Merge branch 'development'

Author: zingale

Make.Microphysics

@@ -102,10 +102,14 @@ ifeq ($(INTEGRATOR_DIR), CVODE)
   LIBRARY_LOCATIONS += $(CVODE_HOME)/lib
   LIBRARIES += -lsundials_cvode -lsundials_sunlinsolband -lsundials_sunlinsolspbcgs -lsundials_sunlinsolsptfqmr -lsundials_sunmatrixsparse -lsundials_nveccuda -lsundials_sunlinsoldense -lsundials_sunlinsolspfgmr -lsundials_sunmatrixband -lsundials_sunnonlinsolfixedpoint -lsundials_nvecserial -lsundials_sunlinsolpcg -lsundials_sunlinsolspgmr -lsundials_sunmatrixdense -lsundials_sunnonlinsolnewton
 
+ifeq ($(USE_CUDA_CVODE),TRUE)
+  LIBRARIES += -rpath=$(CVODE_HOME)/lib
+else
+  LIBRARIES += -Wl,-rpath,$(CVODE_HOME)/lib
+endif
+
   ifeq ($(USE_CUDA_CVODE), TRUE)
     DEFINES += -DCUDA_CVODE
-
-    LIBRARIES += -rpath=$(CVODE_HOME)/lib
   endif
 
   ifeq ($(USE_CVODE_CUSOLVER), TRUE)

integration/VODE90/cuVODE/test/README.md

@@ -14,6 +14,11 @@ your application code that integrates ODEs in a loop over zones.
 
 # Building with CUDA
 
-To build the example with CUDA Fortran, use the PGI compiler and do
-`make COMP=PGI USE_CUDA=TRUE CUDA_VERSION=9.0` if, e.g., you are using
-CUDA 9.
+To build the example with CUDA Fortran, use the PGI compiler and do:
+
+```
+make -j COMP=PGI USE_CUDA=TRUE AMREX_USE_CUDA=TRUE USE_GPU_PRAGMA=TRUE CUDA_VERSION=9.0
+```
+
+This was tested with PGI 18.10 and CUDA 9.2.148.
+

integration/numerical_jacobian.F90

@@ -161,7 +161,7 @@ subroutine test_numerical_jac(state)
     use actual_rhs_module
     use eos_module, only : eos
     use eos_type_module, only : eos_t, eos_input_rt, normalize_abundances
-    use jacobian_sparsity_module, only: get_jac_entry
+    use jacobian_sparsity_module, only: get_jac_entry, scale_jac_entry
 
     type (burn_t) :: state
     type (burn_t) :: state_num
@@ -193,8 +193,10 @@ subroutine test_numerical_jac(state)
     ! nets work with, so we convert it to derivatives with respect to
     ! X and of mass fraction creation rates
     do n = 1, nspec_evolve
-       state % jac(n,:) = state % jac(n,:) * aion(n)
-       state % jac(:,n) = state % jac(:,n) * aion_inv(n)
+       do j = 1, neqs
+          call scale_jac_entry(state, n, j, aion(n))
+          call scale_jac_entry(state, j, n, aion_inv(n))
+       enddo
     enddo
 
     ! Now compute the numerical Jacobian.