cleaning all files

cfg/CentOs6/cmake.profile

-export PATH=/opt/cmake/bin:$PATH
+add2env PATH "/opt/cmake/bin"

cfg/CentOs6/compilers.bashrc

-# this should be done in the .profile but if the shell is dash
-# it does not work.
-# => we call intel cf file  in both places (bashrc & profile)
+add2env PATH "/opt/gcc/bin" front
+add2env LD_LIBRARY_PATH "/opt/gcc/lib64" front
\ No newline at end of file
-
-# recompiled gcc
-export PATH=/opt/gcc/bin:$PATH
-export LD_LIBRARY_PATH=/opt/gcc/lib64:$LD_LIBRARY_PATH
-
-# icc
-#if [ -z "$MKLROOT" ]; then
-#   . /opt/intel/bin/compilervars.sh intel64
-#fi
-

cfg/CentOs6/compilers.profile

-# the .profile is sometimes read by "dash" and we cannot provide 
-# a sourced script with some parameters (it is a "bashism")
-#
-#
-# recompiled gcc
-export PATH=/opt/gcc/bin:$PATH
-export LD_LIBRARY_PATH=/opt/gcc/lib64:$LD_LIBRARY_PATH
-# icc
-#if [ -n "$BASH_VERSION" ]; then
-   #if [ -z "$MKLROOT" ]; then  # pas suffisant! (MKLROOT transmis au "at" mais pas LD_LIBRARY_PATH)
-#      . /opt/intel/bin/compilervars.sh intel64
-   #fi
-#fi
+add2env PATH "/opt/gcc/bin" front
+add2env LD_LIBRARY_PATH "/opt/gcc/lib64" front

cfg/CentOs6/matlab.profile

-PATH=$PATH:/opt/MATLAB/R2012a/bin
-
+add2env PATH "/opt/MATLAB/R2012a/bin"

cfg/CentOs6/mumps.profile

-# $id$
-#
-# configuration to allow CMake to automatically find mumps 
-#
-export LIB=$LIB:/opt/mumps/lib
-export INCLUDE=$INCLUDE:/opt/mumps/include
-
-# not necessary while cmake link with absolute path to libs
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mumps/lib
+add2env LD_LIBRARY_PATH "/opt/mumps/lib"
+add2env LIB "/opt/mumps/lib"
+add2env INCLUDE "/opt/mumps/include"

cfg/CentOs6/parasolid.profile

-# Parasolid
-
-# adds pskernel.so to the PATH
-
-if [ -d /opt/parasolid/shared_object ] ; then
-    if [ -z "${PATH}" ] ; then
-       export PATH="/opt/parasolid/shared_object"
-    else
-       export PATH="/opt/parasolid/shared_object:${PATH}"
-    fi
-    if [ -z "${LD_LIBRARY_PATH}" ] ; then
-       export LD_LIBRARY_PATH="/opt/parasolid/shared_object"
-    else
-       export LD_LIBRARY_PATH="/opt/parasolid/shared_object:${LD_LIBRARY_PATH}"
-    fi
-
-fi
-
-# adds parasolid INCLUDE dir
-
-if [ -d /opt/parasolid ] ; then
-    if [ -z "${INCLUDE}" ] ; then
-       export INCLUDE="/opt/parasolid"
-    else
-       export INCLUDE="/opt/parasolid:${INCLUDE}"
-    fi
-fi
-
+add2env PATH "/opt/parasolid/shared_object"
+add2env INCLUDE "/opt/parasolid"
 export P_SCHEMA=/opt/parasolid/schema
-

cfg/CentOs6/python.profile

-export PATH=/opt/python-2.7.10/bin:$PATH
-export LD_LIBRARY_PATH=/opt/python-2.7.10/lib:$LD_LIBRARY_PATH
+add2env PATH "/opt/python-2.7.10/bin" front
+add2env LD_LIBRARY_PATH "/opt/python-2.7.10/lib" front

cfg/CentOs6/qt.profile

-export PATH=/opt/qt/bin:$PATH
-export LD_LIBRARY_PATH=/opt/qt/lib:$LD_LIBRARY_PATH
+add2env PATH "/opt/qt/bin" front
+add2env LD_LIBRARY_PATH "/opt/qt/bin" front

cfg/CentOs6/samcef.profile

-# Samcef v15.01-3
-
-export SAM_ZONE=200000000
-#PATH=$PATH:/opt/SamcefField/V8.5-01
-PATH=$PATH:/opt/SamcefField/V8.5-01/Samcef-V151i8/lin/bin
-export SAM_USE_FLEXLM=1
-export SAMTECH_LICENSE_FILE=@pegase.ltas.ulg.ac.be
-

cfg/CentOs6/subversion.profile

-export PATH=/opt/subversion-1.8.14/bin:$PATH
+add2env PATH "/opt/subversion-1.8.14/bin" front

cfg/CentOs6/vtk.profile

-
-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/vtk/lib/
-export LD_LIBRARY_PATH
-PYTHONPATH=$PYTHON_PATH:/opt/vtk/lib/python2.7/site-packages
-export PYTHONPATH
+add2env LD_LIBRARY_PATH "/opt/vtk/lib/"
+add2env PYTHON_PATH "/opt/vtk/lib/python2.7/site-packages"

cfg/blueberry/intelCommunity.bashrc

-# this should be done in the .profile but if the shell is dash
-# it does not work.
-# => we call intel cf file  in both places (bashrc & profile)
+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile 
+#  (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash). 
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
 
 if [ -z "$MKLROOT" ]; then
     . /opt/intel/mkl/bin/mklvars.sh intel64

cfg/blueberry/intelCommunity.profile

-# the .profile is sometimes read by "dash" and we cannot provide 
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile 
+#  (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash). 
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
 
 if [ -n "$BASH_VERSION" ]; then
-   #if [ -z "$MKLROOT" ]; then  # pas suffisant! (MKLROOT transmis au "at" mais pas LD_LIBRARY_PATH)
-      . /opt/intel/mkl/bin/mklvars.sh intel64
-   #fi
-   #if [ -z "$TBBROOT" ]; then
-      . /opt/intel/tbb/bin/tbbvars.sh intel64
-   #fi
+    . /opt/intel/mkl/bin/mklvars.sh intel64
+    . /opt/intel/tbb/bin/tbbvars.sh intel64
 fi

cfg/blueberry/mumps.profile

-# MUMPS + MKL-TBB
-
 add2env LD_LIBRARY_PATH "/opt/mumps/lib"
 add2env LIB "/opt/mumps/lib"
 add2env INCLUDE "/opt/mumps/include"
-

cfg/blueberry/parasolid.profile

-# Parasolid
-
 add2env PATH "/opt/parasolid/shared_object"
 add2env INCLUDE "/opt/parasolid"
 export P_SCHEMA=/opt/parasolid/schema
-

cfg/clifton/intelCommunity.bashrc

-# this should be done in the .profile but if the shell is dash
-# it does not work.
-# => we call intel cf file  in both places (bashrc & profile)
+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile 
+#  (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash). 
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
 
 if [ -z "$MKLROOT" ]; then
-#   . /opt/intel/bin/compilervars.sh intel64
     . /opt/intelCommunity2017/mkl/bin/mklvars.sh intel64
 fi
 if [ -z "$TBBROOT" ]; then

cfg/clifton/intelCommunity.profile

-# the .profile is sometimes read by "dash" and we cannot provide 
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile 
+#  (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash). 
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
 
 if [ -n "$BASH_VERSION" ]; then
-   #if [ -z "$MKLROOT" ]; then  # pas suffisant! (MKLROOT transmis au "at" mais pas LD_LIBRARY_PATH)
-      #. /opt/intel/bin/compilervars.sh intel64
-      . /opt/intelCommunity2017/mkl/bin/mklvars.sh intel64
-   #fi
-   #if [ -z "$TBBROOT" ]; then
-      . /opt/intelCommunity2017/tbb/bin/tbbvars.sh intel64
-   #fi
-
+    . /opt/intelCommunity2017/mkl/bin/mklvars.sh intel64
+    . /opt/intelCommunity2017/tbb/bin/tbbvars.sh intel64
 fi

cfg/clifton/matlab.profile

-PATH=$PATH:/opt/MATLAB/R2015a/bin
-
+add2env PATH "/opt/MATLAB/R2015a/bin"

cfg/clifton/mumps.profile

-# $Id$
-#
-# configuration to allow CMake to automatically find mumps 
-#
-LIB=$LIB:/opt/mumps-4.10.0-Tbb/lib
-export LIB
-INCLUDE=$INCLUDE:/opt/mumps-4.10.0-Tbb/include
-export INCLUDE
-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mumps-4.10.0-Tbb/lib
-export LD_LIBRARY_PATH
+add2env LD_LIBRARY_PATH "/opt/mumps-4.10.0-Tbb/lib"
+add2env LIB "/opt/mumps-4.10.0-Tbb/lib"
+add2env INCLUDE "/opt/mumps-4.10.0-Tbb/include"

cfg/clifton/parasolid.profile

 # Parasolid
 
-# adds pskernel.so to the PATH
-
-if [ -d /opt/parasolid-28.1/shared_object ] ; then
-    if [ -z "${PATH}" ] ; then
-       export PATH="/opt/parasolid-28.1/shared_object"
-    else
-       export PATH="/opt/parasolid-28.1/shared_object:${PATH}"
-    fi
-fi
-
-# adds parasolid INCLUDE dir
-
-if [ -d /opt/parasolid-28.1 ] ; then
-    if [ -z "${INCLUDE}" ] ; then
-       export INCLUDE="/opt/parasolid-28.1"
-    else
-       export INCLUDE="/opt/parasolid-28.1:${INCLUDE}"
-    fi
-fi
-
+add2env PATH "/opt/parasolid-28.1/shared_object"
+add2env INCLUDE "/opt/parasolid-28.1"
 export P_SCHEMA=/opt/parasolid-28.1/schema
-