Merge branch 'v2.4' of github.com:plumed/plumed2 into v2.4

CHANGES/v2.4.md

@@ -151,3 +151,9 @@ Fixes after beta release:
   - Fixed a bug in EDS module for restarts, where accumulated rate was not stored to restart file, leading to convergence problems.
   - (developers) `plumed config makefile_conf` can be used to retrieve `Makefile.conf` file a posteriori.
   - Added patch for Quantum ESPRESSO 6.2 (thanks to Ralf Meyer).
+  - (developers) Store `MPIEXEC` variable at configure time and use it later for running regtests. Notice that in case
+    `MPIEXEC` is not specified regtests will be run using the command stored in env var `PLUMED_MPIRUN` or, if this is
+    also not defined, using `mpirun`.
+  - (developers) Added canonical makefile targets `check` and `installcheck`. Notice that `check` runs checks with
+    non-installed plumed whereas `installcheck` uses the installed one, including its correct program name if it
+    was personalized (e.g. with suffixes). Notice that this modifies the previously available `check` target.

Makefile

@@ -13,7 +13,7 @@ SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports vim astyle
 SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
 
      
-.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck distclean all_plus_docs macports codecheck plumedcheck astyle
+.PHONY: all lib clean $(SRCDIRS) doc docclean check installcheck cppcheck distclean all_plus_docs macports codecheck plumedcheck astyle
 
 # if machine dependent configuration has been found:
 ifdef GCCDEP
@@ -59,8 +59,15 @@ docs:
 	$(MAKE) doc
 
 # regtests
-check: src test
-	$(MAKE) -C regtest
+# perform tests using non-installed plumed
+check:
+	PLUMED_PREPEND_PATH="$(realpath .)/src/lib" $(MAKE) -C regtest
+	$(MAKE) -C regtest checkfail
+
+# perform tests using the installed version of plumed
+installcheck:
+	PLUMED_PREPEND_PATH="$(bindir)" PLUMED_PROGRAM_NAME="$(program_name)" $(MAKE) -C regtest
+	$(MAKE) -C regtest checkfail
 
 else
 

Makefile.conf.in

@@ -32,3 +32,4 @@ datarootdir=@datarootdir@
 datadir=@datadir@
 docdir=@docdir@
 htmldir=@htmldir@
+mpiexec=@MPIEXEC@

README.md

@@ -97,37 +97,30 @@ Quick compilation instructions
 ------------------------------
 
 Extensive installation instructions are in the [user documentation](http://www.plumed.org/documentation).
-Configure for your system
+Quick instructions:
 
     ./configure --prefix=$HOME/opt
-    
-    
-If necessary, edit `Makefile.conf`. 
-Configure your environment
-
-    source ./sourceme.sh
-    
-Compile plumed
-
     make
-    
-The `plumed` executable should be now in your execution path
-
-    plumed help
-    
-Compile the manuals.
-
-    make doc
+    make doc # optional
 
 User documentation can be found at `user-doc/html/index.html`.
 Developer documentation can be found at `developer-doc/html/index.html`.
 [Pre-compiled documentation](http://www.plumed.org/documentation) is available online, so this is only required
 if you are working with a modified version of the code!
 
-Install PLUMED in `$HOME/opt` (directory should be set during `./configure`):
+In order to run PLUMED without installing it you should type `source sourceme.sh`. However,
+we recomment installing PLUMED. 
+To install it in `$HOME/opt` (directory should be set during `./configure`):
 
     umask 022
     make install
     
+Now you will be able to run plumed using e.g.
+
+    plumed help
+
+If you compiled your own documentation, paths to the installed documentation can be found with command `plumed info --user-doc`.
+
 A sample modulefile with environment variable will be placed in
-`$HOME/opt/lib/plumed/src/lib/modulefile`. If you compiled your own documentation, paths to the installed documentation can be found with command `plumed info --user-doc`.
+`$HOME/opt/lib/plumed/src/lib/modulefile`. This can be useful if you want to
+install multiple PLUMED versions side by side and select them with env modules.

configure

@@ -651,6 +651,7 @@ CPPFLAGS
 LDFLAGS
 CXXFLAGS
 CXX
+MPIEXEC
 LDSHARED
 STATIC_LIBS
 SOEXT
@@ -735,6 +736,7 @@ target_alias
 SOEXT
 STATIC_LIBS
 LDSHARED
+MPIEXEC
 CXX
 CXXFLAGS
 LDFLAGS
@@ -1409,6 +1411,9 @@ Some influential environment variables:
               configure will add here -ldl if necessary
   LDSHARED    command for linking shared library - configure will use CXX plus
               the proper flags
+  MPIEXEC     command to run mpi programs in tests - default not specified,
+              which means use PLUMED_MPIRUN env var at runtime for backward
+              compatibility
   CXX         C++ compiler command
   CXXFLAGS    C++ compiler flags
   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
@@ -3009,6 +3014,7 @@ fi
 
 
 
+
 # by default use -O flag
 # we override the autoconf default (-g) because in release build we do not want to
 # include symbol information (obj files are huge)
@@ -8365,6 +8371,8 @@ $as_echo "#define _REENTRANT 1" >>confdefs.h
 # these are libraries that should be linked also to MD engines
 
 
+
+
 if test "$shared" == true ; then
   case `(uname)` in
   (Darwin)
@@ -8755,6 +8763,16 @@ fi
 
 fi
 
+if test $mpi_found == ok ; then
+  if test -n "$MPIEXEC" ; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: Regtest suite will use $MPIEXEC command to run MPI tests" >&5
+$as_echo "$as_me: Regtest suite will use $MPIEXEC command to run MPI tests" >&6;}
+  else
+    { $as_echo "$as_me:${as_lineno-$LINENO}: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun)" >&5
+$as_echo "$as_me: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun)" >&6;}
+  fi
+fi
+
 #### This further tests are required to allow linking with non c++ compiler
 { $as_echo "$as_me:${as_lineno-$LINENO}: PLUMED seems to be configured properly!" >&5
 $as_echo "$as_me: PLUMED seems to be configured properly!" >&6;}

configure.ac

@@ -260,6 +260,7 @@ PLUMED_CONFIG_ENABLE([fftw],[search for fftw],[no])
 AC_ARG_VAR(SOEXT,[extension of dynamic libraries (so/dylib)])
 AC_ARG_VAR(STATIC_LIBS,[variables that should be linked statically directly to MD code - configure will add here -ldl if necessary ])
 AC_ARG_VAR(LDSHARED,[command for linking shared library - configure will use CXX plus the proper flags ])
+AC_ARG_VAR(MPIEXEC,[command to run mpi programs in tests - default not specified, which means use PLUMED_MPIRUN env var at runtime for backward compatibility])
 
 
 # by default use -O flag
@@ -673,6 +674,8 @@ AC_SUBST(LDSHARED)
 # these are libraries that should be linked also to MD engines
 AC_SUBST(STATIC_LIBS)
 
+AC_SUBST(MPIEXEC)
+
 if test "$shared" == true ; then
   case `(uname)` in
   (Darwin)
@@ -839,6 +842,14 @@ int main(int argc,char*argv[[]]){
 )
 fi
 
+if test $mpi_found == ok ; then
+  if test -n "$MPIEXEC" ; then
+    AC_MSG_NOTICE([Regtest suite will use $MPIEXEC command to run MPI tests])
+  else
+    AC_MSG_NOTICE([Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun)])
+  fi
+fi
+
 #### This further tests are required to allow linking with non c++ compiler
 AC_MSG_NOTICE([PLUMED seems to be configured properly!])
 AC_MSG_NOTICE([**************************])

macports/Portfile.in

@@ -65,6 +65,11 @@ mpi.setup
 # To enable mpi, replace a configure flag
 if {[mpi_variant_isset]} {
   configure.args-replace --disable-mpi --enable-mpi
+  # command should be included in a pre-configure block to access properly the mpi.exec variable
+  pre-configure {
+  # MPIEXEC is stored so that it can be used to perform tests
+    configure.args-append MPIEXEC="${mpi.exec}"
+  }
 }
 
 # Libraries.

regtest/scripts/run

 #!/bin/bash
 
+if test -n "$PLUMED_PREPEND_PATH" ; then
+  PATH="$PLUMED_PREPEND_PATH:$PATH"
+fi
+
 export valgrind=env
 
 for opt in ${*}
@@ -46,7 +50,7 @@ echo "++ Arguments: $arg"
 echo "++ Processors: $mpiprocs"
 
 mpi=env
-plumed=plumed
+plumed="${PLUMED_PROGRAM_NAME:-plumed}"
 
 root=$($plumed --no-mpi info --root)
 
@@ -63,9 +67,17 @@ cd -
 
 
 if ((mpiprocs>0)); then
-mpi="${PLUMED_MPIRUN:-mpirun} -np $mpiprocs"
+mpi=""
+if $plumed --no-mpi config -q mpiexec
+then
+  mpi="$($plumed --no-mpi config mpiexec)"
+fi
+if test -z "$mpi" ; then
+  mpi="${PLUMED_MPIRUN:-mpirun}"
+fi
+mpi="$mpi -np $mpiprocs"
 
-if ! plumed config -q has mpi
+if ! $plumed config -q has mpi
 then
   echo "NOT_APPLICABLE (MPI NOT INSTALLED)"
   exit 0;
@@ -73,7 +85,7 @@ fi
 
 else
 
-plumed="plumed --no-mpi"
+plumed="$plumed --no-mpi"
 
 fi
 

scripts/config.sh

@@ -50,6 +50,7 @@ do
     ;;
   (has) action=has ;;
   (module) action=module ;;
+  (mpiexec) action=mpiexec ;;
   (makefile_conf)
     echo "$configfile" | awk '{if($1=="makefile_conf") { gsub("^makefile_conf ",""); print} }'
     exit 0
@@ -95,5 +96,15 @@ case $action in
   git=$(echo "$configfile" | grep -v \# | awk '{ if($1=="version" && $2=="git") print $3 }')
   echo "Version: $long (git: $git)"
  ;;
+(mpiexec)
+  mpi=$(echo "$configfile" | grep -v \# | awk '{ if($1=="mpiexec") print $2 }')
+  if test -n "$mpi" ; then
+    retval=0
+    test "$quiet" = no && echo "$mpi"
+  else
+    retval=1
+    test "$quiet" = no && echo "mpiexec not found"
+  fi
+  exit $retval
 esac
 

src/config/Makefile

@@ -23,7 +23,9 @@ obj: all
 
 config.txt: ../../Makefile.conf
 	@echo "Updating config.txt file"
-	@makefile_conf="$(realpath ../../Makefile.conf)" ../maketools/update-config-txt.sh config.txt $(CPPFLAGS)
+	@makefile_conf="$(realpath ../../Makefile.conf)" \
+         mpiexec="$(mpiexec)" \
+         ../maketools/update-config-txt.sh config.txt $(CPPFLAGS)
 
 version.h:
 	@echo "Updating version.h"

src/maketools/update-config-txt.sh

@@ -101,6 +101,8 @@ echo "# version strings"
 echo "# syntax: version short/long/git number"
 echo "$version"
 echo
+echo "mpiexec $mpiexec"
+echo
 echo "# list of 'has' options"
 echo "# syntax: has name on/of"
 echo "# if option xx is on then plumed has beeen compiled with -D__PLUMED_HAS_XX"