I now have a successful build of parallel COGENT (!) on Mac Mavericks, 10.9.4.

Procedure and tools:

Removed macports /opt/local/bin from path so don’t pick up macports versions of tools.
(when Left /opt/local in place, openmpi found the following there: nm, ar, strip, ranlib, nmedit, lipo, otool.  Problem is macports puts opt/local/bin at front of path).

I downloaded hdf5-1.8.13 from the hdf5 site.  
I used my already built gfortran 4.9

I configured openmpi as follows:
./configure --prefix=/usr/local/openmpi CC=gcc CXX=g++ FC=gfortran F77=gfortran mpifort=gfortran --enable-static --with-pic --disable-dlopen --enable-mpirun-prefix-by-default

then make all, make check (all tests passed), make install.

I configured serial and parallel versions of hdf5, in build-ser and build-par subdirectories of hdf5.

for serial: ../configure --prefix=/usr/local/hdf5/ser --enable-fortran --enable-cxx CC=gcc CXX=g++ CFLAGS=-fPIC

for parallel:  ../configure --prefix=/usr/local/hdf5/par CC=mpicc CFLAGS=-fPIC FC=mpifort FCFLAGS=-fPIC CXX=mpicxx CXXFLAGS=-fPIC --enable-parallel --enable-fortran

then make install in both directories.   Ran serial and parallel checks (make check-s and make check-p in appropriate directories).

Next, I  configured and built hypre-2.9.0b, with configure script doconfig_mine as shown below, and then built with script doinstall_mine:

more doinstall_mine 
#!/bin/sh
cd src
make -j4 install
name=$(grep "^prefix='" config.log | sed s/\'//g | sed 's/.*\///')
cd ..
ln -s lib/$name hypre_loc

Next make realclean in Chombo/lib and COGENT/exec, and in COGENT/exec, do
make all -j 2 OPT=TRUE DEBUG=FALSE

and it worked.    Haven't tested anything yet for COGENT.  

hypre, Chombo and COGENT configure files are as pasted below.

Ron
-------------
hypre doconfig script:

 more doconfig_mine
#!/bin/sh

debug="--enable-opt";

mpi_include=`echo '-I/usr/local/openmpi/include' | sed 's/-I//g'`

install_dir=$PWD/lib/darwin-cpp-gfortran-opt

cd src
./configure $debug \
            --with-CC=/usr/local/openmpi/bin/mpicc \
            --with-CFLAGS="-O " \
            --with-CXX=/usr/local/openmpi/bin/mpicxx \
            --with-CXXFLAGS="-O " \
            --with-F77=/usr/local/openmpi/bin/mpifort \
            --with-F77FLAGS="-O " \
            --prefix=$install_dir
cd ..

---------------------
Chombo/lib/make.defs.local:

# -*- Mode: Makefile; Modified: "Fri 29 Jul 2005 15:14:39 by dbs"; -*-
# Ron's mods for Mavericks

makefiles+=Make.defs.local

CXX=mpicxx
FC=mpifort
MPI = TRUE
MPICXX=mpicxx
USE_64=TRUE

CPP=$(CXX) -E

cxxoptflags += -O2 -w
foptflags += -O3
flibflags += -lgfortran 

#/opt/local

# MCP_DIR is openmpi lib
MCP_DIR = /usr/local/openmpi/lib
HDF5_DIR = /usr/local
USE_HDF=TRUE
HDFLIBFLAGS=   -L$(HDF5_DIR)/hdf5/ser/lib -lhdf5 -lhdf5_hl -L$(MCP_DIR) -lz
HDFMPILIBFLAGS=-L$(HDF5_DIR)/hdf5/par/lib -lhdf5 -lhdf5_hl -L$(MCP_DIR) -lz
HDFINCFLAGS=   -I$(HDF5_DIR)/hdf5/ser/include -DH5_USE_16_API
HDFMPIINCFLAGS=-I$(HDF5_DIR)/hdf5/par/include -DH5_USE_16_API
USE_MT        = TRUE
lddbgflags    =  -L$(MCP_DIR)
ldoptflags    =  -L$(MCP_DIR)

LAPACKLIBS = -framework ACCELERATE

--------------------

COGENT GnuMakefile.Multidim
more GNUmakefile.multidim 
# -*- Mode: Makefile;  -*- 

## Define the variables needed by Make.example

# trace the chain of included makefiles
makefiles += cogent

# knowing this can be useful for things which are specific to 
# specific machines
UNAMEN = $(shell uname -n)

# the base name(s) of the application(s) in this directory
mdebase = cogent
# in an example of true silliness, need to define ebase so that the 
# realclean target will also remove my *.ex files...
ebase = bogus

# the location of Chombo lib dir
CHOMBO_HOME = ../../Chombo/lib

#this should be defined in your Make.defs.local file
#LAPACKLIBS = -llapack  -lblas

#LAPACKLIBS = -llapack-3 -llapack_atlas -lm

# names of Chombo libraries needed by this program, in order of search.
1dLibNames =  BoxTools BaseTools
2dLibNames = HOMappedGeometry HOAMRTools AMRTimeDependent AMRTools BoxTools
3dLibNames = HOMappedGeometry HOAMRTools AMRTimeDependent AMRTools BoxTools
4dLibNames = HOMappedGeometry HOAMRTools BoxTools
#5dLibNames = BoxTools
#6dLibNames = BoxTools

# relative paths to source code directories
base_dir = .

2dsrc_dirs =  ../src/coord/configuration ../src/coord/velocity 
2dsrc_dirs += ../src/ibc/configuration ../src/poisson
2dsrc_dirs += ../src/util ../src/ibc

3dsrc_dirs += ../src/util ../src/ibc

4dsrc_dirs =  ../src/core ../src/driver ../src/vlasov ../src/species 
#4dsrc_dirs +=  ../src/collisions ../src/transport
4dsrc_dirs +=  ../src/collisions 
4dsrc_dirs += ../src/coord/phase ../src/ibc/phase ../src/util 
4dsrc_dirs += ../src/advectUtil
4dsrc_dirs += ../src/ibc

#mdsrc_dirs = ../src/ibc

# input file for 'run' target
INPUT = regression.inputs

# shared code for building example programs
include $(CHOMBO_HOME)/mk/Make.example.multidim

# application-specific variables

CXXFLAGS += -DCFG_DIM=2

ifeq ($(MPI),TRUE)
HYPRE_LOC = ../hypre-2.9.0b/hypre_loc
else
HYPRE_LOC = ../hypre-2.9.0b/hypre_loc_serial
endif

XTRACPPFLAGS += -I$(HYPRE_LOC)/include
XTRALIBFLAGS += -L$(HYPRE_LOC)/lib -lHYPRE $(LAPACKLIBS)