Undefined reference to `compress2' and other functions in the HDF5 library - makefile

Question

I am trying to make a code called iPIC3D and it has some prerequisite libraries such as HDF5, H5hut etc. I did everything as instructed. One has to install all the prerequisites and then run the "make" command. But while running the make command, I get a series of errors such as
/usr/local/hdf5/1.8.11-par/lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate':
H5Zdeflate.c:(.text+0xf1): undefined reference to `compress2'
H5Zdeflate.c:(.text+0x1af): undefined reference to `inflateInit_'
H5Zdeflate.c:(.text+0x1c9): undefined reference to `inflate'
H5Zdeflate.c:(.text+0x27a): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x2dc): undefined reference to `inflateEnd'
H5Zdeflate.c:(.text+0x3de): undefined reference to `inflateEnd'
collect2: error: ld returned 1 exit status
make: *** [main] Error 1
Here is a copy of my makefile for reference
PIC_HOME = $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
## SECTION THAT DEPENDS ON THE SYSTEM
# -- Modify this variables according
# -- to your system options.
# -- Possible flags:
# -DPARALLEL_IO Use parallel HDF5
# -DUSEH5HUT Use H5hut (must include also -DPARALLEL_IO)
# -DBATSRUS Coupling with BATS-R-US
CXX = mpicxx
HDF5_HOME = /usr/local/hdf5/1.8.11-par
H5HUT_HOME = /usr/local/H5hut/1.8.11
IPIC_FLAGS = "-DUSEH5HUT -DPARALLEL_IO"
## END OF SECTION
OPTIM = -O3
HDF5_LIB = $(HDF5_HOME)/lib/libhdf5_hl.a $(HDF5_HOME)/lib/libhdf5.a
H5HUT_LIB = $(H5HUT_HOME)/lib/libH5hut.a
H5HUTIO_LIB = $(IPIC_HOME)/H5hut-io/libH5hut-io.a
INC_DIR = ./include
INC_H5HUT = $(H5HUT_HOME)/include
INC_H5HUTIO = $(IPIC_HOME)/H5hut-io/include
INC_HDF5 = $(HDF5_HOME)/include
.SUFFIXES:
.SUFFIXES: .cpp .o .h
SRC = \
$(IPIC_HOME)/grids/Grid3DCU.cpp \
$(IPIC_HOME)/fields/BCStructure.cpp \
$(IPIC_HOME)/fields/EMfields3D.cpp \
$(IPIC_HOME)/inputoutput/phdf5.cpp \
$(IPIC_HOME)/inputoutput/Restart3D.cpp \
$(IPIC_HOME)/inputoutput/ParallelIO.cpp \
$(IPIC_HOME)/inputoutput/Collective.cpp \
$(IPIC_HOME)/performances/Timing.cpp \
$(IPIC_HOME)/PSKOutput3D/PSKhdf5adaptor.cpp \
$(IPIC_HOME)/bc/BcParticles.cpp \
$(IPIC_HOME)/bc/BcFields3D.cpp \
$(IPIC_HOME)/mathlib/EllipticF.cpp \
$(IPIC_HOME)/solvers/CG.cpp \
$(IPIC_HOME)/solvers/GMRES.cpp \
$(IPIC_HOME)/ConfigFile/src/ConfigFile.cpp \
$(IPIC_HOME)/main/iPic3Dlib.cpp \
$(IPIC_HOME)/particles/Particles3Dcomm.cpp \
$(IPIC_HOME)/particles/Particles3D.cpp \
$(IPIC_HOME)/communication/ComNodes3D.cpp \
$(IPIC_HOME)/communication/ComParser3D.cpp \
$(IPIC_HOME)/communication/ComInterpNodes3D.cpp \
$(IPIC_HOME)/communication/ComParticles3D.cpp \
ALLOBJ = $(subst .cpp,.o,$(SRC))
IPIC3D_EXE = $(IPIC_HOME)/iPic3D
IPIC3D_LIB = $(IPIC_HOME)/libiPic3Dlib.a
LDLIBS = $(IPIC3D_LIB) $(H5HUTIO_LIB) $(H5HUT_LIB) $(HDF5_LIB) -ldl
all : io lib main
io :
CXX=$(CXX) HDF5_HOME=$(HDF5_HOME) H5HUT_HOME=$(H5HUT_HOME) IPIC_FLAGS=$(IPIC_FLAGS) $(MAKE) -C $(IPIC_HOME)/H5hut-io
lib : $(ALLOBJ)
$(AR) sr $(IPIC3D_LIB) $(ALLOBJ)
ranlib $(IPIC3D_LIB)
main : iPic3D.o
$(CXX) $(LDFLAGS) -I$(INC_DIR) -I$(INC_HDF6) iPic3D.cpp -o $(IPIC3D_EXE) $(LDLIBS)
clean : cleanio
$(RM) $(ALLOBJ)
$(RM) $(IPIC3D_LIB)
$(RM) iPic3D.o
$(RM) $(IPIC3D_EXE)
cleanio :
$(MAKE) -C $(IPIC_HOME)/H5hut-io clean
%.o : %.cpp
echo " Compiling " $#
$(CXX) $(CXXFLAGS) $(OPTIM) $(IPIC_FLAGS) -I$(INC_DIR) -I$(INC_H5HUTIO) -I$(INC_H5HUT) -I$(INC_HDF5) -c $< -o $#
I am unable to understand what exactly is causing this problem.

Answer 1

I would say you are missing linking in the libz library as this is where the compress2 function should come from. Try adding -lz to your LDLIBS.