "x"; then
NRNBIN=$bindir
fi

export prefix
export bindir
export libdir

MAKEFILEDIR="${bindir}"

if command -v xcrun; then
@NRN_OSX_BUILD_TRUE@export SDKROOT=`xcrun --sdk macosx --show-sdk-path`
@NRN_OSX_BUILD_TRUE@export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
@NRN_OSX_BUILD_TRUE@export MACOSX_DEPLOYMENT_TARGET="@CMAKE_OSX_DEPLOYMENT_TARGET@"
if [ -z "${MACOSX_DEPLOYMENT_TARGET}" ]; then
unset MACOSX_DEPLOYMENT_TARGET
Expand All @@ -55,9 +48,8 @@ UserLDFLAGS=""
UserCOREFLAGS=()

# - options come first but can be in any order.
while test -n "$1" ; do
opt="$1"
case "$opt" in
while [ "$1" ] ; do
case "$1" in
-coreneuron)
# also run nrnivmodl-core
LinkCoreNEURON=true
Expand All @@ -77,14 +69,14 @@ while test -n "$1" ; do
shift
shift;;
-*)
echo "$opt unrecognized"
echo "$1 unrecognized"
exit 1;;
*)
break;;
esac
done

pwd
echo "$PWD"

# Mod file paths may contain spaces which make variable lists of those
# hard to manage as space is the item separator. Furthermore, when a
Expand All @@ -95,214 +87,140 @@ pwd
# of an item, retranslate back to either a space or an escaped space.
# Only do this for cmake

hide_spaces() {
echo "$1" | sed 's/ /+++/g'
}
unhide_spaces() {
echo "$1" | sed 's/+++/ /g'
}
escape_spaces() {
echo "$1" | sed 's/+++/\\ /g'
}
remove_spaces() {
echo "$1" | sed 's/ //g'
}

shopt -s nullglob
# files is the complete list of mod files to process
files=""
if test $# -gt 0 ; then
files=()
if [ $# -gt 0 ] ; then
for i in "$@" ; do
i_hide=`hide_spaces "$i"`
if test -d "$i" ; then
set +e
for j in $(cd "$i"; unset LC_ALL; ls *.mod) ; do
files="$files $i_hide/$j"
done
set -e
if [ -d "$i" ] ; then
files+=( "$i"/*.mod )
elif [ -e "$i" ] || [ -e "$i.mod" ] ; then
files+=( "$i" )
else
if test -e "$i" -o -e "$i.mod" ; then
files="$files $i_hide"
else
echo "Arg Error: \"$i\" is not a folder or mod file name or prefix"

echo ""
echo -n " Mod file, folder args:"
for j in "$@" ; do
echo -n " \"$j\""
done
echo ""
echo "Arg Error: \"$i\" is not a folder or mod file name or prefix"

exit 1
fi
echo ""
echo -n " Mod file, folder args:"
for j in "$@" ; do
echo -n " \"$j\""
done
echo ""

exit 1
fi
done
else
if ls *.mod 1> /dev/null 2> /dev/null ; then # only if there are mod files
# Unset LC_ALL for consistent mod order
files=$(unset LC_ALL; ls *.mod)
fi
files=( *.mod )
fi

files=`echo "$files" | sed 's/^ *//'`

base_names=""
for i in $files ; do
base_names="$base_names `basename $i .mod`"
base_names=()
for i in "${files[@]}" ; do
base_names+=( "$(basename "$i" .mod)" )
done

echo -n "Mod files:"
for i in $files ; do
base_name=`basename "$i" .mod`
dir_name=`dirname "$i"`
echo -n " \"`unhide_spaces $dir_name`/$base_name.mod\""
for i in "${files[@]}" ; do
dir_name=$(dirname "$i")
echo -n " \"$dir_name/${i%.mod}.mod\""
done
echo ""
echo ""


if [ ! -d $MODSUBDIR ] ; then
echo "Creating $MODSUBDIR directory for .o files."
if [ ! -d "$MODSUBDIR" ] ; then
echo "Creating '$MODSUBDIR' directory for .o files."
echo
mkdir $MODSUBDIR
mkdir "$MODSUBDIR"
fi

files=`echo "$files" | sed 's/\.mod//g'`

if test "$files" = '*' ; then
files=""
fi
files=( "${files[@]%.mod}" )

cd $MODSUBDIR
mdir="`pwd`"

# construct file to be included by makefile to specify mod to c rule when
# executed in $MODSUBDIR (child folder of launch location folder)
MODMAKE=makemod2c_inc
echo "" > $MODMAKE
for i in $files ; do
case "$i" in
/*) f=$i;; # absolute, fine as is
*) f=../$i;; # relative
esac
base_name="`basename $f`"
dir_name="`dirname $f`"
# Note: indentation for shell lines in make rules must be a tab
echo "\
./$base_name.c: `escape_spaces "$f.mod"`
mdir="$PWD"

# construct file to be included by makefile to specify mod to c rule when
# executed in $MODSUBDIR (child folder of launch location folder)
MODMAKE=makemod2c_inc
> "$MODMAKE"
for i in "${files[@]}" ; do
case "$i" in
/*) f="$i";; # absolute, fine as is
*) f="../$i";; # relative
esac
base_name="$(basename "$f")"
dir_name="$(dirname "$f")"
# Note: indentation for shell lines in make rules must be a tab
echo "\
./${base_name// /\\ }.c: ${f// /\\ }.mod
@printf \" -> \$(C_GREEN)NMODL\$(C_RESET) \$<\\\n\"
(cd \"`unhide_spaces $dir_name`\"; MODLUNIT=\$(NRNUNITS) \$(NOCMODL) $base_name.mod -o \"$mdir\")
(cd \"$dir_name\"; MODLUNIT=\$(NRNUNITS) \$(NOCMODL) \"$base_name.mod\" -o \"$mdir\")
./$base_name.o: ./$base_name.c
@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
\$(COMPILE) -I\"`unhide_spaces $dir_name`\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
" >> $MODMAKE
done
if test "$nrnivmodl_cfiles" != "" ; then
# I find it very difficult to construct shell variables which are
# space separated lists of items containing spaces. So, for a cmake build,
# the nrnivmodl_cfiles variable is required to be a ';' separated list
# of c files which may contain spaces.
# Save the Internal Field Separator and interpret variables as ';'
# separated list of items (which may contain spaces). Restore after
# processing nrnivmodl_cfiles.
ifs="$IFS"
IFS=';'
for i in $nrnivmodl_cfiles ; do
i_hide=`hide_spaces "$i"`
case "$i_hide" in
/*) f=$i_hide;; # absolute, fine as is
*) f=../$i_hide;; # relative
esac
base_name="`basename $f .c`"
dir_name="`dirname $f`"
echo "\
./$base_name.o: `escape_spaces "$f"`
./${base_name// /\\ }.o: ./${base_name// /\\ }.c
@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
(cd \"`unhide_spaces $dir_name`\"; \$(COMPILE) \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $base_name.c -o \"$mdir/$base_name.o\")
" >> $MODMAKE
done
IFS="$ifs"
fi
\$(COMPILE) -I\"$dir_name\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
" >> "$MODMAKE"
done

COBJS=
MODOBJS=
if [ `echo "\n"` ] ; then
newline="\n"
else
newline="\\\\n"
fi

echo '#include <stdio.h>
{
echo '#include <stdio.h>
#include "hocdec.h"
extern int nrnmpi_myid;
extern int nrn_nobanner_;
#if defined(__cplusplus)
extern "C" {
#endif
' > mod_func.cpp
for i in $base_names ; do
echo 'extern void _'`remove_spaces "$i"`'_reg(void);'
done >> mod_func.cpp
echo '
void modl_reg(){
if (!nrn_nobanner_) if (nrnmpi_myid < 1) {
fprintf(stderr, "Additional mechanisms from files'$newline'");
' >> mod_func.cpp

for i in $files
do
echo ' fprintf(stderr," \"'`unhide_spaces "$i"`'.mod\"");'
done >>mod_func.cpp

echo ' fprintf(stderr, "'$newline'");
}' >>mod_func.cpp

for i in $base_names; do
echo ' _'`remove_spaces "$i"`'_reg();'
MODOBJS="$MODOBJS ./$i.o"
done >> mod_func.cpp

echo "}" >> mod_func.cpp

echo '
'

for i in "${base_names[@]}" ; do
echo "extern void _${i// }_reg(void);"
done

echo ""
echo "void modl_reg() {"
echo " if (!nrn_nobanner_) if (nrnmpi_myid < 1) {"
printf ' fprintf(stderr, "Additional mechanisms from files\\n");\n'

for i in "${files[@]}"
do
echo ' fprintf(stderr, " \"'"$i"'.mod\"");'
done

printf ' fprintf(stderr, "\\n");\n'

echo " }"

for i in "${base_names[@]}" ; do
echo " _${i// }_reg();"
MODOBJS="$MODOBJS ./${i// /\\ }.o"
done

echo "}"

echo '
#if defined(__cplusplus)
}
#endif' >> mod_func.cpp

if test -n "$nrnivmodl_cfiles" ; then
sp=""
COBJS=""
ifs="$IFS"
IFS=';'
for i in $nrnivmodl_cfiles ; do
base_name=`basename "$i" .c`
COBJS="${COBJS}${sp}./${base_name}.o"
sp=" "
done
IFS="$ifs"
fi
echo "COBJS='$COBJS'"
#endif'
} > mod_func.cpp

# call nrnivmodl-core if CoreNEURON is enabled and requested via CLI
UsingCoreNEURON="no"
@CORENEURON_ENABLED_TRUE@UsingCoreNEURON="yes"
UsingCoreNEURON=false
@CORENEURON_ENABLED_TRUE@UsingCoreNEURON=true
if [ "$LinkCoreNEURON" = true ] ; then
if [ "$UsingCoreNEURON" = "yes" ] ; then
cd $USER_PWD
args=""
# pass the nrnivmodl file args to nrnivmodl-core (with spaces escaped)
for i in "$@"; do
j=`hide_spaces "$i"`
j=`escape_spaces "$j"`
args="$args $j"
done
"${cnrn_prefix}/bin/nrnivmodl-core" "${UserCOREFLAGS[@]}" $args
cd $MODSUBDIR
if [ "$UsingCoreNEURON" = true ] ; then
if [ "$#" -gt 1 ] ; then
printf "ERROR : when called with -coreneuron only 1 mod dir is accepted.\n"
exit 1
fi
cd "$USER_PWD"
"${cnrn_prefix}/bin/nrnivmodl-core" "${UserCOREFLAGS[@]}" "$@"
cd "$MODSUBDIR"
else
printf "ERROR : CoreNEURON support is not enabled!\n"
exit 1
fi
fi

make -j 4 -f "${MAKEFILEDIR}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" special &&
make -j 4 -f "${bindir}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" special &&
echo "Successfully created $MODSUBDIR/special"
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