Merge branch 'master' into c++17

.github/workflows/ci.yml

@@ -134,7 +134,9 @@ jobs:
         echo "CXX=mpic++" >> $GITHUB_ENV
         echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV
         echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV
-        echo "MPIEXEC=mpirun --oversubscribe" >> $GITHUB_ENV
+        echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV
+        echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV
+        echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV
         pip install --user mpi4py
         python -c "import mpi4py"
     - name: Build PLUMED
@@ -206,23 +208,21 @@ jobs:
         make -C src/lib/ dirslinks
         make codecheck
 
-  # We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12)
-  fedora37:
-    runs-on: ubuntu-20.04
-    steps:
-    - uses: actions/checkout@v3
-    - name: Build and run tests
-      run: |
-        make -C docker fedora37
-
-  # We test on rockylinux8 as well
-  rocky8:
-    runs-on: ubuntu-20.04
+  docker:
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        # fedora38 (gcc 13)
+        # rockylinux8
+        variant:
+        - fedora38
+        - rocky8
     steps:
     - uses: actions/checkout@v3
     - name: Build and run tests
       run: |
-        make -C docker rocky8
+        make -C docker ${{ matrix.variant }}
 
   macports:
     runs-on: macos-11

docker/Makefile

@@ -1,11 +1,11 @@
 
-.PHONY: ubuntu plumed2.tgz clean fedora37 rocky8
+.PHONY: ubuntu plumed2.tgz clean fedora38 rocky8
 
 ubuntu: plumed2.tgz
 	docker build -t plumed .
 
-fedora37: plumed2.tgz
-	docker build -t plumed -f fedora37 .
+fedora38: plumed2.tgz
+	docker build -t plumed -f fedora38 .
 
 rocky8: plumed2.tgz
 	docker build -t plumed -f rocky8 .

docker/fedora37 → docker/fedora38

@@ -1,4 +1,4 @@
-FROM fedora:37
+FROM fedora:38
 
 # note: at variance with centos7, here we have to explicitly install gcc
 # mdtraj 1.9.7 does not compile with python 3.11 unless installed from source
@@ -27,7 +27,10 @@ COPY plumed2.tgz /home/plumed
 RUN . /etc/bashrc \
  && module load mpi \
  && export OMPI_MCA_btl_base_warn_component_unused=0 \
- && export MPIEXEC="mpirun --oversubscribe" \
+ && export OMPI_MCA_btl_base_verbose=0 \
+ && export OMPI_MCA_plm=isolated \
+ && export OMPI_MCA_btl_vader_single_copy_mechanism=none \
+ && export OMPI_MCA_rmaps_base_oversubscribe=yes \
  && export PATH=$HOME/opt/bin:$PATH \
  && export CPATH=$HOME/opt/include:$CPATH \
  && export INCLUDE=$HOME/opt/include:$INCLUDE \

docker/rocky8

@@ -26,7 +26,10 @@ COPY plumed2.tgz /home/plumed
 RUN . /etc/bashrc \
  && module load mpi \
  && export OMPI_MCA_btl_base_warn_component_unused=0 \
- && export MPIEXEC="mpirun --oversubscribe" \
+ && export OMPI_MCA_btl_base_verbose=0 \
+ && export OMPI_MCA_plm=isolated \
+ && export OMPI_MCA_btl_vader_single_copy_mechanism=none \
+ && export OMPI_MCA_rmaps_base_oversubscribe=yes \
  && export PATH=$HOME/opt/bin:$PATH \
  && export CPATH=$HOME/opt/include:$CPATH \
  && export INCLUDE=$HOME/opt/include:$INCLUDE \

regtest/basic/rt-errormessages/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt-errormessages/config

@@ -0,0 +1,3 @@
+type=make
+# this is needed because we are explicitly checking some exception message
+export PLUMED_STACK_TRACE=no

regtest/basic/rt-errormessages/output.reference

@@ -0,0 +1 @@
+METAD WALKER_MPI : Exception thrown, correct message

regtest/basic/rt-errormessages/testWALKERS_MPI.cpp

@@ -0,0 +1,77 @@
+#include <fstream>
+
+#include "plumed/wrapper/Plumed.h"
+#include "plumed/tools/Communicator.h"
+
+constexpr unsigned nat=10;
+//it is a struct because we don't need getter/setters (for now)
+struct plumedThrowChecker{
+  unsigned natoms=nat;
+  std::vector<double> positions=[](unsigned natoms){
+    std::vector<double> toret(natoms*3,0.0);
+    for(unsigned i=0; i<3*natoms; i++) toret[i]=i;
+    return toret;
+  }(nat);
+  std::vector<double> masses{nat,1.0};
+  std::vector<double> forces{3*nat,0.0};
+  std::vector<double> box{9,0.0};
+  std::vector<double> virial{9,0.0};
+  ///This initializes a new plumed to test each throw in the cleanliest way possible
+  int checkThrow (std::ostream& out,std::string name, std::string cmd, std::string expectedMessage){
+    //GIVEN an initialized Plumed interface
+    PLMD::Plumed plumed;
+
+    plumed.cmd("setNatoms",&natoms);
+    int step=0;
+    plumed.cmd("setLogFile","test.log");
+    plumed.cmd("init");
+    plumed.cmd("setStep",&step);
+    plumed.cmd("setPositions",positions.data());
+    plumed.cmd("setBox",box.data());
+    plumed.cmd("setForces",forces.data());
+    plumed.cmd("setVirial",virial.data());
+    plumed.cmd("setMasses",masses.data());
+
+    plumed.cmd("readInputLine","d: DISTANCE ATOMS=1,2");
+    plumed.cmd("readInputLine","d1: DISTANCE ATOMS={1 2}");
+    ///TODO: expand with a "readInputLines" to give the possibility to test in more situations
+    try {
+      //WHEN the user ask for the given input
+      plumed.cmd("readInputLine",cmd.c_str());
+      //THEN plumed should gracefully exit with a clear error message
+    } catch(PLMD::Plumed::ExceptionError &e) { //correct throw, we are happy
+      std::string exceptionText{e.what()};
+      out << name << " : ";
+      if (exceptionText.find(expectedMessage) != std::string::npos) {
+        out << "Exception thrown, correct message\n";
+        return 0;
+      }
+
+      out << "Exception thrown, wrong message: "
+                << e.what() ;
+      out << "\tExpected message should contain: \""
+                << expectedMessage << "\"\n";
+      return 1;
+    }
+    out  << "Exception not thrown\n";
+    return 1;
+  }
+};
+
+int main(int, char**) {
+  std::ofstream out("output");
+  plumedThrowChecker ptc;
+  //When the user aks for a WALKERS_MPI in the METAD action,
+  //if MPI is not installed then the user must be informed
+  //if MPI is installed then the comunications must be already set up
+  //WHEN PLUMED is not compiled with MPI or the MPI routines are not initialized
+  std::string expectedMessage="WALKERS_MPI flag requires MPI compilation";
+  if (PLMD::Communicator::plumedHasMPI()) {
+    expectedMessage="WALKERS_MPI needs the communicator correctly initialized";
+  }
+  ptc.checkThrow(out,"METAD WALKER_MPI",
+    "METAD ARG=d,d1 SIGMA=0.1,0.2 HEIGHT=0.1 PACE=2 RESTART=YES WALKERS_MPI",
+    expectedMessage);
+
+  //add other throw messages checks
+}

regtest/multicolvar/rt-link/config

@@ -1,2 +1 @@
-mpiprocs=2
 type=make

regtest/multicolvar/rt-link/main.cpp

@@ -1,4 +1,3 @@
-#include "mpi.h"
 #include "plumed/tools/Communicator.h"
 #include "plumed/tools/Tools.h"
 #include "plumed/tools/Vector.h"

regtest/scripts/run

@@ -58,9 +58,14 @@ echo "++ Arguments: $arg"
 echo "++ Processors: $mpiprocs"
 
 mpi=env
+
+# this is the executable used for running the tests:
 plumed="${PLUMED_PROGRAM_NAME:-plumed}"
 
-root=$($plumed --no-mpi info --root)
+# this is the executable used for getting the configuration:
+plumed_nompi="$plumed --no-mpi"
+
+root=$($plumed_nompi info --root)
 
 if test -z "$root" ; then
   echo "FAILURE: plumed executable not available"
@@ -76,16 +81,16 @@ cd -
 
 if ((mpiprocs>0)); then
 mpi=""
-if $plumed --no-mpi config -q mpiexec
+if $plumed_nompi config -q mpiexec
 then
-  mpi="$($plumed --no-mpi config mpiexec)"
+  mpi="$($plumed_nompi config mpiexec)"
 fi
 if test -z "$mpi" ; then
   mpi="${PLUMED_MPIRUN:-mpirun}"
 fi
 mpi="$mpi -np $mpiprocs"
 
-if ! $plumed config -q has mpi
+if ! $plumed_nompi config -q has mpi
 then
     if [ "$TRAVIS" = true ] || [ "$GITHUB_ACTIONS" = true ] ; then
       if [ -z "$PLUMED_ALLOW_SKIP_ON_TRAVIS" ] ; then
@@ -122,7 +127,7 @@ fi
 for need in $plumed_needs
 do
   echo "Checking for $need"
-  if ! $plumed config -q has $need
+  if ! $plumed_nompi config -q has $need
   then
     if [ "$TRAVIS" = true ] || [ "$GITHUB_ACTIONS" = true ] ; then
       if [ -z "$PLUMED_ALLOW_SKIP_ON_TRAVIS" ] ; then
@@ -140,7 +145,7 @@ done
 for module in $plumed_modules
 do
   echo "Checking for $module"
-  if ! $plumed config -q module $module
+  if ! $plumed_nompi config -q module $module
   then
     if [ "$TRAVIS" = true ] || [ "$GITHUB_ACTIONS" = true ] ; then
       if [ -z "$PLUMED_ALLOW_SKIP_ON_TRAVIS" ] ; then
@@ -170,10 +175,12 @@ if type -t plumed_custom_skip 1>/dev/null ; then
   fi
 fi
 
-if $plumed --is-installed ; then
-  export PLUMED_KERNEL="$root/../lib${PLUMED_PROGRAM_NAME:-plumed}Kernel.$($plumed info --soext)"
+if $plumed_nompi --is-installed ; then
+  export PLUMED_KERNEL="$root/../lib${PLUMED_PROGRAM_NAME:-plumed}Kernel.$($plumed_nompi info --soext)"
+  export PLUMED_LIB="$root/../lib${PLUMED_PROGRAM_NAME:-plumed}.$($plumed_nompi info --soext)"
 else
-  export PLUMED_KERNEL="$root/src/lib/libplumedKernel.$($plumed info --soext)"
+  export PLUMED_KERNEL="$root/src/lib/libplumedKernel.$($plumed_nompi info --soext)"
+  export PLUMED_LIB="$root/src/lib/libplumed.$($plumed_nompi info --soext)"
 fi
 if type -t plumed_regtest_before 1>/dev/null ; then
   plumed_regtest_before
@@ -194,12 +201,11 @@ case "$type" in
   $mpi $valgrind $plumed sum_hills $arg > out 2> err
  ;;
 (make)
-  $plumed info --configuration > Makefile.conf
-  $plumed --is-installed || ln -s "$root/src" plumed
+  $plumed_nompi --is-installed || ln -s "$root/src" plumed
   if test "$plumed_language" = fortran || test "$plumed_language" = fortran08 || test "$plumed_language" = c ; then
-    cat <($plumed info --configuration) "$root/src/lib/Plumed.inc.shared" ../../../scripts/exe.make > Makefile 
+    cat <($plumed_nompi info --configuration) "$root/src/lib/Plumed.inc.shared" ../../../scripts/exe.make > Makefile 
   else
-    cat <($plumed info --configuration) "$root/src/lib/Plumed.inc.static" ../../../scripts/exe.make > Makefile 
+    cat <($plumed_nompi info --configuration) "$root/src/lib/Plumed.inc.static" ../../../scripts/exe.make > Makefile 
   fi
   if test "$plumed_language" = fortran || test "$plumed_language" = fortran08 ; then
     if make print-fortran | grep "FC=$" 1>/dev/null ; then
@@ -271,7 +277,7 @@ EOF
   ;;
 (python)
 # make sure the right python module is in the path based on plumed root
-  PYTHONPATH="$root/python:$PYTHONPATH" $($plumed config python_bin) $arg > out 2> err
+  PYTHONPATH="$root/python:$PYTHONPATH" $($plumed_nompi config python_bin) $arg > out 2> err
   ;;
 (*) echo "FAILURE: unknown test type" ; exit 1 ;;
 esac

src/bias/MetaD.cpp

@@ -875,6 +875,12 @@ MetaD::MetaD(const ActionOptions& ao):
   // MPI version
   parseFlag("WALKERS_MPI",walkers_mpi_);
 
+  //If this Action is not compiled with MPI the user is informed and we exit gracefully
+  if(walkers_mpi_) {
+    plumed_assert(Communicator::plumedHasMPI()) << "Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation";
+    plumed_assert(Communicator::initialized()) << "Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.";
+  }
+
   // Flying Gaussian
   parseFlag("FLYING_GAUSSIAN", flying_);
 

src/opes/ECVmultiThermalBaric.cpp

@@ -327,7 +327,7 @@ ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&ao)
   log.printf("   and a pressure range from PRESSURE_MIN=%g to PRESSURE_MAX=%g\n",pres_min,pres_max);
   if(pres_min==pres_max)
     log.printf(" +++ WARNING +++ if you only need a multithermal simulation it is more efficient to set it up with ECV_MULTITHERMAL\n");
-  if(geom_spacing_)
+  if(!geom_spacing_)
     log.printf(" -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n");
   if(coeff_!=0)
     log.printf(" -- CUT_CORNER: ignoring some high temperature and low pressure values\n");

src/opes/OPESexpanded.cpp

@@ -251,6 +251,10 @@ OPESexpanded::OPESexpanded(const ActionOptions&ao)
   parseFlag("WALKERS_MPI",walkers_mpi);
   if(walkers_mpi)
   {
+    //If this Action is not compiled with MPI the user is informed and we exit gracefully
+    plumed_massert(Communicator::plumedHasMPI(),"Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation");
+    plumed_massert(Communicator::initialized(),"Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.");
+
     if(comm.Get_rank()==0) //multi_sim_comm works on first rank only
     {
       NumWalkers_=multi_sim_comm.Get_size();

src/opes/OPESmetad.cpp

@@ -306,7 +306,11 @@ void OPESmetad<mode>::registerKeywords(Keywords& keys)
   keys.use("ARG");
   keys.add("compulsory","TEMP","-1","temperature. If not set, it is taken from MD engine, but not all MD codes provide it");
   keys.add("compulsory","PACE","the frequency for kernel deposition");
-  keys.add("compulsory","SIGMA","ADAPTIVE","the initial widths of the kernels. If not set, adaptive sigma will be used with the given ADAPTIVE_SIGMA_STRIDE");
+  std::string info_sigma("the initial widths of the kernels");
+  if(mode::explore)
+    info_sigma+=", divided by \\f$\\sqrt{\\gamma}\\f$";
+  info_sigma+=". If not set, an adaptive sigma will be used with the given ADAPTIVE_SIGMA_STRIDE";
+  keys.add("compulsory","SIGMA","ADAPTIVE",info_sigma);
   keys.add("compulsory","BARRIER","the free energy barrier to be overcome. It is used to set BIASFACTOR, EPSILON, and KERNEL_CUTOFF to reasonable values");
   keys.add("compulsory","COMPRESSION_THRESHOLD","1","merge kernels if closer than this threshold, in units of sigma");
 //extra options
@@ -554,6 +558,10 @@ OPESmetad<mode>::OPESmetad(const ActionOptions& ao)
   parseFlag("WALKERS_MPI",walkers_mpi);
   if(walkers_mpi)
   {
+    //If this Action is not compiled with MPI the user is informed and we exit gracefully
+    plumed_massert(Communicator::plumedHasMPI(),"Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation");
+    plumed_massert(Communicator::initialized(),"Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.");
+
     if(comm.Get_rank()==0)//multi_sim_comm works on first rank only
     {
       NumWalkers_=multi_sim_comm.Get_size();

src/tools/Communicator.cpp

@@ -28,6 +28,14 @@
 
 namespace PLMD {
 
+bool Communicator::plumedHasMPI() {
+#ifdef __PLUMED_HAS_MPI
+  return true;
+#else
+  return false;
+#endif
+}
+
 Communicator::Communicator()
 #ifdef __PLUMED_HAS_MPI
   : communicator(MPI_COMM_SELF)

src/tools/Communicator.h

@@ -121,6 +121,9 @@ class Communicator {
     }
   };
 public:
+  ///Runtime acces to the __PLUMED_HAS_MPI definition
+  static bool plumedHasMPI();
+
 /// Wrapper class for MPI_Status
   class Status {
     int Get_count(MPI_Datatype)const;

user-doc/Introduction.md

@@ -45,6 +45,7 @@ As far as we know, the following MD codes can be used with PLUMED out of the box
 - [DFTB+](https://www.dftbplus.org/), since release 20.1.
 - [Metalwalls](https://gitlab.com/ampere2/metalwalls)
 - [ASE](https://wiki.fysik.dtu.dk/ase/)
+- [GPUMD](https://gpumd.org/)
 
 Please refer to the documentation of the MD code to know how to use it with the latest PLUMED release.
 If you maintain another MD code that is PLUMED-ready let us know and we will add it to this list.