Merge pull request #2283 from stan-dev/feature/issue-update-sundials-561

Feature/issue update sundials 561

Author: rok-cesnovar

README.md

@@ -105,7 +105,7 @@ SUNDIALS_STATIC_INLINE
 realtype *N_VGetDeviceArrayPointer_Cuda(N_Vector x)
 {
   N_VectorContent_Cuda content = (N_VectorContent_Cuda)x->content;
-  return(content->host_data == NULL ? NULL : (realtype*)content->device_data->ptr);
+  return(content->device_data == NULL ? NULL : (realtype*)content->device_data->ptr);
 }
 
 /*

lib/sundials_5.5.0/CONTRIBUTING.md lib/sundials_5.6.1/CONTRIBUTING.md

@@ -0,0 +1,217 @@
+/* -----------------------------------------------------------------
+ * Programmer(s): Daniel McGreer and Cody J. Balos @ LLNL
+ * -----------------------------------------------------------------
+ * SUNDIALS Copyright Start
+ * Copyright (c) 2002-2020, Lawrence Livermore National Security
+ * and Southern Methodist University.
+ * All rights reserved.
+ *
+ * See the top-level LICENSE and NOTICE files for details.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ * SUNDIALS Copyright End
+ * -----------------------------------------------------------------
+ * This is the header file for the hip implementation of the
+ * NVECTOR module.
+ *
+ * Notes:
+ *
+ *   - The definition of the generic N_Vector structure can be found
+ *     in the header file sundials_nvector.h.
+ *
+ *   - The definitions of the types 'realtype' and 'sunindextype' can
+ *     be found in the header file sundials_types.h, and it may be
+ *     changed (at the configuration stage) according to the user's needs.
+ *     The sundials_types.h file also contains the definition
+ *     for the type 'booleantype'.
+ *
+ *   - N_Vector arguments to arithmetic vector operations need not
+ *     be distinct. For example, the following call:
+ *
+ *       N_VLinearSum_Hip(a,x,b,y,y);
+ *
+ *     (which stores the result of the operation a*x+b*y in y)
+ *     is legal.
+ * -----------------------------------------------------------------*/
+
+#ifndef _NVECTOR_HIP_H
+#define _NVECTOR_HIP_H
+
+#include <stdio.h>
+
+#include <sundials/sundials_hip_policies.hpp>
+#include <sundials/sundials_memory.h>
+#include <sundials/sundials_nvector.h>
+
+#ifdef __cplusplus  /* wrapper to enable C++ usage */
+extern "C" {
+#endif
+
+/*
+ * -----------------------------------------------------------------
+ * hip implementation of N_Vector
+ * -----------------------------------------------------------------
+ */
+
+struct _N_VectorContent_Hip
+{
+  sunindextype       length;
+  booleantype        own_exec;
+  booleantype        own_helper;
+  SUNMemory          host_data;
+  SUNMemory          device_data;
+  SUNHipExecPolicy*  stream_exec_policy;
+  SUNHipExecPolicy*  reduce_exec_policy;
+  SUNMemoryHelper    mem_helper;
+  void*              priv; /* 'private' data */
+};
+
+typedef struct _N_VectorContent_Hip *N_VectorContent_Hip;
+
+/*
+ * -----------------------------------------------------------------
+ * NVECTOR_HIP implementation specific functions
+ * -----------------------------------------------------------------
+ */
+
+SUNDIALS_EXPORT N_Vector N_VNew_Hip(sunindextype length);
+SUNDIALS_EXPORT N_Vector N_VNewManaged_Hip(sunindextype length);
+SUNDIALS_EXPORT N_Vector N_VNewWithMemHelp_Hip(sunindextype length,
+                                               booleantype use_managed_mem,
+                                               SUNMemoryHelper helper);
+SUNDIALS_EXPORT N_Vector N_VNewEmpty_Hip();
+SUNDIALS_EXPORT N_Vector N_VMake_Hip(sunindextype length,
+                                     realtype *h_vdata,
+                                     realtype *d_vdata);
+SUNDIALS_EXPORT N_Vector N_VMakeManaged_Hip(sunindextype length,
+                                            realtype *vdata);
+SUNDIALS_EXPORT void N_VSetHostArrayPointer_Hip(realtype* h_vdata, N_Vector v);
+SUNDIALS_EXPORT booleantype N_VIsManagedMemory_Hip(N_Vector x);
+SUNDIALS_EXPORT int N_VSetKernelExecPolicy_Hip(N_Vector x,
+                                               SUNHipExecPolicy* stream_exec_policy,
+                                               SUNHipExecPolicy* reduce_exec_policy);
+SUNDIALS_EXPORT void N_VCopyToDevice_Hip(N_Vector v);
+SUNDIALS_EXPORT void N_VCopyFromDevice_Hip(N_Vector v);
+SUNDIALS_EXPORT void N_VPrint_Hip(N_Vector v);
+SUNDIALS_EXPORT void N_VPrintFile_Hip(N_Vector v, FILE *outfile);
+
+SUNDIALS_STATIC_INLINE
+sunindextype N_VGetLength_Hip(N_Vector x)
+{
+  N_VectorContent_Hip content = (N_VectorContent_Hip)x->content;
+  return content->length;
+}
+
+SUNDIALS_STATIC_INLINE
+realtype *N_VGetHostArrayPointer_Hip(N_Vector x)
+{
+  N_VectorContent_Hip content = (N_VectorContent_Hip)x->content;
+  return(content->host_data == NULL ? NULL : (realtype*)content->host_data->ptr);
+}
+
+SUNDIALS_STATIC_INLINE
+realtype *N_VGetDeviceArrayPointer_Hip(N_Vector x)
+{
+  N_VectorContent_Hip content = (N_VectorContent_Hip)x->content;
+  return(content->device_data == NULL ? NULL : (realtype*)content->device_data->ptr);
+}
+
+/*
+ * -----------------------------------------------------------------
+ * NVECTOR API functions
+ * -----------------------------------------------------------------
+ */
+
+SUNDIALS_EXPORT N_Vector N_VCloneEmpty_Hip(N_Vector w);
+SUNDIALS_EXPORT N_Vector N_VClone_Hip(N_Vector w);
+SUNDIALS_EXPORT void N_VDestroy_Hip(N_Vector v);
+SUNDIALS_EXPORT void N_VSpace_Hip(N_Vector v, sunindextype *lrw, sunindextype *liw);
+
+/* standard vector operations */
+SUNDIALS_EXPORT void N_VLinearSum_Hip(realtype a, N_Vector x, realtype b, N_Vector y, N_Vector z);
+SUNDIALS_EXPORT void N_VConst_Hip(realtype c, N_Vector z);
+SUNDIALS_EXPORT void N_VProd_Hip(N_Vector x, N_Vector y, N_Vector z);
+SUNDIALS_EXPORT void N_VDiv_Hip(N_Vector x, N_Vector y, N_Vector z);
+SUNDIALS_EXPORT void N_VScale_Hip(realtype c, N_Vector x, N_Vector z);
+SUNDIALS_EXPORT void N_VAbs_Hip(N_Vector x, N_Vector z);
+SUNDIALS_EXPORT void N_VInv_Hip(N_Vector x, N_Vector z);
+SUNDIALS_EXPORT void N_VAddConst_Hip(N_Vector x, realtype b, N_Vector z);
+SUNDIALS_EXPORT realtype N_VDotProd_Hip(N_Vector x, N_Vector y);
+SUNDIALS_EXPORT realtype N_VMaxNorm_Hip(N_Vector x);
+SUNDIALS_EXPORT realtype N_VWrmsNorm_Hip(N_Vector x, N_Vector w);
+SUNDIALS_EXPORT realtype N_VWrmsNormMask_Hip(N_Vector x, N_Vector w, N_Vector id);
+SUNDIALS_EXPORT realtype N_VMin_Hip(N_Vector x);
+SUNDIALS_EXPORT realtype N_VWL2Norm_Hip(N_Vector x, N_Vector w);
+SUNDIALS_EXPORT realtype N_VL1Norm_Hip(N_Vector x);
+SUNDIALS_EXPORT void N_VCompare_Hip(realtype c, N_Vector x, N_Vector z);
+SUNDIALS_EXPORT booleantype N_VInvTest_Hip(N_Vector x, N_Vector z);
+SUNDIALS_EXPORT booleantype N_VConstrMask_Hip(N_Vector c, N_Vector x, N_Vector m);
+SUNDIALS_EXPORT realtype N_VMinQuotient_Hip(N_Vector num, N_Vector denom);
+
+/* fused vector operations */
+SUNDIALS_EXPORT int N_VLinearCombination_Hip(int nvec, realtype* c, N_Vector* X,
+                                             N_Vector Z);
+SUNDIALS_EXPORT int N_VScaleAddMulti_Hip(int nvec, realtype* c, N_Vector X,
+                                         N_Vector* Y, N_Vector* Z);
+SUNDIALS_EXPORT int N_VDotProdMulti_Hip(int nvec, N_Vector x, N_Vector* Y,
+                                        realtype* dotprods);
+
+/* vector array operations */
+SUNDIALS_EXPORT int N_VLinearSumVectorArray_Hip(int nvec,
+                                                realtype a, N_Vector* X,
+                                                realtype b, N_Vector* Y,
+                                                N_Vector* Z);
+SUNDIALS_EXPORT int N_VScaleVectorArray_Hip(int nvec, realtype* c, N_Vector* X,
+                                            N_Vector* Z);
+SUNDIALS_EXPORT int N_VConstVectorArray_Hip(int nvec, realtype c, N_Vector* Z);
+SUNDIALS_EXPORT int N_VScaleAddMultiVectorArray_Hip(int nvec, int nsum,
+                                                    realtype* a, N_Vector* X,
+                                                    N_Vector** Y, N_Vector** Z);
+SUNDIALS_EXPORT int N_VLinearCombinationVectorArray_Hip(int nvec, int nsum,
+                                                        realtype* c,
+                                                        N_Vector** X,
+                                                        N_Vector* Z);
+SUNDIALS_EXPORT int N_VWrmsNormVectorArray_Hip(int nvec, N_Vector* X,
+                                               N_Vector* W, realtype* nrm);
+SUNDIALS_EXPORT int N_VWrmsNormMaskVectorArray_Hip(int nvec, N_Vector* X,
+                                                   N_Vector* W, N_Vector id,
+                                                   realtype* nrm);
+
+/* OPTIONAL local reduction kernels (no parallel communication) */
+SUNDIALS_EXPORT realtype N_VWSqrSumLocal_Hip(N_Vector x, N_Vector w);
+SUNDIALS_EXPORT realtype N_VWSqrSumMaskLocal_Hip(N_Vector x, N_Vector w, N_Vector id);
+
+/* OPTIONAL XBraid interface operations */
+SUNDIALS_EXPORT int N_VBufSize_Hip(N_Vector x, sunindextype *size);
+SUNDIALS_EXPORT int N_VBufPack_Hip(N_Vector x, void *buf);
+SUNDIALS_EXPORT int N_VBufUnpack_Hip(N_Vector x, void *buf);
+
+/* OPTIONAL operations for debugging */
+SUNDIALS_EXPORT void N_VPrint_Hip(N_Vector v);
+SUNDIALS_EXPORT void N_VPrintFile_Hip(N_Vector v, FILE *outfile);
+
+/*
+ * -----------------------------------------------------------------
+ * Enable / disable fused vector operations
+ * -----------------------------------------------------------------
+ */
+
+SUNDIALS_EXPORT int N_VEnableFusedOps_Hip(N_Vector v, booleantype tf);
+
+SUNDIALS_EXPORT int N_VEnableLinearCombination_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableScaleAddMulti_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableDotProdMulti_Hip(N_Vector v, booleantype tf);
+
+SUNDIALS_EXPORT int N_VEnableLinearSumVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableScaleVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableConstVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableWrmsNormVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableWrmsNormMaskVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableScaleAddMultiVectorArray_Hip(N_Vector v, booleantype tf);
+SUNDIALS_EXPORT int N_VEnableLinearCombinationVectorArray_Hip(N_Vector v, booleantype tf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

lib/sundials_5.5.0/LICENSE lib/sundials_5.6.1/LICENSE

@@ -42,6 +42,10 @@ SUNDIALS_EXPORT N_Vector N_VGetLocalVector_MPIPlusX(N_Vector v);
 
 SUNDIALS_EXPORT sunindextype N_VGetLocalLength_MPIPlusX(N_Vector v);
 
+SUNDIALS_STATIC_INLINE
+int N_VEnableFusedOps_MPIPlusX(N_Vector v, booleantype tf)
+{ return N_VEnableFusedOps_MPIManyVector(v, tf); }
+
 #ifdef __cplusplus
 }
 #endif

lib/sundials_5.5.0/NOTICE lib/sundials_5.6.1/NOTICE

@@ -10,6 +10,9 @@
  *
  * SPDX-License-Identifier: BSD-3-Clause
  * SUNDIALS Copyright End
+ * -----------------------------------------------------------------
+ * This is the header file for the RAJA implementation of the
+ * NVECTOR module.
  * -----------------------------------------------------------------*/
 
 #ifndef _NVECTOR_RAJA_H
@@ -18,8 +21,8 @@
 #include <stdio.h>
 
 #include <sundials/sundials_nvector.h>
+#include <sundials/sundials_memory.h>
 #include <sundials/sundials_config.h>
-#include <sunmemory/sunmemory_cuda.h>
 
 #ifdef __cplusplus  /* wrapper to enable C++ usage */
 extern "C" {
@@ -85,7 +88,7 @@ SUNDIALS_STATIC_INLINE
 realtype *N_VGetDeviceArrayPointer_Raja(N_Vector x)
 {
   N_VectorContent_Raja content = (N_VectorContent_Raja)x->content;
-  return(content->host_data == NULL ? NULL : (realtype*)content->device_data->ptr);
+  return(content->device_data == NULL ? NULL : (realtype*)content->device_data->ptr);
 }
 
 

lib/sundials_5.5.0/README.md lib/sundials_5.6.1/README.md

@@ -25,10 +25,10 @@
  * -----------------------------------------------------------------*/
 
 
-#define SUNDIALS_VERSION "5.5.0"
+#define SUNDIALS_VERSION "5.6.1"
 #define SUNDIALS_VERSION_MAJOR 5
-#define SUNDIALS_VERSION_MINOR 5
-#define SUNDIALS_VERSION_PATCH 0
+#define SUNDIALS_VERSION_MINOR 6
+#define SUNDIALS_VERSION_PATCH 1
 #define SUNDIALS_VERSION_LABEL ""
 
 
@@ -70,6 +70,16 @@
  */
 /* #undef SUNDIALS_HAVE_POSIX_TIMERS */
 
+/* CVODE should use fused kernels if utilizing
+  * the CUDA NVector.
+  */
+/* #undef SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS */
+
+
+/* BUILD SUNDIALS with monitoring functionalities
+  * the CUDA NVector.
+  */
+/* #undef SUNDIALS_BUILD_WITH_MONITORING */
 
 /* ------------------------------------------------------------------
  * SUNDIALS TPL macros
@@ -93,17 +103,9 @@
   */
 /* #undef SUNDIALS_TRILINOS_HAVE_MPI */
 
-/* CVODE should use fused kernels if utilizing
-  * the CUDA NVector.
-  */
-/* #undef SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS */
-
-
-/* BUILD SUNDIALS with monitoring functionalities
-  * the CUDA NVector.
-  */
-/* #undef SUNDIALS_BUILD_WITH_MONITORING */
-
+/* RAJA backends */
+/* #undef SUNDIALS_RAJA_BACKENDS_HIP */
+#define SUNDIALS_RAJA_BACKENDS_CUDA
 
 /* ------------------------------------------------------------------
  * SUNDIALS modules enabled

lib/sundials_5.5.0/include/cvodes/cvodes.h lib/sundials_5.6.1/include/cvodes/cvodes.h

@@ -70,6 +70,16 @@
  */
 #cmakedefine SUNDIALS_HAVE_POSIX_TIMERS
 
+/* CVODE should use fused kernels if utilizing
+  * the CUDA NVector.
+  */
+#cmakedefine SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS
+
+
+/* BUILD SUNDIALS with monitoring functionalities
+  * the CUDA NVector.
+  */
+#cmakedefine SUNDIALS_BUILD_WITH_MONITORING
 
 /* ------------------------------------------------------------------
  * SUNDIALS TPL macros
@@ -93,17 +103,9 @@
   */
 #cmakedefine SUNDIALS_TRILINOS_HAVE_MPI
 
-/* CVODE should use fused kernels if utilizing
-  * the CUDA NVector.
-  */
-#cmakedefine SUNDIALS_BUILD_PACKAGE_FUSED_KERNELS
-
-
-/* BUILD SUNDIALS with monitoring functionalities
-  * the CUDA NVector.
-  */
-#cmakedefine SUNDIALS_BUILD_WITH_MONITORING
-
+/* RAJA backends */
+#cmakedefine SUNDIALS_RAJA_BACKENDS_HIP
+#cmakedefine SUNDIALS_RAJA_BACKENDS_CUDA
 
 /* ------------------------------------------------------------------
  * SUNDIALS modules enabled