Merge branch 'master' into refactor

Author: sbryngelson

.github/workflows/frontier/submit.sh

@@ -33,7 +33,7 @@ sbatch <<EOT
 #SBATCH -A CFD154                  # charge account
 #SBATCH -N 1                       # Number of nodes required
 $sbatch_device_opts
-#SBATCH -t 04:59:00                # Duration of the job (Ex: 15 mins)
+#SBATCH -t 05:59:00                # Duration of the job (Ex: 15 mins)
 #SBATCH -o$job_slug.out            # Combined output and error messages file
 #SBATCH -p extended                # Extended partition for shorter queues
 #SBATCH -W                         # Do not exit until the submitted job terminates.

.typos.toml

@@ -19,6 +19,7 @@ strang = "strang"
 Strang = "Strang"
 TKE = "TKE"
 HSA = "HSA"
+infp = "infp"
 
 [files]
 extend-exclude = ["docs/documentation/references*", "tests/", "toolchain/cce_simulation_workgroup_256.sh"]

.vscode/settings.json

@@ -49,7 +49,7 @@
     // Enable ONLY fortls language server
     "fortran.enableLanguageServer": true,
     "fortran.languageServer": "fortls",
-    "fortran.fortls.disabled": false,
+    "fortran.fortls.disabled": true,
     "fortran.fortls.path": "fortls",
 
     // Try to disable any built-in language features

CMakeLists.txt

@@ -328,6 +328,13 @@ macro(HANDLE_SOURCES target useCommon)
                                                "${CMAKE_BINARY_DIR}/modules/${target}/*.fpp")
     if (${useCommon})
         file(GLOB common_FPPs CONFIGURE_DEPENDS "${common_DIR}/*.fpp")
+
+        # If we're building post_process, exclude m_compute_levelset.fpp
+        if("${target}" STREQUAL "post_process")
+            list(FILTER common_FPPs EXCLUDE REGEX ".*/m_compute_levelset\.fpp$")
+            list(FILTER common_FPPs EXCLUDE REGEX ".*/m_ib_patches\.fpp$")
+        endif()
+
         list(APPEND ${target}_FPPs ${common_FPPs})
     endif()
 
@@ -443,7 +450,7 @@ function(MFC_SETUP_TARGET)
 
         if (ARGS_SILO)
             find_package(SILO REQUIRED)
-            target_link_libraries(${a_target} PRIVATE SILO::SILO)
+            target_link_libraries(${a_target} PRIVATE SILO::SILO stdc++)
         endif()
 
         if (ARGS_HDF5)

docs/documentation/gpuParallelization.md

@@ -31,7 +31,7 @@ Note: Ordering is not guaranteed or stable, so use key-value pairing when using
 
 - Data on the GPU has a reference counter
 - When data is referred to being allocated, it means that GPU memory is allocated if it is not already present in GPU memory. If a variable is already present, the reference counter is just incremented.
-- When data is referred to being dellocated, it means that the reference counter is decremented. If the reference counter is zero, then the data is actually deallocated from GPU memory
+- When data is referred to being deallocated, it means that the reference counter is decremented. If the reference counter is zero, then the data is actually deallocated from GPU memory
 - When data is referred to being attached, it means that the device pointer attaches to target if it not already attached. If pointer is already attached, then the attachment counter is just incremented
 - When data is referred to being detached, it means that the attachment counter is decremented. If attachment counter is zero, then actually detached
 

examples/1D_inert_shocktube/case.py

@@ -70,8 +70,8 @@
     "mapped_weno": "T",
     "mp_weno": "T",
     "riemann_solver": 2,
-    "wave_speeds": 2,
-    "avg_state": 1,
+    "wave_speeds": 1,
+    "avg_state": 2,
     "bc_x%beg": -2,
     "bc_x%end": -3,
     # Chemistry

examples/1D_shuosher_analytical/case.py

@@ -57,7 +57,7 @@
             "patch_icpp(1)%pres": 10.3333,
             "patch_icpp(1)%alpha_rho(1)": 3.957143,
             "patch_icpp(1)%alpha(1)": 1.0,
-            # One anlytic patch to take care of -4 < x < 5
+            # One analytic patch to take care of -4 < x < 5
             # Patch 2 Analytic
             "patch_icpp(2)%geometry": 1,
             "patch_icpp(2)%x_centroid": 0.5,

examples/1D_shuosher_old/case.py

@@ -57,7 +57,7 @@
             "patch_icpp(1)%pres": 10.3333,
             "patch_icpp(1)%alpha_rho(1)": 3.957143,
             "patch_icpp(1)%alpha(1)": 1.0,
-            # One anlytic patch to take care of -4 < x < 5
+            # One analytic patch to take care of -4 < x < 5
             # Patch 2 Analytic
             "patch_icpp(2)%geometry": 1,
             "patch_icpp(2)%x_centroid": 0.5,

examples/1D_shuosher_teno5/case.py

@@ -59,7 +59,7 @@
             "patch_icpp(1)%pres": 10.333,
             "patch_icpp(1)%alpha_rho(1)": 3.857,
             "patch_icpp(1)%alpha(1)": 1.0,
-            # One anlytic patch to take care of 1 < x < 10
+            # One analytic patch to take care of 1 < x < 10
             # Patch 2 Analytic
             "patch_icpp(2)%geometry": 1,
             "patch_icpp(2)%x_centroid": 5.5,

examples/1D_shuosher_teno7/case.py

@@ -59,7 +59,7 @@
             "patch_icpp(1)%pres": 10.333,
             "patch_icpp(1)%alpha_rho(1)": 3.857,
             "patch_icpp(1)%alpha(1)": 1.0,
-            # One anlytic patch to take care of 1 < x < 10
+            # One analytic patch to take care of 1 < x < 10
             # Patch 2 Analytic
             "patch_icpp(2)%geometry": 1,
             "patch_icpp(2)%x_centroid": 5.5,