Change to test TSAN with clang and libomp

This permits openmp and simd to be tested with ThreadSanitizer

Used more of the safe gatherLoadUTranspose, since that is required
for Jenkins to pass.

Change-Id: I262a5e61b715679e23cee641cf3be553714644ce

diff --git a/admin/builds/pre-submit-matrix.txt b/admin/builds/pre-submit-matrix.txt
index abff968f5ece738954479bfbb5c7e86640b6df37..d1a9cd16e469fc916d13b96ebe768abd6440fe6e 100644 (file)
--- a/admin/builds/pre-submit-matrix.txt
+++ b/admin/builds/pre-submit-matrix.txt
@@ -32,12 +32,9 @@ gcc-4.8 gpuhw=nvidia cuda-7.0 cmake-3.8.1 mpi npme=1 nranks=2 openmp
 # Test SIMD implementation of pair search for GPU code-path
 gcc-7 gpuhw=nvidia gpu_id=1 cuda-9.2 thread-mpi openmp cmake-3.6.1 release-with-assert simd=avx2_256
 
-# Test with ThreadSanitizer (compiled without OpenMP, even though
-#   this gcc was configured with --disable-linux-futex, because
-#   Redmine #1850 is unresolved, which causes more suspected
-#   false positives than races detected)
-# Test newest gcc at time of release
-gcc-7 tsan no-openmp cmake-3.10.0
+# Test with libcxx
+# Test with ThreadSanitizer + OpenMP + SIMD
+clang-7 no-hwloc tsan libcxx-7 openmp cmake-3.12.1 simd=avx2_256
 
 # Test on MacOS (the gcc-6 and/or x11 flags implicitly steer jobs to the OSX agent)
 # Test X11 build
@@ -91,7 +88,6 @@ gcc-5 openmp simd=avx_128_fma gpuhw=amd opencl-1.2 clFFT-2.14
 # Add OpenMP support to ASAN build (but libomp.so in clang-4 reports leaks, so might need a suitable build or suppression)
 # Test hwloc-2 support
 # Test newest supported LTS Ubuntu
-# Resolve Redmine #1850 so that ThreadSanitizer can test our OpenMP code
 # Test AVX-512 when hardware is available
 # Update to test gcc 8
 # Update to test clang 7

diff --git a/src/gromacs/mdlib/lincs.cpp b/src/gromacs/mdlib/lincs.cpp
index fb3e2c0d7970539f0b8f58472f5ab316118a33c1..f57d901a034b42bf21d1c197848da938e6e014aa 100644 (file)
--- a/src/gromacs/mdlib/lincs.cpp
+++ b/src/gromacs/mdlib/lincs.cpp
@@ -500,6 +500,23 @@ static void lincs_update_atoms(Lincs *li, int th,
 }
 
 #if GMX_SIMD_HAVE_REAL
+//! Helper function so that we can run TSAN with SIMD support (where implemented).
+template <int align>
+static inline void gmx_simdcall
+gatherLoadUTransposeTSANSafe(const real         *base,
+                             const std::int32_t *offset,
+                             SimdReal           *v0,
+                             SimdReal           *v1,
+                             SimdReal           *v2)
+{
+#if (CMAKE_BUILD_TYPE == CMAKE_BUILD_TYPE_TSAN) && GMX_SIMD_X86_AVX2_256
+    // This function is only implemented in this case
+    gatherLoadUTransposeSafe<align>(base, offset, v0, v1, v2);
+#else
+    gatherLoadUTranspose<align>(base, offset, v0, v1, v2);
+#endif
+}
+
 /*! \brief Calculate the constraint distance vectors r to project on from x.
  *
  * Determine the right-hand side of the matrix equation using quantity f.
@@ -541,8 +558,8 @@ calc_dr_x_f_simd(int                       b0,
             offset1[i] = bla[bs*2 + i*2 + 1];
         }
 
-        gatherLoadUTranspose<3>(reinterpret_cast<const real *>(x), offset0, &x0_S, &y0_S, &z0_S);
-        gatherLoadUTranspose<3>(reinterpret_cast<const real *>(x), offset1, &x1_S, &y1_S, &z1_S);
+        gatherLoadUTransposeTSANSafe<3>(reinterpret_cast<const real *>(x), offset0, &x0_S, &y0_S, &z0_S);
+        gatherLoadUTransposeTSANSafe<3>(reinterpret_cast<const real *>(x), offset1, &x1_S, &y1_S, &z1_S);
         rx_S = x0_S - x1_S;
         ry_S = y0_S - y1_S;
         rz_S = z0_S - z1_S;
@@ -558,8 +575,8 @@ calc_dr_x_f_simd(int                       b0,
 
         transposeScatterStoreU<3>(reinterpret_cast<real *>(r + bs), offset2, rx_S, ry_S, rz_S);
 
-        gatherLoadUTranspose<3>(reinterpret_cast<const real *>(f), offset0, &x0_S, &y0_S, &z0_S);
-        gatherLoadUTranspose<3>(reinterpret_cast<const real *>(f), offset1, &x1_S, &y1_S, &z1_S);
+        gatherLoadUTransposeTSANSafe<3>(reinterpret_cast<const real *>(f), offset0, &x0_S, &y0_S, &z0_S);
+        gatherLoadUTransposeTSANSafe<3>(reinterpret_cast<const real *>(f), offset1, &x1_S, &y1_S, &z1_S);
         fx_S = x0_S - x1_S;
         fy_S = y0_S - y1_S;
         fz_S = z0_S - z1_S;
@@ -757,23 +774,6 @@ static void do_lincsp(const rvec *x, rvec *f, rvec *fp, t_pbc *pbc,
 
 #if GMX_SIMD_HAVE_REAL
 
-//! Helper function so that we can run TSAN with SIMD support (where implemented).
-template <int align>
-static inline void gmx_simdcall
-gatherLoadUTransposeTSANSafe(const real         *base,
-                             const std::int32_t *offset,
-                             SimdReal           *v0,
-                             SimdReal           *v1,
-                             SimdReal           *v2)
-{
-#if (CMAKE_BUILD_TYPE == CMAKE_BUILD_TYPE_TSAN) && GMX_SIMD_X86_AVX2_256
-    // This function is only implemented in this case
-    gatherLoadUTransposeSafe<align>(base, offset, v0, v1, v2);
-#else
-    gatherLoadUTranspose<align>(base, offset, v0, v1, v2);
-#endif
-}
-
 /*! \brief Calculate the constraint distance vectors r to project on from x.
  *
  * Determine the right-hand side of the matrix equation using coordinates xp. */