local: KNDEBUG hook to attach a debugger to a running replica

If the KNDEBUG environment variable is set, PlumedMain's constructor spins on a
volatile flag so you can attach a debugger to an already-running MD job and then
release it by flipping holdToDebug from the debugger. Inert otherwise: one
getenv and one branch.

Not upstreamable in this form -- an unbounded sleep loop in a library
constructor is not something PLUMED would accept, and the commented-out
`simulationIndex > 0` condition shows it was meant to be replica-specific. A
polished version (documented, bounded timeout, opt-in at configure time) could
be proposed separately.

Author: aalhossary

src/core/PlumedMain.cpp

@@ -67,6 +67,7 @@
 #include <optional>
 #include <variant>
 #include <filesystem>
+#include <unistd.h>
 
 namespace PLMD {
 
@@ -289,6 +290,19 @@ PlumedMain::PlumedMain():
   stopwatch_fwd(log),
   actionSet_fwd(*this),
   passtools(DataPassingTools::create(sizeof(double))) {
+
+  bool debug = false;
+  const char* debug_val = std::getenv("KNDEBUG");
+  if (debug_val != nullptr) {
+    debug = true;
+  }
+
+  volatile bool holdToDebug = true;
+  while (/*simulationIndex > 0 &&*/ debug && holdToDebug) {
+    sleep(1);
+  }
+
+
   passtools->usingNaturalUnits=false;
   increaseReferenceCounter();
   log.link(comm);