diff --git a/external/external_build.cmake b/external/external_build.cmake
index fa2442b..c28c6db 100644
--- a/external/external_build.cmake
+++ b/external/external_build.cmake
@@ -5,13 +5,9 @@ OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
 IF(ENABLE_OPENMP)
 
   IF (NOT OPENMP_FOUND)
-    MESSAGE(ERROR "No known compiler option for enabling OpenMP")
+    MESSAGE(FATAL_ERROR "No known compiler option for enabling OpenMP")
   ENDIF(NOT OPENMP_FOUND)
 
-  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKED_FLAGS} ${OpenMP_C_FLAGS}")
-
 ENDIF(ENABLE_OPENMP)
 
 SET(BUILD_PREFIX ${CMAKE_BINARY_DIR}/ep_build)
@@ -91,7 +87,11 @@ if (INTERNAL_HDF5)
   ExternalProject_Add(hdf5
     PREFIX ${BUILD_PREFIX}/hdf5-prefix
     URL ${HDF5_URL}
-    CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure --disable-shared --enable-cxx --with-pic --prefix=${HDF5_BIN_DIR} CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+    CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure
+           --disable-shared --enable-cxx --with-pic
+	   --prefix=${HDF5_BIN_DIR} --libdir=${HDF5_BIN_DIR}/lib 
+	   CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} 
+	   CXX=${CMAKE_CXX_COMPILER}
     BUILD_IN_SOURCE 1
     INSTALL_COMMAND make install
   )
@@ -129,7 +129,12 @@ if (INTERNAL_NETCDF)
     DEPENDS ${hdf5_built}
     PREFIX ${BUILD_PREFIX}/netcdf-prefix
     URL ${NETCDF_URL}
-    CONFIGURE_COMMAND ${NETCDF_SOURCE_DIR}/configure --prefix=${NETCDF_BIN_DIR} --enable-netcdf-4  --with-pic --disable-shared --disable-dap --disable-cdmremote --disable-rpc --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+    CONFIGURE_COMMAND ${NETCDF_SOURCE_DIR}/configure
+         --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
+         --enable-netcdf-4  --with-pic --disable-shared --disable-dap 
+         --disable-cdmremote --disable-rpc 
+         --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
+         CXX=${CMAKE_CXX_COMPILER}
     BUILD_IN_SOURCE 1
     INSTALL_COMMAND make install
   )
@@ -146,7 +151,8 @@ ELSE(INTERNAL_NETCDF)
   find_library(NETCDFCPP_LIBRARY netcdf_c++)
   find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
   find_path(NETCDFCPP_INCLUDE_PATH NAMES netcdf)
-  SET(CONFIGURE_CPP_FLAGS ${CONFIGURE_CPP_FLAGS} -I${NETCDF_INCLUDE_PATH} -I${NETCDFCPP_INCLUDE_PATH})
+  SET(CONFIGURE_CPP_FLAGS ${CONFIGURE_CPP_FLAGS} 
+          -I${NETCDF_INCLUDE_PATH} -I${NETCDFCPP_INCLUDE_PATH})
 endif (INTERNAL_NETCDF)
 
 ##################
@@ -158,7 +164,8 @@ if (INTERNAL_BOOST)
   ExternalProject_Add(boost
     URL ${BOOST_URL}
     PREFIX ${BUILD_PREFIX}/boost-prefix
-    CONFIGURE_COMMAND ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
+    CONFIGURE_COMMAND 
+           ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
     BUILD_IN_SOURCE 1
     BUILD_COMMAND ${BOOST_SOURCE_DIR}/b2 --with-exception --with-python
     INSTALL_COMMAND echo "No install"
@@ -176,7 +183,10 @@ IF(INTERNAL_GSL)
   ExternalProject_Add(gsl
     URL ${GSL_URL}
     PREFIX ${BUILD_PREFIX}/gsl-prefix
-    CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure --prefix=${CMAKE_BINARY_DIR}/ext_build/gsl --disable-shared CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
+    CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure
+           --prefix=${CMAKE_BINARY_DIR}/ext_build/gsl --disable-shared
+           --with-pic --libdir=${CMAKE_BINARY_DIR}/ext_build/gsl/lib
+           CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
     BUILD_IN_SOURCE 1
     BUILD_COMMAND make
     INSTALL_COMMAND make install
@@ -224,7 +234,7 @@ ExternalProject_Add(cfitsio
   PREFIX ${BUILD_PREFIX}/cfitsio-prefix
   CONFIGURE_COMMAND 
         ${CMAKE_SOURCE_DIR}/external/cfitsio/configure 
-	    --prefix=${CMAKE_BINARY_DIR}/ext_build/cfitsio 
+	    --prefix=${CMAKE_BINARY_DIR}/ext_build/cfitsio --libdir=${CMAKE_BINARY_DIR}/ext_build/cfitsio/lib
 	    CPPFLAGS=${CONFIGURE_CPP_FLAGS} 
 	    CC=${CMAKE_C_COMPILER} 
 	    CXX=${CMAKE_CXX_COMPILER}
@@ -233,6 +243,7 @@ ExternalProject_Add(cfitsio
   INSTALL_COMMAND make install
 )
 SET(CFITSIO_LIBRARY ${CMAKE_BINARY_DIR}/ext_build/cfitsio/lib/libcfitsio.a)
+SET(CFITSIO_INCLUDE_PATH ${CMAKE_BINARY_DIR}/ext_build/cfitsio/include)
 
 #################
 # Build Healpix 
diff --git a/external/external_python_build.cmake b/external/external_python_build.cmake
index b516577..d934e17 100644
--- a/external/external_python_build.cmake
+++ b/external/external_python_build.cmake
@@ -2,29 +2,58 @@ INCLUDE(FindPythonInterp)
 
 SET(INTERNAL_NETCDF4_PYTHON ON)
 SET(INTERNAL_CYTHON ON)
-
+SET(INTERNAL_HEALPY ON)
+SET(INTERNAL_ARGPARSE ON)
 
 IF(INTERNAL_CYTHON)
   SET(CYTHON_URL "http://cython.org/release/Cython-0.17.1.tar.gz" CACHE STRING "URL to download Cython from")
+  mark_as_advanced(CYTHON_URL)
 ENDIF(INTERNAL_CYTHON)
 
 IF(INTERNAL_NETCDF4_PYTHON)
   SET(NETCDF4_PYTHON_URL "http://netcdf4-python.googlecode.com/files/netCDF4-1.0.1.tar.gz" CACHE STRING "URL to download NetCDF4-python from")
+  mark_as_advanced(NETCDF4_PYTHON_URL)
 ENDIF(INTERNAL_NETCDF4_PYTHON)
 
+IF (INTERNAL_HEALPY)
+  SET(HEALPY_URL "http://github.com/healpy/healpy/archive/1.4.1.tar.gz" CACHE STRING "URL to download Healpy from")
+  mark_as_advanced(HEALPY_URL)
+ENDIF(INTERNAL_HEALPY)
 
+IF(INTERNAL_ARGPARSE)
+  SET(SETUPTOOLS_URL "http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz" CACHE STRING "URL to download setuptools from")
+  SET(ARGPARSE_URL "http://argparse.googlecode.com/files/argparse-1.2.1.tar.gz" CACHE STRING "URL to download argparse from")
+  mark_as_advanced(ARGPARSE_URL SETUPTOOLS_URL)
+ENDIF(INTERNAL_ARGPARSE)
+
+execute_process(
+   COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/external/detect_site.py ${CMAKE_BINARY_DIR}/ext_build/python
+   RESULT_VARIABLE RET_VALUE
+   OUTPUT_VARIABLE PYTHON_LOCAL_SITE_PACKAGE
+)
+IF(RET_VALUE)
+  MESSAGE(FATAL_ERROR "Could not detect the location of site-package in the build directory")
+ENDIF(RET_VALUE)
+
+STRING(REGEX REPLACE "(\r?\n)+$" "" PYTHON_LOCAL_SITE_PACKAGE "${PYTHON_LOCAL_SITE_PACKAGE}")
+MESSAGE(STATUS "Python is installing its packages in ${PYTHON_LOCAL_SITE_PACKAGE}") 
 
 
 
 IF(INTERNAL_CYTHON)
+  SET(BUILD_ENVIRONMENT 
+          ${CMAKE_COMMAND}
+           "-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}"
+           "-DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE}"
+           "-DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python" "-P") 
   ExternalProject_Add(cython
     DEPENDS ${PREV_PYTHON_BUILD}
     URL ${CYTHON_URL}
     PREFIX ${BUILD_PREFIX}/cython-prefix
     CONFIGURE_COMMAND echo "No configure"
     BUILD_IN_SOURCE 1
-    BUILD_COMMAND ${PYTHON_EXECUTABLE} setup.py build
-    INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install --prefix=${CMAKE_BINARY_DIR}/ext_build/python
+    BUILD_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
+    INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
   ) 
   SET(PREV_PYTHON_BUILD ${PREV_PYTHON_BUILD} cython)
 ENDIF(INTERNAL_CYTHON)
@@ -40,10 +69,11 @@ IF(INTERNAL_NETCDF4_PYTHON)
            "-DHDF5_DIR=${HDF5_BIN_DIR}"
            "-DNETCDF4_DIR=${NETCDF_BIN_DIR}"
            "-DPYTHON_LDFLAGS:STRING=${PYTHON_LDFLAGS}"
+           "-DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE}"
            "-DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python" "-P") 
 
   ExternalProject_Add(netcdf4-python
-    DEPENDS ${PREV_PYTHON_BUILD}
+    DEPENDS ${PREV_PYTHON_BUILD} netcdf
     URL ${NETCDF4_PYTHON_URL}
     PREFIX ${BUILD_PREFIX}/netcdf4-python-prefix
     CONFIGURE_COMMAND echo "No configure" 
@@ -51,16 +81,56 @@ IF(INTERNAL_NETCDF4_PYTHON)
     BUILD_COMMAND ${BUILD_ENVIRONMENT}  ${CMAKE_SOURCE_DIR}/external/python_build.cmake
     INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
   )
+  SET(PREV_PYTHON_BUILD ${PREV_PYTHON_BUILD} netcdf4-python) 
 ENDIF(INTERNAL_NETCDF4_PYTHON)
 
+IF(INTERNAL_HEALPY)
+  SET(BUILD_ENVIRONMENT 
+          ${CMAKE_COMMAND}
+           "-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}"
+           "-DPYTHON_CPPFLAGS:STRING=${PYTHON_CPPFLAGS}"
+           "-DCFITSIO_EXT_LIB=${CFITSIO_LIBRARY}"
+           "-DCFITSIO_EXT_INC=${CFITSIO_INCLUDE_PATH}"
+           "-DNETCDF4_DIR=${NETCDF_BIN_DIR}"
+           "-DPYTHON_LDFLAGS:STRING=${PYTHON_LDFLAGS}"
+           "-DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE}"
+           "-DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python" "-P")
 
-execute_process(
-   COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/external/detect_site.py ${CMAKE_BINARY_DIR}/ext_build/python
-   RESULT_VARIABLE RET_VALUE
-   OUTPUT_VARIABLE PYTHON_LOCAL_SITE_PACKAGE
-)
-IF(RET_VALUE)
-  MESSAGE(FATAL_ERROR "Could not detect the location of site-package in the build directory")
-ENDIF(RET_VALUE)
+  ExternalProject_Add(healpy
+    DEPENDS ${PREV_PYTHON_BUILD}
+    URL ${HEALPY_URL}
+    PREFIX ${BUILD_PREFIX}/healpy-prefix
+    CONFIGURE_COMMAND echo "No configure"
+    BUILD_IN_SOURCE 1
+    BUILD_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
+    INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
+  )
+ENDIF(INTERNAL_HEALPY)
 
-MESSAGE(STATUS "Python is installing its packages in ${PYTHON_LOCAL_SITE_PACKAGE}") 
+IF(INTERNAL_ARGPARSE)
+  SET(BUILD_ENVIRONMENT 
+          ${CMAKE_COMMAND}
+           "-DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}"
+           "-DPYTHON_LOCAL_SITE_PACKAGE=${PYTHON_LOCAL_SITE_PACKAGE}"
+           "-DTARGET_PATH=${CMAKE_BINARY_DIR}/ext_build/python" "-P")
+
+  ExternalProject_Add(setuptools
+    URL ${SETUPTOOLS_URL}
+    PREFIX ${BUILD_PREFIX}/setuptools-prefix
+    CONFIGURE_COMMAND echo "No configure"
+    BUILD_IN_SOURCE 1
+    BUILD_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
+    INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
+  )
+
+  ExternalProject_Add(argparse
+    DEPENDS setuptools
+    URL ${ARGPARSE_URL}
+    PREFIX ${BUILD_PREFIX}/argparse-prefix
+    CONFIGURE_COMMAND echo "No configure"
+    BUILD_IN_SOURCE 1
+    BUILD_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_build.cmake
+    INSTALL_COMMAND ${BUILD_ENVIRONMENT} ${CMAKE_SOURCE_DIR}/external/python_install.cmake
+   )
+  SET(AUXILIARY_PYTHON_DEPEND ${AUXILIARY_PYTHON_DEPEND} argparse)
+ENDIF(INTERNAL_ARGPARSE)
diff --git a/external/python_build.cmake b/external/python_build.cmake
index da9b70f..ca9970e 100644
--- a/external/python_build.cmake
+++ b/external/python_build.cmake
@@ -2,9 +2,15 @@ SET(ENV{HDF5_DIR} ${HDF5_DIR})
 SET(ENV{NETCDF4_DIR} ${NETCDF4_DIR})
 SET(ENV{CPPFLAGS} ${PYTHON_CPPFLAGS})
 SET(ENV{LDFLAGS} ${PYTHON_LDFLAGS})
-SET(ENV{PYTHONPATH} ${TARGET_PATH}/lib/python2.7/site-packages:$ENV{PYTHONPATH})
+SET(ENV{VOID_GSL} ${VOID_GSL})
+SET(ENV{PYTHONPATH} ${PYTHON_LOCAL_SITE_PACKAGE}:$ENV{PYTHONPATH})
+SET(ENV{CFITSIO_EXT_INC} ${CFITSIO_EXT_INC})
+SET(ENV{CFITSIO_EXT_LIB} ${CFITSIO_EXT_LIB})
+
+SET(PYTHON_BUILD_COMMAND ${PYTHON_EXECUTABLE} setup.py build)
+MESSAGE(STATUS "Running ${PYTHON_BUILD_COMMAND}")
 execute_process(
-  COMMAND ${PYTHON_EXECUTABLE} setup.py build
+  COMMAND ${PYTHON_BUILD_COMMAND}
   RESULT_VARIABLE RET_VALUE
 )
 
diff --git a/external/python_install.cmake b/external/python_install.cmake
index 4799a98..e33e377 100644
--- a/external/python_install.cmake
+++ b/external/python_install.cmake
@@ -2,8 +2,16 @@ SET(ENV{HDF5_DIR} ${HDF5_DIR})
 SET(ENV{NETCDF4_DIR} ${NETCDF4_DIR})
 SET(ENV{CPPFLAGS} ${PYTHON_CPPFLAGS})
 SET(ENV{LDFLAGS} ${PYTHON_LDFLAGS})
+SET(ENV{VOID_GSL} ${VOID_GSL})
+SET(ENV{CFITSIO_EXT_INC} ${CFITSIO_EXT_INC})
+SET(ENV{CFITSIO_EXT_LIB} ${CFITSIO_EXT_LIB})
+SET(ENV{PYTHONPATH} ${PYTHON_LOCAL_SITE_PACKAGE}:$ENV{PYTHONPATH})
+
+SET(PYTHON_INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install --prefix=${TARGET_PATH} --install-lib=${PYTHON_LOCAL_SITE_PACKAGE})
+
+message(STATUS "Running ${PYTHON_INSTALL_COMMAND}")
 execute_process(
-  COMMAND ${PYTHON_EXECUTABLE} setup.py install --prefix=${TARGET_PATH}
+  COMMAND ${PYTHON_INSTALL_COMMAND}
   RESULT_VARIABLE RET_VALUE
 )
 
diff --git a/pipeline/prepareCatalogs.py b/pipeline/prepareCatalogs.py
index af9d997..bbddc2d 100755
--- a/pipeline/prepareCatalogs.py
+++ b/pipeline/prepareCatalogs.py
@@ -228,7 +228,7 @@ if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
 # first the directly downsampled runs
 # Note: ss0.002   ~ SDSS DR7 dim2
 #       ss0.0004 ~ SDSS DR9 mid 
-baseResolution = numPart/lbox/lbox/lbox # particles/Mpc^3
+baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
 for thisSubSample in subSamples:
 
   keepFraction = float(thisSubSample) / baseResolution
diff --git a/pipeline/prepareGadgetCatalog.py b/pipeline/prepareGadgetCatalog.py
index f0548fa..e3e1ffa 100755
--- a/pipeline/prepareGadgetCatalog.py
+++ b/pipeline/prepareGadgetCatalog.py
@@ -219,7 +219,7 @@ if not os.access(scriptDir, os.F_OK): os.mkdir(scriptDir)
 # first the directly downsampled runs
 # Note: ss0.002   ~ SDSS DR7 dim2
 #       ss0.0004 ~ SDSS DR9 mid 
-baseResolution = numPart/lbox/lbox/lbox # particles/Mpc^3
+baseResolution = float(numPart)/lbox/lbox/lbox # particles/Mpc^3
 for thisSubSample in subSamples:
 
   keepFraction = float(thisSubSample) / baseResolution
diff --git a/python_tools/setup.py b/python_tools/setup.py
index 5e6eebb..bd2a9e9 100644
--- a/python_tools/setup.py
+++ b/python_tools/setup.py
@@ -2,6 +2,9 @@ from distutils.core import setup
 from distutils.extension import Extension
 from Cython.Distutils import build_ext
 import numpy as np
+import os
+
+VOID_GSL=os.environ.get('VOID_GSL')
 
 setup(
     name='void_python_tools',
@@ -15,6 +18,6 @@ setup(
     ext_modules = [
        Extension("void_python_tools.apTools.chi2.velocityProfileFitNative", 
                  ["void_python_tools/apTools/chi2/velocityProfileFitNative.pyx"],
-       libraries=["gsl", "gslcblas"])
+       libraries=["gsl", "gslcblas"], library_dirs=[VOID_GSL+"/lib"], include_dirs=[VOID_GSL+"/include"])
     ]
 )
diff --git a/run_env.sh.in b/run_env.sh.in
new file mode 100644
index 0000000..969bf9c
--- /dev/null
+++ b/run_env.sh.in
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+PYTHONPATH=@PYTHONPATH@
+export PYTHONPATH
+
+$@