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INSTALL - FIX - Make bundled-dependency builds honour FC/CC and embed rpath #279

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INSTALL - FIX - Make bundled-dependency builds honour FC/CC and embed rpath #279

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12 changes: 12 additions & 0 deletions install/DEFAULTS.inc
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Original file line number Diff line number Diff line change
Expand Up @@ -520,6 +520,18 @@ else
endif
endif

# Embed the netcdf library directories in the executables. Without this the
# codes link against $(NETCDFDIR) but resolve at run time against whatever the
# loader finds first, which fails with e.g.
# symbol lookup error: undefined symbol: netcdf_mp_nf90_create_
# when a system netcdf shadows the bundled one, and silently mixes libraries
# when the two were built by different compilers.
NETCDF_RPATH = -Wl,-rpath,$(NETCDFDIR)
ifneq ($(NETCDF_C_DIR),$(NETCDFDIR))
NETCDF_RPATH += -Wl,-rpath,$(NETCDF_C_DIR)
endif
NETCDF_EXTRA_LIBS += $(NETCDF_RPATH)

# Intel specifics
#----------------
# include compiler specific libs for intel fast moves
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8 changes: 6 additions & 2 deletions install/TARGETS.inc
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Expand Up @@ -43,8 +43,9 @@ netcdf-c: v hdf5
cd ../; git submodule update --init deps/src/netcdf-c;
if [ ! -f ../deps/src/netcdf-c/Makefile ]; then \
cd ../deps/src/netcdf-c; \
CC="$(CC)" FC="$(FC)" F77="$(FC)" \
CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
fi
cd ../deps/src/netcdf-c; \
Expand All @@ -56,8 +57,9 @@ netcdf-fortran: v netcdf-c
cd ../; git submodule update --init deps/src/netcdf-fortran;
if [ ! -f ../deps/src/netcdf-fortran/Makefile ]; then \
cd ../deps/src/netcdf-fortran; \
CC="$(CC)" FC="$(FC)" F77="$(FC)" \
CPPFLAGS="-I$(realpath $(DEPSINSTALLDIR))/include" \
LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib" \
LDFLAGS="-L$(realpath $(DEPSINSTALLDIR))/lib -Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
fi
cd ../deps/src/netcdf-fortran; \
Expand All @@ -69,6 +71,8 @@ hdf5: v
cd ../; git submodule update --init deps/src/hdf5;
if [ ! -f ../deps/src/hdf5/Makefile ]; then \
cd ../deps/src/hdf5; \
CC="$(CC)" FC="$(FC)" \
LDFLAGS="-Wl,-rpath,$(realpath $(DEPSINSTALLDIR))/lib" \
./configure --prefix=$(realpath $(DEPSINSTALLDIR)); \
fi
cd ../deps/src/hdf5; \
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16 changes: 16 additions & 0 deletions install/makefile
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Expand Up @@ -116,6 +116,22 @@ realclean: clean clear
# only for regenerating it when source USE/MODULE relationships change, and
# require python3 (used by maintainers and the CI deps job, not end users).
PYTHON ?= python3
# Remove the autotools configuration of the bundled dependencies. The netcdf
# and hdf5 rules only run ./configure when no Makefile is present, so a plain
# `clean` keeps whatever toolchain configured them first. Switching FC/CC
# without this leaves gfortran-built module files in place, and the codes then
# fail with a confusing "module file was not generated by any release of this
# compiler" followed by cascading kind-parameter errors.
.PHONY: depsclean
depsclean:
for d in hdf5 netcdf-c netcdf-fortran; do \
if [ -f ../deps/src/$$d/Makefile ]; then \
(cd ../deps/src/$$d && $(MAKE) distclean >/dev/null 2>&1 || true); \
fi; \
rm -f ../deps/src/$$d/Makefile ../deps/src/$$d/config.cache; \
done
rm -rf ../deps/lib/* ../deps/include/* ../deps/bin/* ../deps/share ../deps/hdf5

.PHONY: deps checkdeps
deps:
$(PYTHON) gen_deps.py > DEPENDENCIES.inc
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