Merge branch 'v2.3' into v2.4

CHANGES/v2.3.md

@@ -233,6 +233,7 @@ For developers:
 For users:
 - Fixed a problem leading to NaN derivatives of \ref switchingfunction `Q` when distance between two atoms is large.
 - GROMACS patch updated to gromacs-2016.5.
+- `./configure` crashes if prefix is set to present working directory (notice that this choice was already leading to issues).
 
 For developers:
 - Fixed small issue in debug options of \ref driver (see \issue{245}).

configure

@@ -8953,6 +8953,21 @@ then
   prefix=/usr/local
 fi
 
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking If prefix is equal to present working directory" >&5
+$as_echo_n "checking If prefix is equal to present working directory... " >&6; }
+
+# ignore cases where the directory does not exist:
+normalized_prefix="`cd "${prefix}" 2>/dev/null && pwd || true`"
+
+if test "`pwd`" = "$normalized_prefix" ; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+  as_fn_error $? "prefix should not be equal to the present working directory" "$LINENO" 5
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
 test "$program_prefix" != NONE &&
   program_transform_name="s&^&$program_prefix&;$program_transform_name"
 # Use a double $ so make ignores it.

configure.ac

@@ -1013,6 +1013,18 @@ then
   prefix=/usr/local
 fi
 
+AC_MSG_CHECKING([If prefix is equal to present working directory])
+
+# ignore cases where the directory does not exist:
+normalized_prefix="`cd "${prefix}" 2>/dev/null && pwd || true`"
+
+if test "`pwd`" = "$normalized_prefix" ; then
+  AC_MSG_RESULT([yes])
+  AC_MSG_ERROR([prefix should not be equal to the present working directory])
+else
+  AC_MSG_RESULT([no])
+fi
+
 AC_ARG_PROGRAM
 
 

user-doc/Installation.md

@@ -433,6 +433,9 @@ variable when installing, PLUMED will be installed in /usr/local.
 The install command should be executed with root permissions (e.g. "sudo make install")
 if you want to install PLUMED on a system directory.
 
+\warning Please **do not** set prefix to the current directory (`./configure --prefix=$PWD`). PLUMED
+expects the installation directory to be a different one! You might want to use something like `./configure --prefix=$PWD/install` instead.
+
 Notice that upon installation PLUMED might need to relink a library.
 This was always true until version 2.1, but in version 2.2 libraries should
 only be relinked if one changes the install prefix during when typing `make install`.