From 7ddaf9f715dde71d7dce5c5a0a5dcfe7161ec596 Mon Sep 17 00:00:00 2001
From: Romain Boman <romain.boman@gmail.com>
Date: Fri, 18 May 2018 13:45:53 +0200
Subject: [PATCH] cleaning all files
---
cfg/CentOs6/cmake.profile | 2 +-
cfg/CentOs6/compilers.bashrc | 15 +----
cfg/CentOs6/compilers.profile | 15 +----
cfg/CentOs6/matlab.profile | 3 +-
cfg/CentOs6/mumps.profile | 12 +---
cfg/CentOs6/parasolid.profile | 31 +----------
cfg/CentOs6/python.profile | 4 +-
cfg/CentOs6/qt.profile | 4 +-
cfg/CentOs6/samcef.profile | 8 ---
cfg/CentOs6/subversion.profile | 2 +-
cfg/CentOs6/vtk.profile | 7 +--
cfg/blueberry/intelCommunity.bashrc | 17 +++++-
cfg/blueberry/intelCommunity.profile | 24 +++++---
cfg/blueberry/mumps.profile | 3 -
cfg/blueberry/parasolid.profile | 3 -
cfg/clifton/intelCommunity.bashrc | 18 ++++--
cfg/clifton/intelCommunity.profile | 26 +++++----
cfg/clifton/matlab.profile | 3 +-
cfg/clifton/mumps.profile | 13 +----
cfg/clifton/parasolid.profile | 23 +-------
cfg/clifton/samcef.profile | 7 +--
cfg/default/aliases.bashrc | 2 -
cfg/default/editor.bashrc | 1 -
cfg/default/functions.bashrc | 2 -
cfg/default/omp.profile | 2 -
cfg/fabulous/lammps.profile | 6 +-
cfg/fabulous/ls_colors.bashrc | 2 -
cfg/fabulous/modules.profile | 2 -
cfg/fabulous/progs_bin.profile | 2 -
cfg/garfield/compilers.bashrc | 18 ++++--
cfg/garfield/compilers.profile | 23 +++++---
cfg/garfield/metafor.bashrc | 2 -
cfg/garfield/metafor.profile | 6 --
cfg/garfield/misc.bashrc | 8 ---
cfg/garfield/mumps.profile | 3 -
cfg/garfield/parasolid.profile | 3 -
cfg/garfield/paraview.bashrc | 2 +-
cfg/garfield/progs_bin.profile | 2 -
cfg/garfield/python.profile | 2 +-
cfg/garfield/samcef.profile | 2 +-
cfg/garfield/trilinos.bashrc | 5 +-
cfg/garfield/vtk.profile | 2 +-
cfg/gaston/intelCommunity.bashrc | 18 ++++--
cfg/gaston/intelCommunity.profile | 20 +++++--
cfg/gaston/mumps.profile | 3 -
cfg/gaston/parasolid.profile | 3 -
cfg/hmem00/git.profile | 5 --
cfg/hmem00/modules.profile | 3 -
cfg/loop.sh | 82 +++++++++++++++++++---------
cfg/master2/git.profile | 2 -
cfg/master2/gmm.profile | 2 -
cfg/master2/gmsh.profile | 2 -
cfg/master2/lammps.profile | 6 +-
cfg/master2/pcre.profile | 2 -
cfg/master2/python.profile | 2 -
cfg/master2/swig.profile | 3 -
cfg/spirou/cmake.profile | 2 -
cfg/spirou/gmsh.profile | 1 -
cfg/spirou/intel.profile | 1 -
cfg/spirou/matlab.bashrc | 2 +-
cfg/spirou/mumps.profile | 2 -
cfg/spirou/parasolid.profile | 3 -
cfg/spirou/prompt.bashrc | 2 -
cfg/spirou/qt.profile | 2 -
cfg/spirou/vtk.profile | 1 -
cfg/spring/compilers.bashrc | 20 +++++--
cfg/spring/compilers.profile | 32 +++++------
cfg/spring/mumps.profile | 3 -
cfg/spring/parasolid.profile | 3 -
cfg/thorgal/intelCommunity.bashrc | 17 +++++-
cfg/thorgal/intelCommunity.profile | 20 +++++--
cfg/thorgal/mumps.profile | 3 -
cfg/thorgal/parasolid.profile | 3 -
cfg/zen/eclipse.profile | 6 +-
cfg/zen/lammps.profile | 6 +-
externalProgramPath.py | 0
externalProgramPathGui.pyw | 0
postProLoop.py | 0
postProLoopGui.pyw | 0
79 files changed, 266 insertions(+), 353 deletions(-)
delete mode 100644 cfg/CentOs6/samcef.profile
delete mode 100644 cfg/fabulous/progs_bin.profile
delete mode 100644 cfg/garfield/metafor.profile
delete mode 100644 cfg/garfield/progs_bin.profile
mode change 100644 => 100755 externalProgramPath.py
mode change 100644 => 100755 externalProgramPathGui.pyw
mode change 100644 => 100755 postProLoop.py
mode change 100644 => 100755 postProLoopGui.pyw
diff --git a/cfg/CentOs6/cmake.profile b/cfg/CentOs6/cmake.profile
index e28887b..c7b8d1f 100644
--- a/cfg/CentOs6/cmake.profile
+++ b/cfg/CentOs6/cmake.profile
@@ -1 +1 @@
-export PATH=/opt/cmake/bin:$PATH
+add2env PATH "/opt/cmake/bin"
diff --git a/cfg/CentOs6/compilers.bashrc b/cfg/CentOs6/compilers.bashrc
index 14a7a3f..4667b38 100644
--- a/cfg/CentOs6/compilers.bashrc
+++ b/cfg/CentOs6/compilers.bashrc
@@ -1,13 +1,2 @@
-# this should be done in the .profile but if the shell is dash
-# it does not work.
-# => we call intel cf file in both places (bashrc & profile)
-
-# recompiled gcc
-export PATH=/opt/gcc/bin:$PATH
-export LD_LIBRARY_PATH=/opt/gcc/lib64:$LD_LIBRARY_PATH
-
-# icc
-#if [ -z "$MKLROOT" ]; then
-# . /opt/intel/bin/compilervars.sh intel64
-#fi
-
+add2env PATH "/opt/gcc/bin" front
+add2env LD_LIBRARY_PATH "/opt/gcc/lib64" front
\ No newline at end of file
diff --git a/cfg/CentOs6/compilers.profile b/cfg/CentOs6/compilers.profile
index 189080c..583bfd3 100644
--- a/cfg/CentOs6/compilers.profile
+++ b/cfg/CentOs6/compilers.profile
@@ -1,13 +1,2 @@
-# 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
diff --git a/cfg/CentOs6/matlab.profile b/cfg/CentOs6/matlab.profile
index 48e86c1..f391a0e 100644
--- a/cfg/CentOs6/matlab.profile
+++ b/cfg/CentOs6/matlab.profile
@@ -1,2 +1 @@
-PATH=$PATH:/opt/MATLAB/R2012a/bin
-
+add2env PATH "/opt/MATLAB/R2012a/bin"
diff --git a/cfg/CentOs6/mumps.profile b/cfg/CentOs6/mumps.profile
index 75ef411..57e0ada 100644
--- a/cfg/CentOs6/mumps.profile
+++ b/cfg/CentOs6/mumps.profile
@@ -1,9 +1,3 @@
-# $id$
-#
-# 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=$LD_LIBRARY_PATH:/opt/mumps/lib
+add2env LD_LIBRARY_PATH "/opt/mumps/lib"
+add2env LIB "/opt/mumps/lib"
+add2env INCLUDE "/opt/mumps/include"
diff --git a/cfg/CentOs6/parasolid.profile b/cfg/CentOs6/parasolid.profile
index c121151..e24e2e8 100644
--- a/cfg/CentOs6/parasolid.profile
+++ b/cfg/CentOs6/parasolid.profile
@@ -1,30 +1,3 @@
-# Parasolid
-
-# adds pskernel.so to the PATH
-
-if [ -d /opt/parasolid/shared_object ] ; then
- if [ -z "${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:${INCLUDE}"
- fi
-fi
-
+add2env PATH "/opt/parasolid/shared_object"
+add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/CentOs6/python.profile b/cfg/CentOs6/python.profile
index b0880e9..e3a2588 100644
--- a/cfg/CentOs6/python.profile
+++ b/cfg/CentOs6/python.profile
@@ -1,2 +1,2 @@
-export PATH=/opt/python-2.7.10/bin:$PATH
-export LD_LIBRARY_PATH=/opt/python-2.7.10/lib:$LD_LIBRARY_PATH
+add2env PATH "/opt/python-2.7.10/bin" front
+add2env LD_LIBRARY_PATH "/opt/python-2.7.10/lib" front
diff --git a/cfg/CentOs6/qt.profile b/cfg/CentOs6/qt.profile
index a395354..cf036d1 100644
--- a/cfg/CentOs6/qt.profile
+++ b/cfg/CentOs6/qt.profile
@@ -1,2 +1,2 @@
-export PATH=/opt/qt/bin:$PATH
-export LD_LIBRARY_PATH=/opt/qt/lib:$LD_LIBRARY_PATH
+add2env PATH "/opt/qt/bin" front
+add2env LD_LIBRARY_PATH "/opt/qt/bin" front
diff --git a/cfg/CentOs6/samcef.profile b/cfg/CentOs6/samcef.profile
deleted file mode 100644
index 2ea188a..0000000
--- a/cfg/CentOs6/samcef.profile
+++ /dev/null
@@ -1,8 +0,0 @@
-# Samcef v15.01-3
-
-export SAM_ZONE=200000000
-#PATH=$PATH:/opt/SamcefField/V8.5-01
-PATH=$PATH:/opt/SamcefField/V8.5-01/Samcef-V151i8/lin/bin
-export SAM_USE_FLEXLM=1
-export SAMTECH_LICENSE_FILE=@pegase.ltas.ulg.ac.be
-
diff --git a/cfg/CentOs6/subversion.profile b/cfg/CentOs6/subversion.profile
index 0167db9..807b808 100644
--- a/cfg/CentOs6/subversion.profile
+++ b/cfg/CentOs6/subversion.profile
@@ -1 +1 @@
-export PATH=/opt/subversion-1.8.14/bin:$PATH
+add2env PATH "/opt/subversion-1.8.14/bin" front
diff --git a/cfg/CentOs6/vtk.profile b/cfg/CentOs6/vtk.profile
index 6e88e22..6b85d7f 100644
--- a/cfg/CentOs6/vtk.profile
+++ b/cfg/CentOs6/vtk.profile
@@ -1,5 +1,2 @@
-
-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"
diff --git a/cfg/blueberry/intelCommunity.bashrc b/cfg/blueberry/intelCommunity.bashrc
index 55a8521..09fe18c 100644
--- a/cfg/blueberry/intelCommunity.bashrc
+++ b/cfg/blueberry/intelCommunity.bashrc
@@ -1,6 +1,17 @@
-# 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 "$MKLROOT" ]; then
. /opt/intel/mkl/bin/mklvars.sh intel64
diff --git a/cfg/blueberry/intelCommunity.profile b/cfg/blueberry/intelCommunity.profile
index d2bff7e..3fa6997 100644
--- a/cfg/blueberry/intelCommunity.profile
+++ b/cfg/blueberry/intelCommunity.profile
@@ -1,11 +1,19 @@
-# the .profile is sometimes read by "dash" and we cannot provide
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile
+# (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash).
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
if [ -n "$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
diff --git a/cfg/blueberry/mumps.profile b/cfg/blueberry/mumps.profile
index 2d94cb9..57e0ada 100644
--- a/cfg/blueberry/mumps.profile
+++ b/cfg/blueberry/mumps.profile
@@ -1,6 +1,3 @@
-# MUMPS + MKL-TBB
-
add2env LD_LIBRARY_PATH "/opt/mumps/lib"
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/blueberry/parasolid.profile b/cfg/blueberry/parasolid.profile
index 5f9e03b..e24e2e8 100644
--- a/cfg/blueberry/parasolid.profile
+++ b/cfg/blueberry/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/opt/parasolid/shared_object"
add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/clifton/intelCommunity.bashrc b/cfg/clifton/intelCommunity.bashrc
index 6b5efc4..7b93b13 100644
--- a/cfg/clifton/intelCommunity.bashrc
+++ b/cfg/clifton/intelCommunity.bashrc
@@ -1,9 +1,19 @@
-# 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
diff --git a/cfg/clifton/intelCommunity.profile b/cfg/clifton/intelCommunity.profile
index 8d2cadb..c74dbb2 100644
--- a/cfg/clifton/intelCommunity.profile
+++ b/cfg/clifton/intelCommunity.profile
@@ -1,13 +1,19 @@
-# 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 "$TBBROOT" ]; then
- . /opt/intelCommunity2017/tbb/bin/tbbvars.sh intel64
- #fi
-
+ . /opt/intelCommunity2017/mkl/bin/mklvars.sh intel64
+ . /opt/intelCommunity2017/tbb/bin/tbbvars.sh intel64
fi
diff --git a/cfg/clifton/matlab.profile b/cfg/clifton/matlab.profile
index df9a228..58f04e5 100644
--- a/cfg/clifton/matlab.profile
+++ b/cfg/clifton/matlab.profile
@@ -1,2 +1 @@
-PATH=$PATH:/opt/MATLAB/R2015a/bin
-
+add2env PATH "/opt/MATLAB/R2015a/bin"
diff --git a/cfg/clifton/mumps.profile b/cfg/clifton/mumps.profile
index e4ff5f5..98a366c 100644
--- a/cfg/clifton/mumps.profile
+++ b/cfg/clifton/mumps.profile
@@ -1,10 +1,3 @@
-# $Id$
-#
-# 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=$LD_LIBRARY_PATH:/opt/mumps-4.10.0-Tbb/lib
-export LD_LIBRARY_PATH
+add2env LD_LIBRARY_PATH "/opt/mumps-4.10.0-Tbb/lib"
+add2env LIB "/opt/mumps-4.10.0-Tbb/lib"
+add2env INCLUDE "/opt/mumps-4.10.0-Tbb/include"
diff --git a/cfg/clifton/parasolid.profile b/cfg/clifton/parasolid.profile
index 8dfef6f..158db8d 100644
--- a/cfg/clifton/parasolid.profile
+++ b/cfg/clifton/parasolid.profile
@@ -1,24 +1,5 @@
# Parasolid
-# adds pskernel.so to the PATH
-
-if [ -d /opt/parasolid-28.1/shared_object ] ; then
- if [ -z "${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:${INCLUDE}"
- fi
-fi
-
+add2env PATH "/opt/parasolid-28.1/shared_object"
+add2env INCLUDE "/opt/parasolid-28.1"
export P_SCHEMA=/opt/parasolid-28.1/schema
-
diff --git a/cfg/clifton/samcef.profile b/cfg/clifton/samcef.profile
index 121ccc7..b504e28 100644
--- a/cfg/clifton/samcef.profile
+++ b/cfg/clifton/samcef.profile
@@ -1,7 +1,2 @@
-# Samcef v17.1 i8
-
export SAM_ZONE=200000000
-PATH=$PATH:/opt/Samv17i8/
-#export SAM_USE_FLEXLM=1
-#export SAMTECH_LICENSE_FILE=@pegase.ltas.ulg.ac.be
-
+add2env PATH "/opt/Samv17i8"
diff --git a/cfg/default/aliases.bashrc b/cfg/default/aliases.bashrc
index 98c206b..9cc8ef1 100644
--- a/cfg/default/aliases.bashrc
+++ b/cfg/default/aliases.bashrc
@@ -1,3 +1 @@
-
alias verif='cd ~/dev/oo_meta/apps/verif'
-
diff --git a/cfg/default/editor.bashrc b/cfg/default/editor.bashrc
index ea04dba..e0560ad 100644
--- a/cfg/default/editor.bashrc
+++ b/cfg/default/editor.bashrc
@@ -1,3 +1,2 @@
-
export EDITOR=vim
alias vi='vim'
diff --git a/cfg/default/functions.bashrc b/cfg/default/functions.bashrc
index 2b177c4..30bb21f 100644
--- a/cfg/default/functions.bashrc
+++ b/cfg/default/functions.bashrc
@@ -1,5 +1,3 @@
-# Fonctions generales
-
function backup()
{
ARC=backup-profile-bin.tar.gz
diff --git a/cfg/default/omp.profile b/cfg/default/omp.profile
index 4b6bf3f..ea8dc08 100644
--- a/cfg/default/omp.profile
+++ b/cfg/default/omp.profile
@@ -1,3 +1 @@
-
export OMP_NUM_THREADS=1
-
diff --git a/cfg/fabulous/lammps.profile b/cfg/fabulous/lammps.profile
index 07f77ad..348d0d9 100644
--- a/cfg/fabulous/lammps.profile
+++ b/cfg/fabulous/lammps.profile
@@ -1,5 +1 @@
-
-if [ -d ~/dev/lammps/src ] ; then
- PATH=$PATH:~/dev/lammps/src
-fi
-
+add2env PATH "~/dev/lammps/src"
diff --git a/cfg/fabulous/ls_colors.bashrc b/cfg/fabulous/ls_colors.bashrc
index f80ed49..8971679 100644
--- a/cfg/fabulous/ls_colors.bashrc
+++ b/cfg/fabulous/ls_colors.bashrc
@@ -1,4 +1,2 @@
-
LS_COLORS='di=01;34:ln=01;36:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.axa=00;36:*.oga=00;36:*.spx=00;36:*.xspf=00;36'
export LS_COLORS
-
diff --git a/cfg/fabulous/modules.profile b/cfg/fabulous/modules.profile
index 9185c6a..08634cb 100644
--- a/cfg/fabulous/modules.profile
+++ b/cfg/fabulous/modules.profile
@@ -3,14 +3,12 @@ module load slurm
module load git subversion
module load gcc cmake swig
module load python qt vtk parasolid mumps
-#module load gmm trilinos
module load samcef gmsh
module load isosurf tetgen triangle
module load matlab scilab
# intel community
-#. /cm/shared/apps/intel-community/2017.2/bin/compilervars.sh intel64
. /cm/shared/apps/intel-community/2017.2/mkl/bin/mklvars.sh intel64
. /cm/shared/apps/intel-community/2017.2/tbb/bin/tbbvars.sh intel64
diff --git a/cfg/fabulous/progs_bin.profile b/cfg/fabulous/progs_bin.profile
deleted file mode 100644
index 3d34ff0..0000000
--- a/cfg/fabulous/progs_bin.profile
+++ /dev/null
@@ -1,2 +0,0 @@
-
-add2env PATH "$HOME/dev/progs/bin" front
diff --git a/cfg/garfield/compilers.bashrc b/cfg/garfield/compilers.bashrc
index 6f6574b..3f73074 100644
--- a/cfg/garfield/compilers.bashrc
+++ b/cfg/garfield/compilers.bashrc
@@ -1,9 +1,19 @@
-# 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 "$MKLROOT" ]; then
- #. /opt/intel/bin/compilervars.sh intel64 # mets intel mpi par defaut!
. /opt/intel/mkl/bin/mklvars.sh intel64
. /opt/intel/tbb/bin/tbbvars.sh intel64
fi
diff --git a/cfg/garfield/compilers.profile b/cfg/garfield/compilers.profile
index a046a25..3fa6997 100644
--- a/cfg/garfield/compilers.profile
+++ b/cfg/garfield/compilers.profile
@@ -1,10 +1,19 @@
-# the .profile is sometimes read by "dash" and we cannot provide
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile
+# (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash).
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
if [ -n "$BASH_VERSION" ]; then
- #if [ -z "$MKLROOT" ]; then # pas suffisant! (MKLROOT transmis au "at" mais pas LD_LIBRARY_PATH)
- #. /opt/intel/bin/compilervars.sh intel64 # mets intel mpi par defaut!
- . /opt/intel/mkl/bin/mklvars.sh intel64
- . /opt/intel/tbb/bin/tbbvars.sh intel64
- #fi
+ . /opt/intel/mkl/bin/mklvars.sh intel64
+ . /opt/intel/tbb/bin/tbbvars.sh intel64
fi
diff --git a/cfg/garfield/metafor.bashrc b/cfg/garfield/metafor.bashrc
index 05ffa73..5ada172 100644
--- a/cfg/garfield/metafor.bashrc
+++ b/cfg/garfield/metafor.bashrc
@@ -1,6 +1,4 @@
-
function mtfconfig
{
cmake -C ../oo_meta/CMake/ubuntu.cmake ../oo_meta
}
-
diff --git a/cfg/garfield/metafor.profile b/cfg/garfield/metafor.profile
deleted file mode 100644
index 33f66eb..0000000
--- a/cfg/garfield/metafor.profile
+++ /dev/null
@@ -1,6 +0,0 @@
-# permet d'installer un metafor compilé
-# (plus très utile depuis scripts Luc?)
-
-#add2env LD_LIBRARY_PATH "$HOME/MetaforBIN"
-#add2env PATH "$HOME/MetaforBIN"
-
diff --git a/cfg/garfield/misc.bashrc b/cfg/garfield/misc.bashrc
index 5f2964a..352e8fc 100644
--- a/cfg/garfield/misc.bashrc
+++ b/cfg/garfield/misc.bashrc
@@ -1,10 +1,2 @@
-# misc aliases
-
alias a2ps='a2ps --pro=color --line-numbers=5'
alias plotdigitizer='java -Xmx256m -jar /opt/PlotDigitizer/PlotDigitizer.jar'
-
-function mnt_Shared()
-{
- sudo mount -t vboxsf Shared /mnt
-}
-
diff --git a/cfg/garfield/mumps.profile b/cfg/garfield/mumps.profile
index 2d94cb9..57e0ada 100644
--- a/cfg/garfield/mumps.profile
+++ b/cfg/garfield/mumps.profile
@@ -1,6 +1,3 @@
-# MUMPS + MKL-TBB
-
add2env LD_LIBRARY_PATH "/opt/mumps/lib"
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/garfield/parasolid.profile b/cfg/garfield/parasolid.profile
index 5f9e03b..e24e2e8 100644
--- a/cfg/garfield/parasolid.profile
+++ b/cfg/garfield/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/opt/parasolid/shared_object"
add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/garfield/paraview.bashrc b/cfg/garfield/paraview.bashrc
index ac9fb65..2272019 100644
--- a/cfg/garfield/paraview.bashrc
+++ b/cfg/garfield/paraview.bashrc
@@ -1,2 +1,2 @@
-
alias paraview='/opt/paraview/bin/paraview'
+alias pvserver='/opt/paraview/bin/pvserver'
diff --git a/cfg/garfield/progs_bin.profile b/cfg/garfield/progs_bin.profile
deleted file mode 100644
index 3d34ff0..0000000
--- a/cfg/garfield/progs_bin.profile
+++ /dev/null
@@ -1,2 +0,0 @@
-
-add2env PATH "$HOME/dev/progs/bin" front
diff --git a/cfg/garfield/python.profile b/cfg/garfield/python.profile
index 668d279..67b3efb 100644
--- a/cfg/garfield/python.profile
+++ b/cfg/garfield/python.profile
@@ -1,2 +1,2 @@
-# binaires ajouté par pip par exemple (pip lui-meme ou yapf)
+# binaires ajoute par pip par exemple (pip lui-meme ou yapf)
add2env PATH "$HOME/.local/bin" front
diff --git a/cfg/garfield/samcef.profile b/cfg/garfield/samcef.profile
index e52e31a..542f794 100644
--- a/cfg/garfield/samcef.profile
+++ b/cfg/garfield/samcef.profile
@@ -4,7 +4,7 @@ add2env PATH "/opt/samcef"
# pas besoin de definir LMS_LICENSE
# (deja defini dans "/opt/samcef/site" lors de l'install)
-
+# -----------------------------------------------------------
# version "russe"
#add2env PATH "/opt/sfield/V8.5-01/Samcef-V151i8/lin/bin"
#export SAMTECH_LICENSE_FILE=/opt/sfield/V8.5-01/SAMTECH.lic
\ No newline at end of file
diff --git a/cfg/garfield/trilinos.bashrc b/cfg/garfield/trilinos.bashrc
index d49863c..a26619a 100644
--- a/cfg/garfield/trilinos.bashrc
+++ b/cfg/garfield/trilinos.bashrc
@@ -1,4 +1,3 @@
-# Trilinos custom compilé localement
-
+# Trilinos custom compile localement
# (permet le FIND_PACKAGE(Trilinos) dans CMake)
-add2env CMAKE_PREFIX_PATH "/opt/trilinos" front
+#add2env CMAKE_PREFIX_PATH "/opt/trilinos" front
diff --git a/cfg/garfield/vtk.profile b/cfg/garfield/vtk.profile
index 2f2befc..cb69d4c 100644
--- a/cfg/garfield/vtk.profile
+++ b/cfg/garfield/vtk.profile
@@ -1,2 +1,2 @@
-# vtk custom compilé localement
+# vtk custom compile localement
#add2env LD_LIBRARY_PATH "/usr/local/lib/vtk-5.10"
diff --git a/cfg/gaston/intelCommunity.bashrc b/cfg/gaston/intelCommunity.bashrc
index 55a8521..7fb2eff 100644
--- a/cfg/gaston/intelCommunity.bashrc
+++ b/cfg/gaston/intelCommunity.bashrc
@@ -1,6 +1,17 @@
-# 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
@@ -8,4 +19,3 @@ fi
if [ -z "$TBBROOT" ]; then
. /opt/intel/tbb/bin/tbbvars.sh intel64
fi
-
diff --git a/cfg/gaston/intelCommunity.profile b/cfg/gaston/intelCommunity.profile
index d2bff7e..2501156 100644
--- a/cfg/gaston/intelCommunity.profile
+++ b/cfg/gaston/intelCommunity.profile
@@ -1,11 +1,19 @@
-# the .profile is sometimes read by "dash" and we cannot provide
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile
+# (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash).
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
if [ -n "$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
fi
diff --git a/cfg/gaston/mumps.profile b/cfg/gaston/mumps.profile
index 2d94cb9..57e0ada 100644
--- a/cfg/gaston/mumps.profile
+++ b/cfg/gaston/mumps.profile
@@ -1,6 +1,3 @@
-# MUMPS + MKL-TBB
-
add2env LD_LIBRARY_PATH "/opt/mumps/lib"
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/gaston/parasolid.profile b/cfg/gaston/parasolid.profile
index 5f9e03b..e24e2e8 100644
--- a/cfg/gaston/parasolid.profile
+++ b/cfg/gaston/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/opt/parasolid/shared_object"
add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/hmem00/git.profile b/cfg/hmem00/git.profile
index 4871e7a..e984471 100644
--- a/cfg/hmem00/git.profile
+++ b/cfg/hmem00/git.profile
@@ -1,6 +1 @@
-
-
unset SSH_ASKPASS
-
-
-
diff --git a/cfg/hmem00/modules.profile b/cfg/hmem00/modules.profile
index 6c80be2..d263785 100644
--- a/cfg/hmem00/modules.profile
+++ b/cfg/hmem00/modules.profile
@@ -1,5 +1,2 @@
-
module load cmake python
module load intel/compiler
-
-
diff --git a/cfg/loop.sh b/cfg/loop.sh
index ca61df1..e3b00ca 100755
--- a/cfg/loop.sh
+++ b/cfg/loop.sh
@@ -1,4 +1,3 @@
-# $Id: loop.sh 1755 2013-05-30 12:18:36Z boman $
#
# usage:
# add the following calls to the end of the .bashrc/.profile cfg files
@@ -7,32 +6,36 @@
# .bashrc: (interactive stuffs)
# . $HOME/bin/cfg/loop.sh ; fct_loop bashrc $* ; unset fct_loop
#
-# arg1 is the extension of the files to be loaded
-# arg2 is the name of the master node if needed (clusters)
-#
# if this script is sometimes run with dash (not bash!)
-# (by gnome on ubuntu for the .profile)
+# (by gnome on ubuntu/debian for the .profile)
# => avoid bashisms (e.g. ~ becomes $HOME)
-#
-# RoBo 2013
-
function add2env()
{
+ #verb=1 #uncomment to debug script
+
if [ $# -lt 2 ] || [ $# -gt 3 ] ; then
echo "add2env VARNAME folder [front]"
return
fi
- if [ -d $2 ] ; then # if the second arg is an existing folder
- if [ -z ${!1} ] ; then # if the first arg is an empty variable
+
+ ndir=${2%/} # remove trailing space
+ if [ -d $ndir ] ; then # if the second arg is an existing folder
+ if [ -z ${!1} ] ; then # if the first arg is an empty env variable
#echo $1 is empty
- eval export $1="$2"
+ eval export $1="$ndir"
else
#echo $1 is not empty
- if [ "$3" == "front" ] ; then
- eval export $1="$2:\$$1" # add folder to the front
+ if ! eval echo \$$1 | grep -E -q "(^|:)$ndir($|:)" ; then # if ndir is not already present in the variable
+ if [ "$3" == "front" ] ; then
+ eval export $1="$ndir:\$$1" # add folder to the front
+ else
+ eval export $1="\$$1:$ndir" # add folder to the end
+ fi
else
- eval export $1="\$$1:$2" # add folder to the end
+ if [ -n "$verb" ] ; then
+ echo "! $1 already contains $ndir"
+ fi
fi
fi
else
@@ -42,14 +45,21 @@ function add2env()
}
+# arg1 is the extension of the files to be loaded
+# arg2 is the name of the master node if needed (clusters)
+
function fct_loop()
{
umask 007
- #echo "Execute loop.sh"
- #echo "script=$0"
- #echo "nargs=$#"
- #echo "arguments=$*"
+ #verb=1 #uncomment to debug script
+
+ if [ -n "$verb" ] ; then
+ echo "Executing \"loop.sh $*\" with shell=$0"
+ #echo "script=$0"
+ #echo "nargs=$#"
+ #echo "arguments=$*"
+ fi
#for var in "$@"; do
# echo "var=$var"
#done
@@ -66,14 +76,16 @@ function fct_loop()
# default cfg
for i in $thisdir/default/*.$1 ; do
- #echo "testing script $i ..."
- if [ -r $i ]; then
- # do not read file if a file with the same name exists in the "myhost" folder
- if [ ! -f $thisdir/$myhost/`basename $i` ] ; then
- #echo " =>loading script $i ..."
- . $i
+ #echo "testing script $i ..."
+ if [ -r $i ]; then
+ # do not read file if a file with the same name exists in the "myhost" folder
+ if [ ! -f $thisdir/$myhost/`basename $i` ] ; then
+ if [ -n "$verb" ] ; then
+ echo " =>loading script $i ..."
+ fi
+ . $i
+ fi
fi
- fi
done
# machine-dependent cfg
@@ -81,9 +93,27 @@ function fct_loop()
for i in $thisdir/$myhost/*.$1 ; do
#echo "testing script $i ..."
if [ -r $i ]; then
- #echo " =>loading script $i ..."
+ if [ -n "$verb" ] ; then
+ echo " =>loading script $i ..."
+ fi
. $i
fi
done
unset i
+
+
+ # remove duplicate entries in env vars ----
+ # see https://unix.stackexchange.com/questions/40749/remove-duplicate-path-entries-with-awk-command
+
+ # - initial version
+ #LD_LIBRARY_PATH=$(printf %s "$LD_LIBRARY_PATH" | awk -v RS=: '{ if (!arr[$0]++) {printf("%s%s",!ln++?"":":",$0)}}')
+ # - loop version
+ for var in PATH LD_LIBRARY_PATH INTEL_LICENSE_FILE CPATH INFOPATH NLSPATH LIBRARY_PATH MANPATH CLASSPATH MIC_LIBRARY_PATH MIC_LD_LIBRARY_PATH
+ do
+ if [ -n "$(eval echo \$$var)" ] ; then # if var is set
+ cmd="$var=\$(printf %s \"\$$var\" | awk -v RS=: '{ if (!arr[\$0]++) {printf(\"%s%s\",!ln++?\"\":\":\",\$0)}}')"
+ eval $(echo $cmd)
+ fi
+ done
+
}
diff --git a/cfg/master2/git.profile b/cfg/master2/git.profile
index bee69f7..07acaaf 100644
--- a/cfg/master2/git.profile
+++ b/cfg/master2/git.profile
@@ -1,3 +1 @@
-
module load git
-
diff --git a/cfg/master2/gmm.profile b/cfg/master2/gmm.profile
index 266b12b..a3259ca 100644
--- a/cfg/master2/gmm.profile
+++ b/cfg/master2/gmm.profile
@@ -1,4 +1,2 @@
# gmm compile localement
-
add2env INCLUDE "/home/ulg/nlcm/rboman/local/gmm/include" front
-
diff --git a/cfg/master2/gmsh.profile b/cfg/master2/gmsh.profile
index 7505f59..b54f563 100644
--- a/cfg/master2/gmsh.profile
+++ b/cfg/master2/gmsh.profile
@@ -1,4 +1,2 @@
# gmsh compile par RB
-
add2env PATH "/home/ulg/nlcm/rboman/local/gmsh/bin" front
-
diff --git a/cfg/master2/lammps.profile b/cfg/master2/lammps.profile
index 07f77ad..348d0d9 100644
--- a/cfg/master2/lammps.profile
+++ b/cfg/master2/lammps.profile
@@ -1,5 +1 @@
-
-if [ -d ~/dev/lammps/src ] ; then
- PATH=$PATH:~/dev/lammps/src
-fi
-
+add2env PATH "~/dev/lammps/src"
diff --git a/cfg/master2/pcre.profile b/cfg/master2/pcre.profile
index b98426c..e81830e 100644
--- a/cfg/master2/pcre.profile
+++ b/cfg/master2/pcre.profile
@@ -1,6 +1,4 @@
# pcre (swig) compile localement par RB
-
add2env LIB "/home/ulg/nlcm/rboman/local/pcre/lib" front
add2env INCLUDE "/home/ulg/nlcm/rboman/local/pcre/include" front
add2env LD_LIBRARY_PATH "/home/ulg/nlcm/rboman/local/pcre/lib" front
-
diff --git a/cfg/master2/python.profile b/cfg/master2/python.profile
index 5d06da1..dcbf334 100644
--- a/cfg/master2/python.profile
+++ b/cfg/master2/python.profile
@@ -1,6 +1,4 @@
-
module load python/2.7.10
# trucs qui manquent dans le modulefile de David
add2env CMAKE_PREFIX_PATH "/cm/shared/apps/python/2.7.10" front
-
diff --git a/cfg/master2/swig.profile b/cfg/master2/swig.profile
index b99ddb6..3a1acae 100644
--- a/cfg/master2/swig.profile
+++ b/cfg/master2/swig.profile
@@ -1,4 +1 @@
-# swig recompile localement par RB
-
add2env PATH "/home/ulg/nlcm/rboman/local/swig-3.0.11/bin" front
-
diff --git a/cfg/spirou/cmake.profile b/cfg/spirou/cmake.profile
index 2b5121c..732d4fe 100644
--- a/cfg/spirou/cmake.profile
+++ b/cfg/spirou/cmake.profile
@@ -1,3 +1 @@
-
-
add2env PATH "/Applications/CMake.app/Contents/bin"
diff --git a/cfg/spirou/gmsh.profile b/cfg/spirou/gmsh.profile
index 6950dac..3b40fed 100644
--- a/cfg/spirou/gmsh.profile
+++ b/cfg/spirou/gmsh.profile
@@ -1,2 +1 @@
-
add2env PATH "/Applications/Gmsh.app/Contents/MacOS"
diff --git a/cfg/spirou/intel.profile b/cfg/spirou/intel.profile
index 33b60d9..202314b 100644
--- a/cfg/spirou/intel.profile
+++ b/cfg/spirou/intel.profile
@@ -1,4 +1,3 @@
-
. /opt/intel/compilers_and_libraries/mac/mkl/bin/mklvars.sh intel64
. /opt/intel/compilers_and_libraries/mac/tbb/bin/tbbvars.sh intel64
diff --git a/cfg/spirou/matlab.bashrc b/cfg/spirou/matlab.bashrc
index f218f35..9a3e351 100644
--- a/cfg/spirou/matlab.bashrc
+++ b/cfg/spirou/matlab.bashrc
@@ -1 +1 @@
-alias matlab='/Applications/MATLAB_R2016b.app/bin/matlab'
\ No newline at end of file
+alias matlab='/Applications/MATLAB_R2016b.app/bin/matlab'
diff --git a/cfg/spirou/mumps.profile b/cfg/spirou/mumps.profile
index 9163d49..92cbf63 100644
--- a/cfg/spirou/mumps.profile
+++ b/cfg/spirou/mumps.profile
@@ -1,4 +1,2 @@
-
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/spirou/parasolid.profile b/cfg/spirou/parasolid.profile
index 5663431..e81e5c2 100644
--- a/cfg/spirou/parasolid.profile
+++ b/cfg/spirou/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/usr/local/parasolid/shared_object"
add2env INCLUDE "/usr/local/parasolid"
export P_SCHEMA=/usr/local/parasolid/schema
-
diff --git a/cfg/spirou/prompt.bashrc b/cfg/spirou/prompt.bashrc
index cf9ee21..8583cd5 100644
--- a/cfg/spirou/prompt.bashrc
+++ b/cfg/spirou/prompt.bashrc
@@ -1,3 +1 @@
-
export PS1="\[$(tput bold)\]\u@\h:\w$ \[$(tput sgr0)\]"
-
diff --git a/cfg/spirou/qt.profile b/cfg/spirou/qt.profile
index 558cc5b..59d39de 100644
--- a/cfg/spirou/qt.profile
+++ b/cfg/spirou/qt.profile
@@ -1,4 +1,2 @@
-
add2env PATH "/usr/local/qt-5.8.0/bin"
add2env DYLD_LIBRARY_PATH "/usr/local/qt-5.8.0/lib"
-
diff --git a/cfg/spirou/vtk.profile b/cfg/spirou/vtk.profile
index d8acaf9..2718ac5 100644
--- a/cfg/spirou/vtk.profile
+++ b/cfg/spirou/vtk.profile
@@ -1,3 +1,2 @@
-
add2env PYTHONPATH "/usr/local/vtk-7.1.0/lib/python2.7/site-packages"
add2env DYLD_LIBRARY_PATH "/usr/local/vtk-7.1.0/lib"
diff --git a/cfg/spring/compilers.bashrc b/cfg/spring/compilers.bashrc
index 78f2ef9..09e595a 100644
--- a/cfg/spring/compilers.bashrc
+++ b/cfg/spring/compilers.bashrc
@@ -1,10 +1,18 @@
-# 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 "$MKLROOT" ]; then
. /opt/intel/bin/compilervars.sh intel64
- #. /opt/intel/mkl/bin/mklvars.sh intel64
- #. /opt/intel/tbb/bin/tbbvars.sh intel64
fi
-
diff --git a/cfg/spring/compilers.profile b/cfg/spring/compilers.profile
index a08a1fb..f8c5c50 100644
--- a/cfg/spring/compilers.profile
+++ b/cfg/spring/compilers.profile
@@ -1,22 +1,18 @@
-# the .profile is sometimes read by "dash" and we cannot provide
-# a sourced script with some parameters (it is a "bashism")
+# Intel compiler and/or TBB/MKL
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile
+# (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash).
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
if [ -n "$BASH_VERSION" ]; then
- #if [ -z "$MKLROOT" ]; then # pas suffisant! (MKLROOT transmis au "at" mais pas LD_LIBRARY_PATH)
. /opt/intel/bin/compilervars.sh intel64 # mets intel mpi par defaut!
- #. /opt/intel/mkl/bin/mklvars.sh intel64
- #. /opt/intel/tbb/bin/tbbvars.sh intel64
- #fi
fi
-
-# remove duplicate entries in LD_LIBRARY_PATH
-# see https://unix.stackexchange.com/questions/40749/remove-duplicate-path-entries-with-awk-command
-
-# -version initiale
-#LD_LIBRARY_PATH=$(printf %s "$LD_LIBRARY_PATH" | awk -v RS=: '{ if (!arr[$0]++) {printf("%s%s",!ln++?"":":",$0)}}')
-# -version "boucle"
-for var in PATH LD_LIBRARY_PATH INTEL_LICENSE_FILE CPATH INFOPATH NLSPATH LIBRARY_PATH MANPATH CLASSPATH
-do
- cmd="$var=\$(printf %s \"\$$var\" | awk -v RS=: '{ if (!arr[\$0]++) {printf(\"%s%s\",!ln++?\"\":\":\",\$0)}}')"
- eval $(echo $cmd)
-done
\ No newline at end of file
diff --git a/cfg/spring/mumps.profile b/cfg/spring/mumps.profile
index 2d94cb9..57e0ada 100644
--- a/cfg/spring/mumps.profile
+++ b/cfg/spring/mumps.profile
@@ -1,6 +1,3 @@
-# MUMPS + MKL-TBB
-
add2env LD_LIBRARY_PATH "/opt/mumps/lib"
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/spring/parasolid.profile b/cfg/spring/parasolid.profile
index 5f9e03b..e24e2e8 100644
--- a/cfg/spring/parasolid.profile
+++ b/cfg/spring/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/opt/parasolid/shared_object"
add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/thorgal/intelCommunity.bashrc b/cfg/thorgal/intelCommunity.bashrc
index 55a8521..09fe18c 100644
--- a/cfg/thorgal/intelCommunity.bashrc
+++ b/cfg/thorgal/intelCommunity.bashrc
@@ -1,6 +1,17 @@
-# this should be done in the .profile but if the shell is dash
-# it does not work.
-# => we call intel cf file in both places (bashrc & profile)
+# Intel compiler and/or TBB/MKL
+#
+# EXPLANATIONS [RB]:
+# In practise, the call to "compilervars.sh" or ("mklvars.sh", etc) should be done in .profile
+# (it sets PATH, LD_LIBRARY_PATH, etc.)
+#
+# BUT, if the login shell is dash, it does not work (we cannot add an extra argument to a sourced script with dash).
+# => we call the scripts in both places (.bashrc & .profile)
+# => the env is cleaned in "loop.sh", removing duplicates if the .profile was actually read by bash
+#
+# SPECIAL CASE: "at" job
+# => the environment is OK and kept, but "LD_LIBRARY_PATH" is set to nothing by "at"
+# => the .profile is then rerun manually in our scripts (with bash)
+# => duplicates are finally removed by loop.sh
if [ -z "$MKLROOT" ]; then
. /opt/intel/mkl/bin/mklvars.sh intel64
diff --git a/cfg/thorgal/intelCommunity.profile b/cfg/thorgal/intelCommunity.profile
index d2bff7e..2501156 100644
--- a/cfg/thorgal/intelCommunity.profile
+++ b/cfg/thorgal/intelCommunity.profile
@@ -1,11 +1,19 @@
-# 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 "$TBBROOT" ]; then
. /opt/intel/tbb/bin/tbbvars.sh intel64
- #fi
fi
diff --git a/cfg/thorgal/mumps.profile b/cfg/thorgal/mumps.profile
index 2d94cb9..57e0ada 100644
--- a/cfg/thorgal/mumps.profile
+++ b/cfg/thorgal/mumps.profile
@@ -1,6 +1,3 @@
-# MUMPS + MKL-TBB
-
add2env LD_LIBRARY_PATH "/opt/mumps/lib"
add2env LIB "/opt/mumps/lib"
add2env INCLUDE "/opt/mumps/include"
-
diff --git a/cfg/thorgal/parasolid.profile b/cfg/thorgal/parasolid.profile
index 5f9e03b..e24e2e8 100644
--- a/cfg/thorgal/parasolid.profile
+++ b/cfg/thorgal/parasolid.profile
@@ -1,6 +1,3 @@
-# Parasolid
-
add2env PATH "/opt/parasolid/shared_object"
add2env INCLUDE "/opt/parasolid"
export P_SCHEMA=/opt/parasolid/schema
-
diff --git a/cfg/zen/eclipse.profile b/cfg/zen/eclipse.profile
index 989a22d..3861d00 100644
--- a/cfg/zen/eclipse.profile
+++ b/cfg/zen/eclipse.profile
@@ -1,5 +1 @@
-
-if [ -d ~/local/eclipse/cpp-mars/eclipse ] ; then
- PATH=$PATH:~/local/eclipse/cpp-mars/eclipse
-fi
-
+add2env PATH "~/local/eclipse/cpp-mars/eclipse"
diff --git a/cfg/zen/lammps.profile b/cfg/zen/lammps.profile
index 07f77ad..348d0d9 100644
--- a/cfg/zen/lammps.profile
+++ b/cfg/zen/lammps.profile
@@ -1,5 +1 @@
-
-if [ -d ~/dev/lammps/src ] ; then
- PATH=$PATH:~/dev/lammps/src
-fi
-
+add2env PATH "~/dev/lammps/src"
diff --git a/externalProgramPath.py b/externalProgramPath.py
old mode 100644
new mode 100755
diff --git a/externalProgramPathGui.pyw b/externalProgramPathGui.pyw
old mode 100644
new mode 100755
diff --git a/postProLoop.py b/postProLoop.py
old mode 100644
new mode 100755
diff --git a/postProLoopGui.pyw b/postProLoopGui.pyw
old mode 100644
new mode 100755
--
GitLab