From 1e082db5f91eda9313be7a386e61ab6733934be8 Mon Sep 17 00:00:00 2001
From: Amr ALHOSSARY <amr_alhossary@hotmail.com>
Date: Thu, 30 Jul 2026 07:38:23 -0400
Subject: [PATCH] PathMSDBase: drop four omp simd pragmas that cannot vectorize

Building with clang and OpenMP emits, four times:

    PathMSDBase.cpp:160:19: warning: loop not vectorized: the optimizer was
    unable to perform the requested transformation ... [-Wpass-failed=transform-warning]

All four remarks are attributed to calculate()'s opening line, which hides which
loops are at fault. Isolating them by keeping one pragma at a time shows exactly
four contributors, and two pragmas that are fine:

    line 176  imgVec[i].property = ... ; imgVec[i].index = i;      1 warning
    line 234  tmp_derivs2[i*nat+j] = tmp_derivs[j];                1 warning
    line 244  (the same loop again)                                1 warning
    line 266  (the same loop again)                                1 warning
    line 335  derivs_s[i] += tmp*it.distder[i];                    0 - vectorizes
    line 340  derivs_z[i] += ...;                                  0 - vectorizes

Neither failing case can be vectorized, and asking for it is misleading:

- Line 176 is not merely hard to vectorize, it is meaningless. ImagePath::property
  is a std::vector<double>, so `imgVec[i].property = indexvec[i]` is a vector
  copy-assignment that ALLOCATES. There is no SIMD work in that loop.

- The other three are the same contiguous copy of Vector elements written out by
  hand. std::copy_n says what is meant, and lets the compiler emit a memmove
  instead of an element loop the vectorizer then declines to transform.

Fixing the source rather than silencing the diagnostic means the warning is gone
for every compiler, and a build using -Werror no longer fails here. Behaviour is
unchanged: std::copy_n over [0,nat) is exactly the loop it replaces, and the
remaining two pragmas, which do vectorize, are untouched.

Verified with clang 20.1.1:
  clang++ -std=c++17 -O3 -fopenmp -march=skylake-avx512 -Wall \
      -c colvar/PathMSDBase.cpp -I.
4 warnings before, 0 after. GCC is unaffected either way (its 17 warnings here
are pre-existing -Wunknown-pragmas from `#pragma acc` in headers, which PLUMED's
own build silences).
---
 src/colvar/PathMSDBase.cpp | 20 +++++++-------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index 65c99b78bd..0cc00b38e3 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -28,6 +28,8 @@
 #include "tools/RMSD.h"
 #include "tools/Tools.h"
 
+#include <algorithm>
+
 namespace PLMD {
 namespace colvar {
 
@@ -173,7 +175,8 @@ void PathMSDBase::calculate() {
   // resize the list to full
   if(imgVec.empty()) { // this is the signal that means: recalculate all
     imgVec.resize(nframes);
-    #pragma omp simd
+    // No `omp simd` here: ImagePath::property is a std::vector<double>, so this body performs a
+    // vector copy-assignment, i.e. it allocates. There is nothing for a SIMD unit to do.
     for(unsigned i=0; i<nframes; i++) {
       imgVec[i].property=indexvec[i];
       imgVec[i].index=i;
@@ -231,20 +234,14 @@ void PathMSDBase::calculate() {
       for(unsigned i=rank; i<imgVec.size(); i+=stride) {
         tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
         plumed_assert(tmp_derivs.size()==nat);
-        #pragma omp simd
-        for(unsigned j=0; j<nat; j++) {
-          tmp_derivs2[i*nat+j]=tmp_derivs[j];
-        }
+        std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
       }
     } else {
       //approximate distance with saved rotation matrices
       for(unsigned i=rank; i<imgVec.size(); i+=stride) {
         tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
         plumed_assert(tmp_derivs.size()==nat);
-        #pragma omp simd
-        for(unsigned j=0; j<nat; j++) {
-          tmp_derivs2[i*nat+j]=tmp_derivs[j];
-        }
+        std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
         if (debugClose) {
           double withclose = tmp_distances[i];
           RMSD opt;
@@ -263,10 +260,7 @@ void PathMSDBase::calculate() {
     for(unsigned i=rank; i<imgVec.size(); i+=stride) {
       tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
       plumed_assert(tmp_derivs.size()==nat);
-      #pragma omp simd
-      for(unsigned j=0; j<nat; j++) {
-        tmp_derivs2[i*nat+j]=tmp_derivs[j];
-      }
+      std::copy_n(tmp_derivs.begin(), nat, tmp_derivs2.begin()+i*nat);
     }
   }