Fix handling of generated rotation matrix sets in parallel with the '…

…rotate' command (Amber-MD#1112)

* Fix accessing the internal rotation matrix data set in parallel for
'rotate'

* Class to choose correct frame number in parallel based on whether a
data set exists or is being generated

* Use ParallelSetFrameNum

* Hide debug info

* 6.29.6. Revision bump for fixed handling of input rotation matrix data
set in rotate command.

src/Action_Rotate.cpp

@@ -38,6 +38,7 @@ int Action_Rotate::Get3x3Set(DataSetList const& DSL, std::string const& dsname)
     mprinterr("Error: No 3x3 matrices data set '%s'\n", dsname.c_str());
     return 1;
   }
+  parallelNum_.SetForParallel( rmatrices_ );
   return 0;
 }
 
@@ -201,29 +202,31 @@ Action::RetType Action_Rotate::DoAction(int frameNum, ActionFrame& frm) {
     if (all_atoms_selected_)
       frm.ModifyFrm().ModifyBox().RotateUcell( RotMatrix_ );
   } else if (mode_ == DATASET) {
+    int dsidx = parallelNum_.ParallelFrameNum(frameNum, frm.TrajoutNum());
     // Rotate coordinates using rotation matrices in DataSet
-    if (frm.TrajoutNum() >= (int)rmatrices_->Size()) {
-      mprintf("Warning: Frame %i out of range for set '%s'\n",
+    if (dsidx >= (int)rmatrices_->Size()) {
+      rprintf("Warning: Frame %i out of range for set '%s'\n",
               frm.TrajoutNum()+1, rmatrices_->legend());
       return Action::ERR;
     }
     if (inverse_) {
-      frm.ModifyFrm().InverseRotate((*rmatrices_)[frm.TrajoutNum()], mask_);
+      frm.ModifyFrm().InverseRotate((*rmatrices_)[dsidx], mask_);
       if (all_atoms_selected_)
-        frm.ModifyFrm().ModifyBox().InverseRotateUcell( (*rmatrices_)[frm.TrajoutNum()] );
+        frm.ModifyFrm().ModifyBox().InverseRotateUcell( (*rmatrices_)[dsidx] );
     } else {
-      frm.ModifyFrm().Rotate((*rmatrices_)[frm.TrajoutNum()], mask_);
+      frm.ModifyFrm().Rotate((*rmatrices_)[dsidx], mask_);
       if (all_atoms_selected_)
-        frm.ModifyFrm().ModifyBox().RotateUcell( (*rmatrices_)[frm.TrajoutNum()] );
+        frm.ModifyFrm().ModifyBox().RotateUcell( (*rmatrices_)[dsidx] );
     }
   } else if (mode_ == CALC) {
+    int dsidx = parallelNum_.ParallelFrameNum(frameNum, frm.TrajoutNum());
     // Calculate rotations around X Y and Z axes from rotation matrices in DataSet
-    if (frm.TrajoutNum() >= (int)rmatrices_->Size()) {
-      mprintf("Warning: Frame %i out of range for set '%s'\n",
+    if (dsidx >= (int)rmatrices_->Size()) {
+      rprintf("Warning: Frame %i out of range for set '%s'\n",
               frm.TrajoutNum()+1, rmatrices_->legend());
       return Action::ERR;
     }
-    Matrix_3x3 const& RM = (*rmatrices_)[frm.TrajoutNum()];
+    Matrix_3x3 const& RM = (*rmatrices_)[dsidx];
     double tx, ty, tz;
     RM.RotationAngles(tx, ty, tz);
     tx *= Constants::RADDEG;

src/Action_Rotate.h

@@ -1,6 +1,7 @@
 #ifndef INC_ACTION_ROTATE_H
 #define INC_ACTION_ROTATE_H
 #include "Action.h"
+#include "ParallelSetFrameNum.h"
 class DataSet_Mat3x3;
 /// Rotate coordinates or calculate rotations from rotation matrices
 class Action_Rotate : public Action {
@@ -33,5 +34,6 @@ class Action_Rotate : public Action {
     DataSet* dsout_ty_;         ///< Hold output theta Y (calc)
     DataSet* dsout_tz_;         ///< Hold output theta Z (calc)
     DataSet* dsout_t_;          ///< Hold output theta (calc)
+    Cpptraj::ParallelSetFrameNum parallelNum_;
 };
 #endif

src/ParallelSetFrameNum.cpp

@@ -0,0 +1,21 @@
+#include "ParallelSetFrameNum.h"
+#include "CpptrajStdio.h"
+#include "DataSet.h"
+using namespace Cpptraj;
+
+void ParallelSetFrameNum::SetForParallel(DataSet const* setIn) {
+  set_ = setIn;
+# ifdef MPI
+  // In parallel, number to use will depend on whether the set exists or not
+  if (set_->Size() > 0)
+    exists_ = true;
+  else
+    exists_ = false;
+# ifdef DEBUG_CPPTRAJ_PARALLELSETFRAMENUM
+  if (!exists_)
+    rprintf("DEBUG: Set '%s' does not yet exist.\n", set_->legend());
+  else
+    rprintf("DEBUG: Set '%s' exists with size %zu.\n", set_->legend(), set_->Size());
+# endif
+# endif /*MPI */
+}

src/ParallelSetFrameNum.h

@@ -0,0 +1,38 @@
+#ifndef INC_PARALLELSETFRAMENUM_H
+#define INC_PARALLELSETFRAMENUM_H
+class DataSet;
+namespace Cpptraj {
+/// Used to pick the correct frame from a data set in parallel
+/** In parallel, Actions that access data from DataSets need to handle
+  * two cases:
+  *   1) The data set exists already before trajectory processing.
+  *   2) The data set is being created during trajectory processing.
+  * In case 1, the data set should be accessed using ActionFrame::TrajoutNum().
+  * In case 2, the data set should be accessed using the frameNum variable
+  * since the set has not yet been synced.
+  */
+class ParallelSetFrameNum {
+  public:
+    /// CONSTRUCTOR
+    ParallelSetFrameNum() : set_(0), exists_(false) {}
+    /// Initialize with DataSet, record if it has any data yet.
+    void SetForParallel(DataSet const*);
+    /// \return Correct frame number in parallel based on whether set exists or is being generated
+    int ParallelFrameNum(int frameNum, int trajoutNum) const {
+#     ifdef MPI
+      // In parallel, number to use depends on whether the set is being generated or not.
+      if (exists_)
+        return trajoutNum;
+      else
+        return frameNum;
+#     else
+      // In serial, just return the frame number.
+      return frameNum;
+#     endif
+    }
+  private:
+    DataSet const* set_; ///< The DataSet in question
+    bool exists_;  ///< True if set exists, false if it is being generated.
+};
+} // END namespace Cpptraj
+#endif

src/Version.h

@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.29.5"
+#define CPPTRAJ_INTERNAL_VERSION "V6.29.6"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

src/cpptrajfiles

@@ -368,6 +368,7 @@ COMMON_SOURCES= \
         PairList.cpp \
         Parallel.cpp \
         ParallelNetcdf.cpp \
+        ParallelSetFrameNum.cpp \
         ParmFile.cpp \
         Parm_Amber.cpp \
         Parm_CharmmPsf.cpp \