Merge branch 'v2.9'

CHANGES/v2.8.md

@@ -112,4 +112,5 @@ Changes from version 2.7 which are relevant for users:
 - Fixed an error in checking array shapes in the interface. Arrays with shape (N,4) should not be accepted for positions or forces.
 - Small fix in Python, where we do not assume anymore that strings are null terminated.
 - Environment variables such as `PLUMED_INCLUDEDIR` and similar are sanitized before they are used for running commands.
+- Fixed a bug leading to a crash when using python selectors (e.g., `@mda:` or `@mdt:`) and multiple MPI processes per replica.
 

regtest/basic/rt32b-mpi/Makefile

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

regtest/basic/rt32b-mpi/config

@@ -0,0 +1,32 @@
+type=driver
+mpiprocs=2
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --debug-dd yes"
+extra_files="
+  ../rt32b/colvar.reference
+  ../rt32b/helix.pdb
+  ../rt32b/test.gro.reference
+  ../rt32b/test1.gro.reference
+  ../rt32b/test2.gro.reference
+  ../rt32b/test3.gro.reference
+  ../rt32b/test4.gro.reference
+  ../rt32b/test5.gro.reference
+  ../rt32b/ala12_trajectory.xyz
+  ../rt32b/plumed.dat
+"
+
+
+function plumed_custom_skip() {
+   if test -n "$PLUMED_PYTHON_SELECT" ; then
+      export PLUMED_PYTHON_BIN="$PLUMED_PYTHON_SELECT"
+      return 1
+   fi
+   for python_bin in python3 python3.12 python3.11 python3.10 python3.9 python3.8 python3.7 python ; do
+     if $python_bin -c "import MDAnalysis; import mdtraj" 2>/dev/null ; then
+       if [ $python_bin != python ] ; then
+         export PLUMED_PYTHON_BIN=$python_bin
+       fi
+       return 1
+     fi
+   done
+   return 0
+}

regtest/basic/rt32b/config

@@ -2,11 +2,13 @@ type=driver
 arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
 
 function plumed_custom_skip() {
-   if test -n "$PLUMED_PYTHON_SELECT" ; then
-      export PLUMED_PYTHON_BIN="$PLUMED_PYTHON_SELECT"
-      return 1
+   if test -n "$PYTHON_BIN" ; then
+     if $PYTHON_BIN -c "import MDAnalysis; import mdtraj" 2>/dev/null ; then
+       export PLUMED_PYTHON_BIN=$PYTHON_BIN
+       return 1
+     fi
    fi
-   for python_bin in python python2.7 python3.6 python3.7 ; do
+   for python_bin in python3 python3.12 python3.11 python3.10 python3.9 python3.8 python3.7 python ; do
      if $python_bin -c "import MDAnalysis; import mdtraj" 2>/dev/null ; then
        if [ $python_bin != python ] ; then
          export PLUMED_PYTHON_BIN=$python_bin

src/core/GenericMolInfo.cpp

@@ -250,14 +250,17 @@ void GenericMolInfo::interpretSymbol( const std::string& symbol, std::vector<Ato
     plumed_assert(enablePythonInterpreter);
 
     log<<"  symbol " + symbol + " will be sent to python interpreter\n";
-    if(!selector) {
+    if(!selector_running) {
       log<<"  MOLINFO "<<getLabel()<<": starting python interpreter\n";
       if(comm.Get_rank()==0) {
         selector=Tools::make_unique<Subprocess>(pythonCmd+" \""+config::getPlumedRoot()+"\"/scripts/selector.sh --pdb " + reference);
         selector->stop();
       }
+      selector_running=true;
     }
 
+    atoms.resize(0);
+
     if(comm.Get_rank()==0) {
       int ok=0;
       std::string error_msg;
@@ -279,7 +282,6 @@ void GenericMolInfo::interpretSymbol( const std::string& symbol, std::vector<Ato
           if(!words.empty() && words[0]=="Selection:") break;
         }
         words.erase(words.begin());
-        atoms.resize(0);
         for(const auto & w : words) {
           int n;
           if(w.empty()) continue;
@@ -313,6 +315,7 @@ void GenericMolInfo::interpretSymbol( const std::string& symbol, std::vector<Ato
       }
       size_t nat=0;
       comm.Bcast(nat,0);
+      atoms.resize(nat);
       comm.Bcast(atoms,0);
     }
     log<<"  selection interpreted using ";
@@ -359,9 +362,10 @@ bool GenericMolInfo::isWhole() const {
 }
 
 void GenericMolInfo::prepare() {
-  if(selector) {
+  if(selector_running) {
     log<<"  MOLINFO "<<getLabel()<<": killing python interpreter\n";
     selector.reset();
+    selector_running=false;
   }
 }
 

src/core/GenericMolInfo.h

@@ -56,6 +56,9 @@ class GenericMolInfo :
   std::string pythonCmd;
 /// Selector subprocess
   std::unique_ptr<Subprocess> selector;
+/// Track is selector is running
+/// Needed on Get_rank()>0
+  bool selector_running=false;
 /// Structure in pdb file is whole
   bool iswhole_;
 public: