From c8258a48bdc77fd53e96a4fd7890a8d755e0d807 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 25 Mar 2015 11:42:15 +0100
Subject: [PATCH 1/6] Upgrade irpf90

---
 scripts/upgrade_irpf90.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/upgrade_irpf90.sh b/scripts/upgrade_irpf90.sh
index a3aeac48..5735754f 100755
--- a/scripts/upgrade_irpf90.sh
+++ b/scripts/upgrade_irpf90.sh
@@ -1,7 +1,7 @@
-#!/bin/bash
+#!/bin/bash 
 # 
 # Upgrades IRPF90 from the web.
-# Tue Nov  4 00:53:13 CET 2014
+# Wed Mar 25 11:41:04 CET 2015
 
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
@@ -10,9 +10,9 @@ then
 fi
 
 cd -- ${QPACKAGE_ROOT}
-mv -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
+mv -f -- ${QPACKAGE_ROOT}/irpf90 ${QPACKAGE_ROOT}/irpf90.old
 
-make irpf90 
+${QPACKAGE_ROOT}/scripts/install_irpf90.sh
 
 if [[ $? -eq 0 ]]
 then

From 6b2496d0ed7e99b41672a990fde13d7be7246121 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Wed, 25 Mar 2015 23:03:51 +0100
Subject: [PATCH 2/6] Lots of cleaning in scripts and Makefiles

---
 .gitignore                        |   3 +-
 scripts/archive_ezfio.sh          |  78 ---------------
 scripts/build_modules.sh          |  34 +++++++
 scripts/check_dependencies.sh     |  14 +--
 scripts/clean_modules.sh          |  36 +++++++
 scripts/create_Makefile.sh        |  14 +--
 scripts/create_Makefile_depend.sh |  12 ++-
 scripts/create_Needed_modules.sh  |  12 ++-
 scripts/create_gitignore.sh       |  10 ++
 scripts/create_module.sh          |  21 ++--
 scripts/create_rst_templates.sh   |  21 ++--
 scripts/ezfio_interface.py        |  57 +++++++----
 scripts/get_basis.sh              |  12 ++-
 scripts/install_curl.sh           |   7 +-
 scripts/install_emsl.sh           |   8 +-
 scripts/install_ezfio.sh          |   8 +-
 scripts/install_ocaml.sh          |   4 +-
 scripts/prepare_ezfio.sh          |  18 ++++
 scripts/prepare_module.sh         |  15 ---
 scripts/qp_include.sh             |  80 +++++++++++++++
 scripts/run_Makefile_common.sh    |  69 +++++++++++++
 scripts/run_Makefile_global.sh    |  81 +++++++++++++++
 scripts/save_current_mos.sh       |   7 ++
 scripts/unarchive_ezfio.sh        |  54 ----------
 scripts/upgrade_ezfio.sh          |   2 +-
 setup_environment.sh              |   3 +
 src/AOs/Makefile                  |   2 -
 src/BiInts/Makefile               |   2 -
 src/Bitmask/Makefile              |   2 -
 src/CAS_SD_selected/Makefile      |   2 -
 src/CID/Makefile                  |   2 -
 src/CID_SC2_selected/Makefile     |   2 -
 src/CID_selected/Makefile         |   2 -
 src/CIS/Makefile                  |   2 -
 src/CISD/Makefile                 |   2 -
 src/CISD_SC2_selected/Makefile    |   2 -
 src/CISD_selected/Makefile        |   2 -
 src/DDCI_selected/Makefile        |   2 -
 src/Dets/Makefile                 |   2 -
 src/Electrons/Makefile            |   2 -
 src/Ezfio_files/Makefile          |   2 -
 src/FCIdump/Makefile              |   2 -
 src/Full_CI/Makefile              |   2 -
 src/Generators_CAS/Makefile       |   2 -
 src/Generators_full/Makefile      |   2 -
 src/Generators_restart/Makefile   |   2 -
 src/Hartree_Fock/Makefile         |   2 -
 src/MOGuess/Makefile              |   2 -
 src/MOs/Makefile                  |   2 -
 src/MP2/Makefile                  |   2 -
 src/Makefile                      |  37 ++++---
 src/Makefile.common               | 160 +++---------------------------
 src/Molden/Makefile               |   2 -
 src/MonoInts/Makefile             |   2 -
 src/NEEDED_MODULES                |   2 +-
 src/Nuclei/Makefile               |   2 -
 src/Output/Makefile               |   2 -
 src/Perturbation/Makefile         |   2 -
 src/Properties/Makefile           |   2 -
 src/Selectors_full/Makefile       |   2 -
 src/Selectors_no_sorted/Makefile  |   2 -
 src/SingleRefMethod/Makefile      |   2 -
 src/Utils/Makefile                |   2 -
 63 files changed, 491 insertions(+), 456 deletions(-)
 delete mode 100755 scripts/archive_ezfio.sh
 create mode 100755 scripts/build_modules.sh
 create mode 100755 scripts/clean_modules.sh
 create mode 100755 scripts/prepare_ezfio.sh
 delete mode 100755 scripts/prepare_module.sh
 create mode 100644 scripts/qp_include.sh
 create mode 100755 scripts/run_Makefile_common.sh
 create mode 100755 scripts/run_Makefile_global.sh
 delete mode 100755 scripts/unarchive_ezfio.sh

diff --git a/.gitignore b/.gitignore
index e096320a..cdcdc6d8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@ EMSL_Basis
 bin/
 *.log
 quantum_package_static.tar.gz
-
+resultsFile
+opam_installer.sh
diff --git a/scripts/archive_ezfio.sh b/scripts/archive_ezfio.sh
deleted file mode 100755
index eb0298fc..00000000
--- a/scripts/archive_ezfio.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/bin/bash
-#
-# Computes the MD5 digest of an EZFIO file, and creates a tar.
-# Thu Apr  3 16:55:50 CEST 2014
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  print "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-fi
-
-function archive()
-{
-  FILE="$1"
-  MD5="$2"
-  ARCHIVE="${QPACKAGE_ROOT}/data/cache/$MD5"
-  if [[ -f "$ARCHIVE" ]]
-  then
-    if ! diff "$FILE" "${QPACKAGE_ROOT}/data/cache/$MD5" &> /dev/null
-    then
-      echo "Something went wrong. The file"
-      echo "${QPACKAGE_ROOT}/data/cache/$MD5"
-      echo "is different from $FILE"
-      echo "Aborting"
-      return 1
-    fi
-  else
-    cp "$FILE" "${QPACKAGE_ROOT}/data/cache/$MD5"
-  fi
-}
-
-
-
-
-EZFIO_FILE=$(basename ${1})
-
-if [[ -z ${EZFIO_FILE} ]]
-then
-  echo "Usage: $(basename $0) <EZFIO_FILE>"
-  exit 1
-fi
-
-
-cd "${QPACKAGE_ROOT}/EZFIO/src"
-FILES=($(python << EOF | sort
-from read_config import * 
-for group in groups:
-  if group == "ezfio":
-    continue
-  for d in groups[group]:
-    if d[2] == ():
-      suffix = ""
-    else:
-      suffix = ".gz"
-    print group+'/'+d[0]+suffix
-print "ezfio/creation"
-print "ezfio/library"
-EOF
-))
-cd $OLDPWD
-
-MD5_FILE=$(basename "${EZFIO_FILE}" .ezfio).md5
-rm -f -- "${MD5_FILE}"
-for FILE in ${FILES[@]}
-do
-  FILE="${EZFIO_FILE}/${FILE}"
-  MD5=$(md5sum "${FILE}" 2>/dev/null | cut -d ' ' -f 1)
-  if [[ ! -z $MD5 ]]
-  then
-    if ! archive "$FILE" "$MD5"
-    then
-      rm -- "${MD5_FILE}"
-      exit 1
-    fi
-    echo "$MD5" "$FILE" >> "${MD5_FILE}"
-  fi
-done
-
diff --git a/scripts/build_modules.sh b/scripts/build_modules.sh
new file mode 100755
index 00000000..5aedc105
--- /dev/null
+++ b/scripts/build_modules.sh
@@ -0,0 +1,34 @@
+#!/bin/bash 
+#
+# This script should run from the directory $QPACKAGE_ROOT/src
+
+source ${QPACKAGE_ROOT}/scripts/run_Makefile_global.sh
+
+NPROC=$(cat /proc/cpuinfo | grep MHz | wc -l)
+
+export IN_MAKE=1
+
+for MODULE in $@
+do
+  if [[ ! -d ${MODULE} ]]
+  then
+    error "Module ${MODULE} doesn't exist"
+  fi
+  cd ${MODULE}
+  echo ${MODULE}  
+  ${QPACKAGE_ROOT}/scripts/run_Makefile_common.sh
+  if [[ $# -eq 1 ]] 
+  then
+    env make -j ${NPROC} all 
+  else
+    env make -j ${NPROC} all &> make.log 
+    if [[ $? -ne 0 ]]
+    then
+      cat make.log
+      error "
+Build failed for module $MODULE
+"
+    fi
+  fi
+  cd ${OLDPWD}
+done
diff --git a/scripts/check_dependencies.sh b/scripts/check_dependencies.sh
index 9e856c41..f21dbc40 100755
--- a/scripts/check_dependencies.sh
+++ b/scripts/check_dependencies.sh
@@ -10,13 +10,13 @@
 # read in the Makefile.
 # Thu Apr  3 01:44:23 CEST 2014
 
-function unique_list()
-{
-  for d in $@
-  do
-    echo $d
-  done | sort | uniq
-}
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 
 if [[ -z $1 ]]
 then
diff --git a/scripts/clean_modules.sh b/scripts/clean_modules.sh
new file mode 100755
index 00000000..cc25cede
--- /dev/null
+++ b/scripts/clean_modules.sh
@@ -0,0 +1,36 @@
+#!/bin/bash 
+#
+# Cleans a module directory 
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+function do_clean()
+{
+  rm -rf -- \
+    IRPF90_temp IRPF90_man Makefile.depend $(cat NEEDED_MODULES) include \
+    ezfio_interface.irp.f irpf90.make irpf90_entities tags $(ls_exe)
+}
+
+if [[ -z $1 ]]
+then
+  check_current_dir_is_module
+  do_clean
+else
+  check_current_dir_is_src
+  for i in $@
+  do
+    if [[ -d $i ]]
+    then
+       cd $i
+       do_clean
+       cd $OLDPWD
+    fi
+  done
+fi
+
diff --git a/scripts/create_Makefile.sh b/scripts/create_Makefile.sh
index f0cbf963..e04b99fc 100755
--- a/scripts/create_Makefile.sh
+++ b/scripts/create_Makefile.sh
@@ -6,17 +6,17 @@
 # module directory.
 # Thu Apr  3 01:44:41 CEST 2014
 
-MODULE=$(basename "$PWD")
-
-if [[ "$MODULE" == "src" ]]
+if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "Error: This script should not be run in the src directory."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
 
 cat << EOF > Makefile
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/scripts/create_Makefile_depend.sh b/scripts/create_Makefile_depend.sh
index 6edd9843..56e1c5e0 100755
--- a/scripts/create_Makefile_depend.sh
+++ b/scripts/create_Makefile_depend.sh
@@ -6,9 +6,19 @@
 # files included by including other modules.
 # Thu Apr  3 01:44:09 CEST 2014
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
 SRC=""
 OBJ=""
-DEPS="$(cat NEEDED_MODULES)"
+DEPS="$NEEDED_MODULES"
 
 for M in ${DEPS}
 do
diff --git a/scripts/create_Needed_modules.sh b/scripts/create_Needed_modules.sh
index 9b08b127..026eadab 100755
--- a/scripts/create_Needed_modules.sh
+++ b/scripts/create_Needed_modules.sh
@@ -4,13 +4,15 @@
 # This script is supposed to run in a module directory.
 # Thu Apr  3 13:38:38 CEST 2014
 
-MODULE=$(basename $PWD)
-
-if [[ $MODULE == "src" ]]
+if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "Error: This script should not be run in the src directory."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
 
 OUTPUT=$(${QPACKAGE_ROOT}/scripts/check_dependencies.sh $@)
 echo ${OUTPUT} > NEEDED_MODULES
diff --git a/scripts/create_gitignore.sh b/scripts/create_gitignore.sh
index 2c249bb6..605b0ab8 100755
--- a/scripts/create_gitignore.sh
+++ b/scripts/create_gitignore.sh
@@ -5,6 +5,16 @@
 # Tue Jan 13 14:18:05 CET 2015
 #
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
 cat << EOF > .gitignore
 #
 # Do not modify this file. Add your ignored files to the gitignore
diff --git a/scripts/create_module.sh b/scripts/create_module.sh
index 74362bc7..dbddc3d3 100755
--- a/scripts/create_module.sh
+++ b/scripts/create_module.sh
@@ -7,7 +7,17 @@
 # All remaining aruments are dependencies.
 # Thu Apr  3 01:44:58 CEST 2014
 
-DEBUG=1
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_src
+
+DEBUG=0
 
 # If DEBUG=1, the print debug info.
 function debug()
@@ -36,13 +46,6 @@ function fail()
 }
 
 
-if [[ -z $QPACKAGE_ROOT ]]
-then
-  echo "Error:"
-  echo "QPACKAGE_ROOT environment variable is not set."
-  echo "source quantum_package.rc"
-  exit 1
-fi
 
 MODULE=$1
 
@@ -68,7 +71,7 @@ debug "Module does not already exist: OK"
 
 
 # Set up dependencies
-ALL_MODULES="$(cat NEEDED_MODULES)"
+ALL_MODULES="${NEEDED_MODULES}"
 echo "Select which modules you are sure you will need:  (press q to quit)"  
 NEEDED_MODULES=""
 select M in ${ALL_MODULES}
diff --git a/scripts/create_rst_templates.sh b/scripts/create_rst_templates.sh
index d78f49f3..931701ee 100755
--- a/scripts/create_rst_templates.sh
+++ b/scripts/create_rst_templates.sh
@@ -3,24 +3,15 @@
 # Creates the rst files when creating a new module.
 # Thu Apr  3 11:54:16 CEST 2014
 
-MODULE=$(basename $PWD)
-
-if [[ $MODULE == "src" ]]
+if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "Error: This script should not be run in the src directory."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
 
-function asksure() {
-  echo -n $@ "(Y/N) "
-  answer=w
-  while [[ $answer != [YyNn] ]]
-  do
-     read answer
-     [[ $answer = [Yy] ]] && retval=0 || retval=1
-  done
-  return $retval
-}
+check_current_dir_is_module
 
 README="True"
 if [[ -f README.rst ]]
diff --git a/scripts/ezfio_interface.py b/scripts/ezfio_interface.py
index beebd8a2..ed7ebfc9 100755
--- a/scripts/ezfio_interface.py
+++ b/scripts/ezfio_interface.py
@@ -184,15 +184,26 @@ def save_ezfio_provider(path_head, dict_code_provider):
 
     path = "{0}/ezfio_interface.irp.f".format(path_head)
 
-    print "Path = {}".format(path)
+#    print "Path = {}".format(path)
 
-    with open(path, "w") as f:
-        f.write("!DO NOT MODIFY BY HAND \n")
-        f.write("!Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py \n")
-        f.write("!from file {0}/EZFIO.cfg\n".format(path_head))
-        f.write("\n")
-        for provider_name, code in dict_code_provider.iteritems():
-            f.write(code + "\n")
+    try:
+        f = open(path, "r")
+    except IOError:
+        old_output = ""
+    else:
+        old_output = f.read()
+        f.close()
+
+    output =   "! DO NOT MODIFY BY HAND\n" + \
+               "! Created by $QPACKAGE_ROOT/scripts/ezfio_interface.py\n" + \
+               "! from file {0}/EZFIO.cfg\n".format(path_head) + \
+               "\n" 
+    for provider_name, code in dict_code_provider.iteritems():
+        output += code + "\n"
+
+    if output != old_output:
+        with open(path, "w") as f:
+            f.write(output)
 
 
 def create_ezfio_config(dict_ezfio_cfg, opt, folder):
@@ -220,10 +231,19 @@ def save_ezfio_config(folder, str_ezfio_config):
     path = "{0}/config/{1}.ezfio_interface_config".format(ezfio_dir,
                                                           folder)
 
-    print "Path = {}".format(path)
+#    print "Path = {}".format(path)
 
-    with open(path, "w") as f:
-        f.write(str_ezfio_config)
+    try:
+        f = open(path, "r")
+    except IOError:
+        old_output = ""
+    else:
+        old_output = f.read()
+        f.close()
+
+    if str_ezfio_config != old_output:
+        with open(path, "w") as f:
+            f.write(str_ezfio_config)
 
 def main():
     """Take in argument a EZFIO.cfg"""
@@ -238,28 +258,25 @@ def main():
     path = os.path.expanduser(path)
     path = os.path.expandvars(path)
     path = os.path.abspath(path)
-    print path
+#    print path
 
     path_dirname = os.path.dirname(path)
     folder = [i for i in path_dirname.split("/") if i][-1]
     folder = folder.lower()
 
-    print "Find a EZFIO.cfg in {}".format(path)
+#    print "Found a EZFIO.cfg in {}".format(path)
     dict_info_provider = get_dict_config_file(path,folder)
 
-    print "Generating the ezfio_interface.irp.f: \n"
+#    print "Generating the ezfio_interface.irp.f: \n"
     d_config = create_ezfio_provider(dict_info_provider)
-#    for provider, code in d_config.iteritems():
-#        print code
 
-    print "Saving the ezfio_interface.irp.f"
+#    print "Saving the ezfio_interface.irp.f"
     save_ezfio_provider(path_dirname, d_config)
 
-    print "Generating the ezfio_config"
+#    print "Generating the ezfio_config"
     config_ezfio = create_ezfio_config(dict_info_provider, "config", folder)
-#    print config_ezfio
 
-    print "Saving ezfio_config"
+#    print "Saving ezfio_config"
     save_ezfio_config(folder, config_ezfio)
 
 
diff --git a/scripts/get_basis.sh b/scripts/get_basis.sh
index d6182799..51b0a4f0 100755
--- a/scripts/get_basis.sh
+++ b/scripts/get_basis.sh
@@ -8,6 +8,13 @@
 # Prints in stdout the name of a temporary file containing the basis set.
 #
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+
 export EMSL_API_ROOT="${QPACKAGE_ROOT}"/EMSL_Basis/
 export PYTHONPATH="${EMSL_API_ROOT}":${PYTHONPATH}
 
@@ -15,8 +22,11 @@ tmpfile="$1"
 shift
 
 # Case insensitive basis in input
-basis=$( ${EMSL_API_ROOT}/EMSL_api.py list_basis | cut -d "'" -f 2 | grep -i "^${1}\$")
+#basis=$( ${EMSL_API_ROOT}/EMSL_api.py list_basis | cut -d "'" -f 2 | grep -i "^${1}\$")
+
+basis="$1"
 shift
+
 atoms=""
 
 for atom in $@
diff --git a/scripts/install_curl.sh b/scripts/install_curl.sh
index afe49839..20033f77 100755
--- a/scripts/install_curl.sh
+++ b/scripts/install_curl.sh
@@ -6,12 +6,11 @@
 CURL="curl-7.30.0.ermine"
 CURL_URL="http://qmcchem.ups-tlse.fr/files/scemama/${CURL}.tar.bz2"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}
diff --git a/scripts/install_emsl.sh b/scripts/install_emsl.sh
index dae8f670..dff002a1 100755
--- a/scripts/install_emsl.sh
+++ b/scripts/install_emsl.sh
@@ -6,18 +6,18 @@
 BASE="EMSL_Basis_Set_Exchange_Local"
 URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}
 
 ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
+rm -rf EMSL_Basis
 mv ${BASE}-master EMSL_Basis
 
 
diff --git a/scripts/install_ezfio.sh b/scripts/install_ezfio.sh
index e43363cf..0f7a6505 100755
--- a/scripts/install_ezfio.sh
+++ b/scripts/install_ezfio.sh
@@ -6,17 +6,15 @@
 BASE="ezfio"
 URL="https://github.com/LCPQ/${BASE}/archive/master.tar.gz"
 
-# Check the QPACKAGE_ROOT directory
 if [[ -z ${QPACKAGE_ROOT} ]]
 then
-  echo "The QPACKAGE_ROOT environment variable is not set."
-  echo "Please reload the quantum_package.rc file."
-  exit 1
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
 fi
 
 cd ${QPACKAGE_ROOT}
 
-
 rm -rf -- EZFIO
 ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${URL} ${QPACKAGE_ROOT}/${BASE}.tar.gz
 tar -zxf ${BASE}.tar.gz && rm ${BASE}.tar.gz ||exit 1
diff --git a/scripts/install_ocaml.sh b/scripts/install_ocaml.sh
index 3c695df4..9e89fb68 100755
--- a/scripts/install_ocaml.sh
+++ b/scripts/install_ocaml.sh
@@ -45,7 +45,8 @@ then
     done
   fi
 fi
-scripts/fetch_from_web.py "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
+${QPACKAGE_ROOT}/scripts/fetch_from_web.py \
+   "https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh" opam_installer.sh
 chmod +x opam_installer.sh
 echo N | ./opam_installer.sh ${QPACKAGE_ROOT}/bin 
 
@@ -53,6 +54,7 @@ if [[ ! -f ${QPACKAGE_ROOT}/bin/opam ]]; then
    echo "Installation of OPAM failed"
    exit 2
 fi
+rm opam_installer.sh
 ${QPACKAGE_ROOT}/bin/opam config setup -a --dot-profile ${QPACKAGE_ROOT}/quantum_package.rc 
 
 source ${QPACKAGE_ROOT}/quantum_package.rc
diff --git a/scripts/prepare_ezfio.sh b/scripts/prepare_ezfio.sh
new file mode 100755
index 00000000..c01bacd3
--- /dev/null
+++ b/scripts/prepare_ezfio.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+# Prepares the EZFIO library before running make
+# Wed Mar 25 21:25:11 CET 2015
+
+echo "Building EZFIO library"
+echo "=-=-=-=-=-=-=-=-=-=-=-"
+
+# Interpret all the EZFIO.cfg files
+for dir in ${QPACKAGE_ROOT}/src/*/ 
+do 
+  cd $dir || exit -1
+  ${QPACKAGE_ROOT}/scripts/ezfio_interface.py
+done
+
+# For old-style directories. Will be removed some day...
+cp ${QPACKAGE_ROOT}/src{/*,}/*.ezfio_config ${QPACKAGE_ROOT}/EZFIO/config 
+
+
diff --git a/scripts/prepare_module.sh b/scripts/prepare_module.sh
deleted file mode 100755
index 287c3663..00000000
--- a/scripts/prepare_module.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-# This script is used by module Makefiles, and should not be used by users.
-# Checks if all the other module directories are properly linked in the
-# current directory. If not, the links are created.
-# Wed Apr  2 14:35:42 CEST 2014
-
-for dir in $@
-do
-  if [[ ! -h $dir ]] ;
-  then
-    ln -s ../$dir $dir
-  fi
-done
-
-
diff --git a/scripts/qp_include.sh b/scripts/qp_include.sh
new file mode 100644
index 00000000..467baca8
--- /dev/null
+++ b/scripts/qp_include.sh
@@ -0,0 +1,80 @@
+#!/bin/bash
+#
+# Useful functions in all scripts
+
+# Make a list unique
+function unique_list()
+{
+  for d in $@
+  do
+    echo $d
+  done | sort | uniq
+}
+
+function check_current_dir_is_src()
+{
+  if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
+  then
+     return 0
+  else
+     echo "Current directory should be \$QPACKAGE_ROOT/src"
+     exit -1
+  fi
+}
+
+function check_current_dir_is_module()
+{
+  cd ..
+  if [[ "${PWD}" == "${QPACKAGE_ROOT}/src" ]]
+  then
+     cd $OLDPWD
+     return 0
+  else
+     cd $OLDPWD
+     echo "Current directory should be \$QPACKAGE_ROOT/src"
+     exit -1
+  fi
+}
+if [[ -f NEEDED_MODULES ]]
+then
+  NEEDED_MODULES=$(cat NEEDED_MODULES)
+fi
+
+# List of executables in the current directory
+function ls_exe()
+{
+  find . -perm /u+x -type f
+}
+
+function asksure() {
+  echo -n $@ "(Y/N) "
+  answer=w
+  while [[ $answer != [YyNn] ]]
+  do
+     read answer
+     [[ $answer = [Yy] ]] && retval=0 || retval=1
+  done
+  return $retval
+}
+
+function error()
+{
+  echo "-------------------- Error --------------------"
+  printf "$@\n"
+  echo "-----------------------------------------------"
+  exit -1
+}
+
+if [[ -z ${DEBUG} ]]
+then
+  function info ()
+  {
+    :
+  }
+else
+  function info ()
+  {
+    echo "$@"
+  }
+fi
+
diff --git a/scripts/run_Makefile_common.sh b/scripts/run_Makefile_common.sh
new file mode 100755
index 00000000..0a579a94
--- /dev/null
+++ b/scripts/run_Makefile_common.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+#
+# Checks to run in every Module directory before building
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_module
+
+# Check if the NEEDED_MODULES file is consistent
+INCLUDE_DIRS="${NEEDED_MODULES} include"
+NEEDED_MODULES_OK=$( ${QPACKAGE_ROOT}/scripts/check_dependencies.sh ${NEEDED_MODULES} )
+if [[ $? -ne 0 ]] 
+then
+  error "
+Your NEEDED_MODULES file is inconsistent. It should be
+${NEEDED_MODULES_OK}
+"
+else
+  info "NEEDED_MODULES files is consistent"
+fi
+
+# Check if README.rst exists
+if [[ ! -f README.rst ]] 
+then
+  ${QPACKAGE_ROOT}/scripts/create_rst_templates.sh
+  error "
+README.rst was not present, so I created a
+default one for you.
+You should document it before you compile, as
+well as the ASSUMPTIONS.rst file.
+"
+else
+  info "README.rst is present"
+fi
+
+
+# Check if ASSUMPTIONS.rst exists
+if [[ ! -f ASSUMPTIONS.rst ]] 
+then
+  error "This is a Bug. At that point, the ASSUMPTIONS.rst) file should exist."
+else
+  info "ASSUMPTIONS.rst is present."
+fi
+
+
+# Create symbolic links of other modules
+if [[ $PWD != ${QPACKAGE_ROOT}/src ]]
+then
+  for dir in ${INCLUDE_DIRS}
+  do
+    if [[ ! -h $dir ]] ;
+    then
+      ln -s ../$dir $dir
+    fi
+  done
+fi
+
+# Update Makefile.depend
+${QPACKAGE_ROOT}/scripts/create_Makefile_depend.sh
+
+# Update EZFIO interface
+${QPACKAGE_ROOT}/scripts/ezfio_interface.py
+
diff --git a/scripts/run_Makefile_global.sh b/scripts/run_Makefile_global.sh
new file mode 100755
index 00000000..82dee8ab
--- /dev/null
+++ b/scripts/run_Makefile_global.sh
@@ -0,0 +1,81 @@
+#!/bin/bash
+# Makes several checks before compiling.
+# Wed Mar 25 21:22:18 CET 2015
+
+# Required EZFIO version
+EZFIO_REQUIRED_VERSION=1.1
+
+# Required IRPF90 version
+IRPF90_REQUIRED_VERSION=1.5
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+check_current_dir_is_src
+
+
+# Check if the user's config exists
+if [[ ! -f  ${QPACKAGE_ROOT}/src/Makefile.config ]] 
+then
+  error "
+Makefile.config is not present.
+You can create Makefile.config
+by modifying Makefile.config.example
+"
+else
+  info "Makefile.config is present"
+fi
+
+
+IRPF90_VERSION=$( ${IRPF90} -v )
+python << EOF
+import sys
+irp_version = float("${IRPF90_VERSION}".rsplit('.',1)[0])
+irp_required_version = float($IRPF90_REQUIRED_VERSION)
+if irp_version < irp_required_version:
+  sys.exit(-1)
+EOF
+
+if [[ $? -ne 0 ]]
+then
+  error "
+Current IRPF90 version :
+\$ ${IRPF90} -v
+${IRPF90_VERSION}.
+
+IRPF90 version >= ${IRPF90_REQUIRED_VERSION} is required.
+To upgrade IRPF90, run :                       
+  ${QPACKAGE_ROOT}/scripts/upgrade_irpf90.sh   
+"
+else
+  info "irpf90 version is OK"
+fi
+
+
+# Check EZFIO version
+EZFIO_VERSION=$(cat ${QPACKAGE_ROOT}/EZFIO/version | cut -d '=' -f 2)
+python << EOF
+import sys
+ezfio_version = float("${EZFIO_VERSION}".rsplit('.',1)[0])
+ezfio_required_version = float($EZFIO_REQUIRED_VERSION)
+if ezfio_version < ezfio_required_version:
+  sys.exit(-1)
+EOF
+
+if [[ $? -ne 0 ]]
+then
+  error "
+Current EZFIO version : ${EZFIO_VERSION}
+EZFIO version >= ${EZFIO_REQUIRED_VERSION} is required.
+To upgrade EZFIO, run :                       
+  ${QPACKAGE_ROOT}/scripts/upgrade_ezfio.sh   
+"
+else
+  info "EZFIO version is OK"
+fi
+
diff --git a/scripts/save_current_mos.sh b/scripts/save_current_mos.sh
index 941f4ed8..36149ae2 100755
--- a/scripts/save_current_mos.sh
+++ b/scripts/save_current_mos.sh
@@ -4,6 +4,13 @@
 # directory, where xxx is the corresponding mo_label.
 # Wed Apr  2 14:35:15 CEST 2014
 
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+
 EZFIO=$1
 
 if [[ -z ${EZFIO} ]]
diff --git a/scripts/unarchive_ezfio.sh b/scripts/unarchive_ezfio.sh
deleted file mode 100755
index 7f70fa6e..00000000
--- a/scripts/unarchive_ezfio.sh
+++ /dev/null
@@ -1,54 +0,0 @@
-#!/bin/bash
-#
-# Reads a *.md5 file, then fetches the proper data in the
-# cache and re-creates the EZFIO database.
-# If the cache data is not present, download it from 
-# $QPACKAGE_CACHE_URL
-# Fri Apr  4 01:02:53 CEST 2014
-
-if [[ -z ${QPACKAGE_ROOT} ]]
-then
-  print "The QPACKAGE_ROOT environment variable is not set."
-  print "Please reload the quantum_package.rc file."
-fi
-
-EZFIO_FILE=$(basename $(basename ${1} .md5))
-
-if [[ -z $1 ]]
-then
-  echo "Usage: $(basename $0) <EZFIO_FILE.md5>"
-  exit 1
-fi
-
-if [[ ! -f ${EZFIO_FILE}.md5 ]]
-then
-  echo "Error: ${EZFIO_FILE}.md5 does not exist."
-  exit 1
-fi
-
-key=($(cut -d ' ' -f 1 ${EZFIO_FILE}.md5))
-filename=($(cut -d ' ' -f 2 ${EZFIO_FILE}.md5))
-
-if [[ -z ${QPACKAGE_CACHE_URL} ]]
-then
-  echo "Error: The QPACKAGE_CACHE_URL environment variable is not set."  
-  exit 1
-fi
-
-VERSION=$( cut -d '=' -f 2 < ${QPACKAGE_ROOT}/EZFIO/version)
-for i in ${!key[@]}
-do
-  MD5=${key[$i]}
-  file=${filename[$i]}
-  if [[ ! -d $file ]]
-  then
-    mkdir -p $(dirname $file)
-    echo ${VERSION} > $(dirname $file)/.version
-  fi
-  if [[ ! -f ${QPACKAGE_ROOT}/data/cache/${MD5} ]]
-  then
-    ${QPACKAGE_ROOT}/scripts/fetch_from_web.py ${QPACKAGE_CACHE_URL}/${MD5} ${QPACKAGE_ROOT}/data/cache/${MD5}
-  fi
-  cp ${QPACKAGE_ROOT}/data/cache/${MD5} ${file}
-done
-echo ${VERSION} > ${EZFIO_FILE}.ezfio/.version
diff --git a/scripts/upgrade_ezfio.sh b/scripts/upgrade_ezfio.sh
index daa51405..4a9af403 100755
--- a/scripts/upgrade_ezfio.sh
+++ b/scripts/upgrade_ezfio.sh
@@ -12,7 +12,7 @@ fi
 cd -- ${QPACKAGE_ROOT}
 mv -- ${QPACKAGE_ROOT}/EZFIO ${QPACKAGE_ROOT}/EZFIO.old
 
-make EZFIO
+${QPACKAGE_ROOT}/scripts/install_ezfio.sh
 
 if [[ $? -eq 0 ]]
 then
diff --git a/setup_environment.sh b/setup_environment.sh
index c0d8b0ce..9fe24c96 100755
--- a/setup_environment.sh
+++ b/setup_environment.sh
@@ -75,6 +75,9 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
 " $BLACK
 
 
+mkdir -f install_logs
+mv *.log install_logs/
+
 if [[ $1 == "--robot" ]] ; 
 then
   exit 0
diff --git a/src/AOs/Makefile b/src/AOs/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/AOs/Makefile
+++ b/src/AOs/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/BiInts/Makefile b/src/BiInts/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/BiInts/Makefile
+++ b/src/BiInts/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Bitmask/Makefile b/src/Bitmask/Makefile
index fa91d467..d230cb0c 100644
--- a/src/Bitmask/Makefile
+++ b/src/Bitmask/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=bitmasks_module.f90
diff --git a/src/CAS_SD_selected/Makefile b/src/CAS_SD_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CAS_SD_selected/Makefile
+++ b/src/CAS_SD_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CID/Makefile b/src/CID/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CID/Makefile
+++ b/src/CID/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CID_SC2_selected/Makefile b/src/CID_SC2_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CID_SC2_selected/Makefile
+++ b/src/CID_SC2_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CID_selected/Makefile b/src/CID_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CID_selected/Makefile
+++ b/src/CID_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CIS/Makefile b/src/CIS/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CIS/Makefile
+++ b/src/CIS/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CISD/Makefile b/src/CISD/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CISD/Makefile
+++ b/src/CISD/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CISD_SC2_selected/Makefile b/src/CISD_SC2_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CISD_SC2_selected/Makefile
+++ b/src/CISD_SC2_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/CISD_selected/Makefile b/src/CISD_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/CISD_selected/Makefile
+++ b/src/CISD_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/DDCI_selected/Makefile b/src/DDCI_selected/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/DDCI_selected/Makefile
+++ b/src/DDCI_selected/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Dets/Makefile b/src/Dets/Makefile
index f97f77c0..092d879d 100644
--- a/src/Dets/Makefile
+++ b/src/Dets/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=H_apply_template.f
diff --git a/src/Electrons/Makefile b/src/Electrons/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Electrons/Makefile
+++ b/src/Electrons/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Ezfio_files/Makefile b/src/Ezfio_files/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Ezfio_files/Makefile
+++ b/src/Ezfio_files/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/FCIdump/Makefile b/src/FCIdump/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/FCIdump/Makefile
+++ b/src/FCIdump/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Full_CI/Makefile b/src/Full_CI/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Full_CI/Makefile
+++ b/src/Full_CI/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Generators_CAS/Makefile b/src/Generators_CAS/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Generators_CAS/Makefile
+++ b/src/Generators_CAS/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Generators_full/Makefile b/src/Generators_full/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Generators_full/Makefile
+++ b/src/Generators_full/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Generators_restart/Makefile b/src/Generators_restart/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Generators_restart/Makefile
+++ b/src/Generators_restart/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Hartree_Fock/Makefile b/src/Hartree_Fock/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Hartree_Fock/Makefile
+++ b/src/Hartree_Fock/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/MOGuess/Makefile b/src/MOGuess/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/MOGuess/Makefile
+++ b/src/MOGuess/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/MOs/Makefile b/src/MOs/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/MOs/Makefile
+++ b/src/MOs/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/MP2/Makefile b/src/MP2/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/MP2/Makefile
+++ b/src/MP2/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Makefile b/src/Makefile
index 307197fe..cd8ce65b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,19 +1,24 @@
-default: all
+ifndef QPACKAGE_ROOT
+  $(error "QPACKAGE_ROOT is not defined. Please source quantum_package.rc")
+endif
 
-SRC=
-OBJ=
+include Makefile.config
 
 ALL_MODULES=$(shell cat NEEDED_MODULES)
+EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
+EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 
-.PHONY: executables all all_clean $(ALL_MODULES)
+.PHONY: $(ALL_MODULES)
 
-all: $(ALL_MODULES)
 
-all_clean:
-	@for i in $(ALL_MODULES) ; do cd $$i ; make veryclean ; make clean_links ; cd .. ; done
+default: $(EZFIO)
+	$(QPACKAGE_ROOT)/scripts/build_modules.sh $(ALL_MODULES)
 
-$(ALL_MODULES): FORCE
-	cd $@ ; make -j $$(cat /proc/cpuinfo | grep MHz | wc -l)
+veryclean:
+	$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
+
+$(ALL_MODULES): $(EZFIO)
+	$(QPACKAGE_ROOT)/scripts/build_modules.sh $@ 
 
 executables: $(ALL_MODULES)
 	rm -f executables ; \
@@ -21,7 +26,15 @@ executables: $(ALL_MODULES)
 	  do printf "%-30s %s\n" $$(basename $$EXE) $$EXE | sed "s|$(QPACKAGE_ROOT)|\$$QPACKAGE_ROOT|g" >> executables ;\
 	done
 
-# Dummy rule to enable to force recompilation
-FORCE:
+# Define the EZFIO rules
+$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
+	$(QPACKAGE_ROOT)/scripts/prepare_ezfio.sh
+	cd $(EZFIO_DIR);\
+	export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ;\
+	$(MAKE) ;\
+	$(MAKE) Python
+
+# Frequent typos
+clena: clean
+veryclena: veryclean
 
-veryclean: all_clean
diff --git a/src/Makefile.common b/src/Makefile.common
index 7b63f772..9ecc93c0 100644
--- a/src/Makefile.common
+++ b/src/Makefile.common
@@ -1,160 +1,34 @@
-.PHONY: default
+.PHONY: default silent
+
+ifneq ($(IN_MAKE),1) 
+
+default:
+	@$(MAKE) -C $(QPACKAGE_ROOT)/src $$(basename $(PWD))
+
+veryclean:
+	 clean_modules.sh
+
+else  # Called by scripts/build_module.sh
 
 default: all .gitignore
 
-# Required EZFIO version
-EZFIO_VERSION=1.1
-
-# Required IRPF90 version
-IRPF90_VERSION=1.4
-
-# Check if QPACKAGE_ROOT is defined
-
-ifndef QPACKAGE_ROOT
-$(info  -------------------- Error --------------------)
-$(info  QPACKAGE_ROOT undefined. Run the setup_environment.sh script)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  QPACKAGE_ROOT is defined.)
-endif
-
-
-# Check if the user's config exists
-
-MAKEFILE_OK=$(shell ls $(QPACKAGE_ROOT)/src/Makefile.config 2> /dev/null && echo True || echo False)
-ifeq ($(MAKEFILE_OK),False)
-$(info  -------------------- Error --------------------)
-$(info Makefile.config is not present.)
-$(info You can create Makefile.config)
-$(info by modifying Makefile.config.example)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  Makefile.config is present.)
-endif
-
-
 # Include the user's config
-
 include $(QPACKAGE_ROOT)/src/Makefile.config
 
-
-# Check the  version of IRPF90
-
-IRP_VERSION_OK=$(shell $(IRPF90) -v | python -c "import sys ; print float(sys.stdin.readline().rsplit('.',1)[0]) >= $(IRPF90_VERSION)")
-ifeq ($(IRP_VERSION_OK),False)
-$(info  -------------------- Error --------------------)
-$(info  IRPF90 version >= $(IRPF90_VERSION) is required)
-$(info  To upgrade IRPF90, run :                       )
-$(info    $(QPACKAGE_ROOT)/scripts/upgrade_irpf90.sh   )
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  irpf90 version is OK.)
-endif
-
-
 # Create the NEEDED_MODULES variable, needed for IRPF90
-
 NEEDED_MODULES=$(shell cat NEEDED_MODULES)
 
-
-# Check if the NEEDED_MODULES file is consistent
-
-NEEDED_MODULES_OK=$(shell X=`$(QPACKAGE_ROOT)/scripts/check_dependencies.sh $(NEEDED_MODULES)` && echo OK || echo $$X)
-ifneq ($(NEEDED_MODULES_OK),OK)
-$(info  -------------------- Error --------------------)
-$(info Your NEEDED_MODULES file is inconsistent. It should be)
-$(info $(NEEDED_MODULES_OK))
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  NEEDED_MODULES files is consistent.)
-endif
-
-
 # Check and update dependencies
-
 include Makefile.depend
 
 
-# Check if README.rst exists
-
-README_RST_OK=$(shell ls README.rst 2>/dev/null || echo False)
-ifeq ($(README_RST_OK), False)
-$(shell $(QPACKAGE_ROOT)/scripts/create_rst_templates.sh)
-$(info  -------------------- Error --------------------)
-$(info  README.rst was not present, so I created a)
-$(info  default one for you.)
-$(info  You should document it before you compile, as)
-$(info  well as the ASSUMPTIONS.rst file.)
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  README.rst is present.)
-endif
-
-
-# Check if ASSUMPTIONS.rst exists
-
-ASSUMPTIONS_RST_OK=$(shell ls ASSUMPTIONS.rst || echo False)
-ifeq ($(ASSUMPTIONS_RST_OK), False)
-$(info  -------------------- Error --------------------)
-$(info This is a Bug. At that point, the ASSUMPTIONS.rst)
-$(info file should exist.)
-$(info  -----------------------------------------------)
-#else
-#$(info  ASSUMPTIONS.rst is present.)
-endif
-
-
 # Define the Makefile common variables
-
 EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
 EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 INCLUDE_DIRS=$(NEEDED_MODULES) include
 
-# Check EZFIO version
-
-EZFIO_VERSION_OK=$(shell cat $(EZFIO_DIR)/version | cut -d '=' -f 2 | python -c "import sys ; print float(sys.stdin.readline().rsplit('.',1)[0]) >= $(EZFIO_VERSION)")
-ifeq ($(EZFIO_VERSION_OK),False)
-$(info  -------------------- Error --------------------)
-$(info  EZFIO version >= $(EZFIO_VERSION) is required  )
-$(info  To upgrade EZFIO, run :                        )
-$(info    $(QPACKAGE_ROOT)/scripts/upgrade_ezfio.sh    )
-$(info  -----------------------------------------------)
-$(error )
-#else
-#$(info  EZFIO version is OK.)
-endif
-
-# Define the EZFIO rules
-
-$(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
-	@echo Building EZFIO library
-	@echo =-=-=-=-=-=-=-=-=-=-=-
-	for dir in $(QPACKAGE_ROOT)/src/*/ ;\
-	do \
-	        cd $$dir && \
-		$(QPACKAGE_ROOT)/scripts/ezfio_interface.py && \
-		cd .. ;\
-	done
-	cp $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/*.ezfio_config) $(EZFIO_DIR)/config 
-	cd $(EZFIO_DIR) ; export FC="$(FC)" ; export FCFLAGS="$(FCFLAGS)" ; export IRPF90="$(IRPF90)" ; $(MAKE) ; $(MAKE) Python
-
-ezfio: $(EZFIO)
-
-
-# Create symbolic links of other modules
-
-ifneq ($(PWD),$(QPACKAGE_ROOT)/src)
-$(shell $(QPACKAGE_ROOT)/scripts/prepare_module.sh $(INCLUDE_DIRS))
 clean_links:
 	rm -f $(INCLUDE_DIRS) $$(basename $$PWD)
-else
-clean_links:
-endif
 
 LIB+=$(EZFIO) $(MKL)
 IRPF90+=$(patsubst %, -I %, $(INCLUDE_DIRS)) $(IRPF90_FLAGS)
@@ -163,22 +37,14 @@ irpf90.make: $(filter-out IRPF90_temp/%, $(wildcard */*.irp.f)) $(wildcard *.irp
 	- $(IRPF90)
 	- update_README.py
 
-Makefile.depend: Makefile
-	$(QPACKAGE_ROOT)/scripts/create_Makefile_depend.sh
-
-ifneq ( $(PWD), $($(QPACKAGE_ROOT)/src))
 include irpf90.make
+
 endif
 
-# Dummy rule to enable to force recompilation
-FORCE:
-
-vercylean: veryclean
-
 .gitignore:
 	$(QPACKAGE_ROOT)/scripts/create_gitignore.sh 
 
-
 # Frequent typos
 clena: clean
 veryclena: veryclean
+vercylean: veryclean
diff --git a/src/Molden/Makefile b/src/Molden/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Molden/Makefile
+++ b/src/Molden/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/MonoInts/Makefile b/src/MonoInts/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/MonoInts/Makefile
+++ b/src/MonoInts/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/NEEDED_MODULES b/src/NEEDED_MODULES
index 84057d07..3df2ab88 100644
--- a/src/NEEDED_MODULES
+++ b/src/NEEDED_MODULES
@@ -1 +1 @@
-AOs BiInts Bitmask Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD_selected DDCI_selected
+AOs BiInts Bitmask CID CID_SC2_selected CID_selected CIS CISD CISD_selected CISD_SC2_selected Dets Electrons Ezfio_files Full_CI Generators_full Hartree_Fock MOGuess MonoInts MOs MP2 Nuclei Output Selectors_full Utils Molden FCIdump Generators_CAS CAS_SD_selected DDCI_selected
diff --git a/src/Nuclei/Makefile b/src/Nuclei/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Nuclei/Makefile
+++ b/src/Nuclei/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Output/Makefile b/src/Output/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Output/Makefile
+++ b/src/Output/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Perturbation/Makefile b/src/Perturbation/Makefile
index ea95cbf1..b668f388 100644
--- a/src/Perturbation/Makefile
+++ b/src/Perturbation/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=perturbation_template.f
diff --git a/src/Properties/Makefile b/src/Properties/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Properties/Makefile
+++ b/src/Properties/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Selectors_full/Makefile b/src/Selectors_full/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Selectors_full/Makefile
+++ b/src/Selectors_full/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Selectors_no_sorted/Makefile b/src/Selectors_no_sorted/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/Selectors_no_sorted/Makefile
+++ b/src/Selectors_no_sorted/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/SingleRefMethod/Makefile b/src/SingleRefMethod/Makefile
index b2ea1de1..06dc50ff 100644
--- a/src/SingleRefMethod/Makefile
+++ b/src/SingleRefMethod/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=
diff --git a/src/Utils/Makefile b/src/Utils/Makefile
index 69065f55..aac09429 100644
--- a/src/Utils/Makefile
+++ b/src/Utils/Makefile
@@ -1,5 +1,3 @@
-default: all
-
 # Define here all new external source files and objects.Don't forget to prefix the
 # object files with IRPF90_temp/
 SRC=map_module.f90

From c7765043fefc0f3526acb04b978c68afa836bda2 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Mar 2015 01:17:37 +0100
Subject: [PATCH 3/6] Improved setup

---
 scripts/install_irpf90.sh |  1 -
 setup_environment.sh      | 73 +++++++++++++++++++++++++++++++++++----
 2 files changed, 66 insertions(+), 8 deletions(-)

diff --git a/scripts/install_irpf90.sh b/scripts/install_irpf90.sh
index 04513ca8..d93340d2 100755
--- a/scripts/install_irpf90.sh
+++ b/scripts/install_irpf90.sh
@@ -27,4 +27,3 @@ echo '${QPACKAGE_ROOT}/irpf90/bin/irpman $@' > bin/irpman
 chmod +x bin/irpf90 bin/irpman
 
 
-
diff --git a/setup_environment.sh b/setup_environment.sh
index 9fe24c96..ca853fdf 100755
--- a/setup_environment.sh
+++ b/setup_environment.sh
@@ -41,22 +41,81 @@ export PATH=\${PATH}:"\${QPACKAGE_ROOT}"/ocaml
 source "\${QPACKAGE_ROOT}"/bin/irpman &> /dev/null
 EOF
 
+
 source quantum_package.rc
-make EZFIO
+
+echo "${BLUE}===== Installing IRPF90 ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_irpf90.sh     | tee install_irpf90.log
+if [[ ! -d ${QPACKAGE_ROOT}/irpf90 ]]
+then
+  echo $RED "Error in IRPF90 installation" $BLACK
+  exit 1
+fi
+
+if [[ ! -x ${QPACKAGE_ROOT}/bin/irpf90 ]]
+then
+  echo $RED "Error in IRPF90 installation" $BLACK
+  exit 1
+fi
+
+
+if [[ ! -x ${QPACKAGE_ROOT}/bin/irpman ]]
+then
+  echo $RED "Error in IRPF90 installation" $BLACK
+  exit 1
+fi
+
+
+echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
+
 if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
 then
   echo $RED "Error in EZFIO installation" $BLACK
   exit 1
 fi
 
-make ocaml
-if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
+
+echo "${BLUE}===== Installing Zlib ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_zlib.sh       | tee install_zlib.log
+
+echo "${BLUE}===== Installing Curl ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_curl.sh       | tee install_curl.log
+
+echo "${BLUE}===== Installing M4 ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_m4.sh         | tee install_m4.log
+
+echo "${BLUE}===== Installing EMSL Basis set library ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_emsl.sh       | tee install_emsl.log
+
+if [[ ! -d ${QPACKAGE_ROOT}/EMSL_Basis ]]
 then
-  echo $RED "Error in ocaml installation" $BLACK
+  echo $RED "Error in EMSL Basis set library installation" $BLACK
   exit 1
 fi
 
-make resultsFile
+echo "${BLUE}===== Installing EZFIO ===== ${BLACK}"
+
+${QPACKAGE_ROOT}/scripts/install_ezfio.sh | tee install_ezfio.log
+if [[ ! -d ${QPACKAGE_ROOT}/EZFIO ]]
+then
+  echo $RED "Error in EZFIO installation" $BLACK
+  exit 1
+fi
+
+
+echo "${BLUE}===== Installing Ocaml compiler and libraries ===== ${BLACK}"
+rm -f -- ocaml/Qptypes.ml
+${QPACKAGE_ROOT}/scripts/install_ocaml.sh | tee install_ocaml.log
+
+if [[ ! -f ${QPACKAGE_ROOT}/ocaml/Qptypes.ml ]]
+then
+  echo $RED "Error in Ocaml installation" $BLACK
+  exit 1
+fi
+
+echo "${BLUE}===== Installing resultsFile Python library ===== ${BLACK}"
+${QPACKAGE_ROOT}/scripts/install_resultsFile.sh
 if [[ ! -d ${QPACKAGE_ROOT}/resultsFile ]]
 then
   echo $RED "Error in resultsFile installation" $BLACK
@@ -75,8 +134,8 @@ source ${QPACKAGE_ROOT}/quantum_package.rc
 " $BLACK
 
 
-mkdir -f install_logs
-mv *.log install_logs/
+mkdir -p ${QPACKAGE_ROOT}/install_logs
+mv ${QPACKAGE_ROOT}/*.log ${QPACKAGE_ROOT}/install_logs/
 
 if [[ $1 == "--robot" ]] ; 
 then

From a500848a8b721902a67d052397b3dc28945fc672 Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Mar 2015 01:33:32 +0100
Subject: [PATCH 4/6] Improved Ocaml makefile

---
 ocaml/Makefile                     |  7 +++----
 scripts/create_executables_list.sh | 26 ++++++++++++++++++++++++++
 src/Makefile                       | 14 +++++---------
 3 files changed, 34 insertions(+), 13 deletions(-)
 create mode 100755 scripts/create_executables_list.sh

diff --git a/ocaml/Makefile b/ocaml/Makefile
index 18788a1b..be763cbd 100644
--- a/ocaml/Makefile
+++ b/ocaml/Makefile
@@ -1,7 +1,6 @@
-# Check if QPACKAGE_ROOT is defined
-
 .NOPARALLEL:
 
+# Check if QPACKAGE_ROOT is defined
 ifndef QPACKAGE_ROOT
 $(info  -------------------- Error --------------------)
 $(info  QPACKAGE_ROOT undefined. Source the quantum_package.rc script)
@@ -30,8 +29,8 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 	   echo $$i ; \
 	done >> .gitignore
 
-executables: 
-	$(MAKE) -C $(QPACKAGE_ROOT)/data executables
+executables: $(QPACKAGE_ROOT)/data/executables
+	$(QPACKAGE_ROOT)/scripts/create_executables_list.sh
 
 external_libs:
 	opam install cryptokit core
diff --git a/scripts/create_executables_list.sh b/scripts/create_executables_list.sh
new file mode 100755
index 00000000..b4aa4244
--- /dev/null
+++ b/scripts/create_executables_list.sh
@@ -0,0 +1,26 @@
+#!/bin/bash 
+#
+# Thu Mar 26 01:27:14 CET 2015
+
+if [[ -z ${QPACKAGE_ROOT} ]]
+then
+  print "The QPACKAGE_ROOT environment variable is not set."
+  print "Please reload the quantum_package.rc file."
+  exit -1
+fi
+source ${QPACKAGE_ROOT}/scripts/qp_include.sh
+
+cd ${QPACKAGE_ROOT}/data
+
+rm -f executables
+EXES=$(find ${QPACKAGE_ROOT}/src -perm /u+x -type f | grep -e "${QPACKAGE_ROOT}/src/[^/]*/[^/]*$" |sort ) 
+
+for EXE in $EXES
+do
+   printf "%-30s %s\n" $(basename $EXE) $EXE | sed "s|${QPACKAGE_ROOT}|\$QPACKAGE_ROOT|g" >> executables 
+done
+
+
+
+
+
diff --git a/src/Makefile b/src/Makefile
index cd8ce65b..298cc134 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -8,24 +8,18 @@ ALL_MODULES=$(shell cat NEEDED_MODULES)
 EZFIO_DIR=$(QPACKAGE_ROOT)/EZFIO
 EZFIO=$(EZFIO_DIR)/lib/libezfio_irp.a
 
-.PHONY: $(ALL_MODULES)
+.PHONY: $(ALL_MODULES) ezfio
 
 
-default: $(EZFIO)
+default: ezfio
 	$(QPACKAGE_ROOT)/scripts/build_modules.sh $(ALL_MODULES)
 
 veryclean:
 	$(QPACKAGE_ROOT)/scripts/clean_modules.sh $(ALL_MODULES)
 
-$(ALL_MODULES): $(EZFIO)
+$(ALL_MODULES): ezfio
 	$(QPACKAGE_ROOT)/scripts/build_modules.sh $@ 
 
-executables: $(ALL_MODULES)
-	rm -f executables ; \
-	for EXE in $$(find $(QPACKAGE_ROOT)/src -perm /u+x -type f | grep -e "$(QPACKAGE_ROOT)/src/[^/]*/[^/]*$$" |sort ) ; \
-	  do printf "%-30s %s\n" $$(basename $$EXE) $$EXE | sed "s|$(QPACKAGE_ROOT)|\$$QPACKAGE_ROOT|g" >> executables ;\
-	done
-
 # Define the EZFIO rules
 $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_ROOT)/src/*/EZFIO.cfg)
 	$(QPACKAGE_ROOT)/scripts/prepare_ezfio.sh
@@ -34,6 +28,8 @@ $(EZFIO): $(wildcard $(QPACKAGE_ROOT)/src/*.ezfio_config) $(wildcard $(QPACKAGE_
 	$(MAKE) ;\
 	$(MAKE) Python
 
+ezfio: $(EZFIO)
+
 # Frequent typos
 clena: clean
 veryclena: veryclean

From ded78166db5d511172ff90990fcabd9662610ddf Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Mar 2015 02:03:01 +0100
Subject: [PATCH 5/6] Corrected ocaml makefile

---
 ocaml/Makefile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ocaml/Makefile b/ocaml/Makefile
index be763cbd..2c3fae01 100644
--- a/ocaml/Makefile
+++ b/ocaml/Makefile
@@ -30,6 +30,8 @@ default: $(ALL_TESTS) $(ALL_EXE) .gitignore
 	done >> .gitignore
 
 executables: $(QPACKAGE_ROOT)/data/executables
+
+$(QPACKAGE_ROOT)/data/executables:
 	$(QPACKAGE_ROOT)/scripts/create_executables_list.sh
 
 external_libs:

From abff0f0c44e58d3314abaae0323975081753042d Mon Sep 17 00:00:00 2001
From: Anthony Scemama <scemama@irsamc.ups-tlse.fr>
Date: Thu, 26 Mar 2015 02:16:12 +0100
Subject: [PATCH 6/6] Fixed static build with gfortran

---
 scripts/make_binary.sh | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/scripts/make_binary.sh b/scripts/make_binary.sh
index 8ac6495d..832be596 100755
--- a/scripts/make_binary.sh
+++ b/scripts/make_binary.sh
@@ -123,8 +123,12 @@ echo "Copying dynamic libraries"
 #     --------------------------
 
 MKL_LIBS=$(find_libs ${FORTRAN_EXEC} | grep libmkl | head -1)
-MKL_LIBS=$(dirname ${MKL_LIBS})
-MKL_LIBS=$(ls ${MKL_LIBS}/libmkl_{def,avx,avx2}.so)
+if [[ -n ${MKL_LIBS} ]]
+then
+  MKL_LIBS=$(dirname ${MKL_LIBS})
+  MKL_LIBS=$(ls ${MKL_LIBS}/libmkl_{def,avx,avx2}.so)
+fi
+
 ALL_LIBS=$(find_libs ${OCAML_EXEC} ${FORTRAN_EXEC})
 cp -- ${ALL_LIBS} ${MKL_LIBS} ${QPACKAGE_STATIC}/extra_lib
 if [[ $? -ne 0 ]] ;
@@ -133,12 +137,7 @@ then
   exit 1
 fi
 
-cp -- ${QPACKAGE_STATIC}/extra_lib/{libiomp*,libmkl*} ${QPACKAGE_STATIC}/lib/
-if [[ $? -ne 0 ]] ;
-then
-  echo 'mv -- ${QPACKAGE_STATIC}/extra_lib/{libiomp*,libmkl*} ${QPACKAGE_STATIC}/lib/'
-  exit 1
-fi
+cp -- ${QPACKAGE_STATIC}/extra_lib/lib{[gi]omp*,mkl*,lapack*,blas*,z*} ${QPACKAGE_STATIC}/lib/
 
 #
 echo "Copying EMSL_Basis directory"