divine debugging #1030
divine debugging #1030
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📝 WalkthroughWalkthroughA new debugging utility class, Changes
Sequence Diagram(s)sequenceDiagram
participant HybridHybridMessengerStrategy
participant DEBUGOD
participant SAMRAI_PatchHierarchy
HybridHybridMessengerStrategy->>DEBUGOD: DEBUGOD::INSTANCE()
HybridHybridMessengerStrategy->>DEBUGOD: inspect("EM_B_x", point)
DEBUGOD->>SAMRAI_PatchHierarchy: Access patch data for "EM_B_x" at point
DEBUGOD-->>HybridHybridMessengerStrategy: Return GodExtract (inspected data)
HybridHybridMessengerStrategy->>DEBUGOD: print(GodExtract)
sequenceDiagram
participant HybridHybridMessengerStrategy
participant DEBUGOD
participant SAMRAI_PatchHierarchy
HybridHybridMessengerStrategy->>DEBUGOD: inspect("EM_B_x", lower_point, upper_point)
DEBUGOD->>SAMRAI_PatchHierarchy: Access patch data in bounding box
DEBUGOD-->>HybridHybridMessengerStrategy: Return GodExtract (inspected data)
HybridHybridMessengerStrategy->>DEBUGOD: print(GodExtract)
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Actionable comments posted: 9
🧹 Nitpick comments (2)
src/amr/debugod.hpp (1)
48-66: Complete the inspect method implementation.The inspect method is incomplete - it iterates through levels and patches but doesn't actually extract or store any debugging data.
The method needs to:
- Access the field data by name
- Extract values at the specified coordinates
- Populate the GodValue structures
Would you like me to help implement the complete inspection logic?
src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp (1)
650-661: Consider removing debugging code before production.This appears to be temporary debugging code with hardcoded values and specific conditions. Consider wrapping it in a debug macro or removing it entirely for production builds.
#ifdef PHARE_DEBUG_MODE // debugging code here #endif
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
src/amr/messengers/hybrid_hybrid_messenger_strategy.hppsrc/amr/debugod.hpp
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src/amr/debugod.hpp
Outdated
| { | ||
| auto& coords = v.coords; | ||
| auto& loc_idx = v.loc_index; | ||
| auto& amr_idx v.loc_index; |
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Fix missing assignment operator.
Missing = operator in variable assignment.
Apply this diff to fix the syntax:
-auto& amr_idx v.loc_index;
+auto& amr_idx = v.amr_index;Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In src/amr/debugod.hpp at line 86, the assignment statement is missing the '='
operator between the variable and the value. Add the '=' operator to correctly
assign v.loc_index to amr_idx.
src/amr/debugod.cpp
Outdated
| DEBUGOD& DEBUGOD::INSTANCE() | ||
| { | ||
| static DEBUGOD instance; | ||
| return instance; | ||
| } |
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Fix template instantiation for compilation.
The DEBUGOD class is a template but this implementation doesn't specify the template parameter, which will cause compilation errors.
Since this is a template class, either move the implementation to the header file or provide explicit template instantiations. Here's the fix to move it to the header:
-namespace PHARE::amr
-{
-DEBUGOD& DEBUGOD::INSTANCE()
-{
- static DEBUGOD instance;
- return instance;
-}
-}; // namespace PHARE::amrAnd add this implementation in debugod.hpp after the class definition:
template<std::size_t dim>
DEBUGOD<dim>& DEBUGOD<dim>::INSTANCE()
{
static DEBUGOD<dim> instance;
return instance;
}🤖 Prompt for AI Agents
In src/amr/debugod.cpp around lines 6 to 10, the implementation of the template
class DEBUGOD's INSTANCE method lacks the template parameter, causing
compilation errors. To fix this, move the implementation of the INSTANCE method
to the header file debugod.hpp after the class definition, and specify the
template parameter explicitly as template<std::size_t dim>. Implement INSTANCE
as a template method returning a static instance of DEBUGOD<dim>.
| auto& god = DEBUGOD::INSTANCE(); | ||
| if (god.time_is("EM_B_x", 0.225)) | ||
| { | ||
| auto bx_dbg = god.inpect("EM_B_x", {12.2, 13.5}); | ||
| god.print(bx_dbg); | ||
| for (auto& [ilvl, value] : bx_dbg) | ||
| { | ||
| god.print(value) | ||
| } | ||
| auto bx_dbg_rge = god.inpect("EM_B_x", {12.2, 8.0}, {12.6, 9.}); | ||
| } | ||
|
|
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Add missing include and fix multiple syntax errors in debugging code.
The debugging code block has several critical issues that prevent compilation.
Apply this diff to fix the issues:
+#include "amr/debugod.hpp"
+
// (add at top of file with other includes)
- auto& god = DEBUGOD::INSTANCE();
- if (god.time_is("EM_B_x", 0.225))
- {
- auto bx_dbg = god.inpect("EM_B_x", {12.2, 13.5});
- god.print(bx_dbg);
- for (auto& [ilvl, value] : bx_dbg)
- {
- god.print(value)
- }
- auto bx_dbg_rge = god.inpect("EM_B_x", {12.2, 8.0}, {12.6, 9.});
- }
+ auto& god = DEBUGOD<dimension>::INSTANCE();
+ god.setHierarchy(hierarchy_);
+ if (time == 0.225) // Check time directly instead of undefined method
+ {
+ PHARE::core::Point<double, dimension> point1{12.2, 13.5};
+ auto bx_dbg = god.inspect("EM_B_x", point1);
+ god.print(bx_dbg);
+ for (auto& [ilvl, values] : bx_dbg)
+ {
+ for (auto& value : values)
+ {
+ // Print individual value details here
+ }
+ }
+ PHARE::core::Point<double, dimension> lower{12.2, 8.0};
+ PHARE::core::Point<double, dimension> upper{12.6, 9.0};
+ auto bx_dbg_rge = god.inspect("EM_B_x", lower, upper);
+ }🤖 Prompt for AI Agents
In src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp around lines 650 to
661, the debugging code has missing include directives and multiple syntax
errors such as missing semicolons and typos in function names. Add the necessary
include for the DEBUGOD class, correct the function name from "inpect" to
"inspect", add missing semicolons after statements, and fix any other syntax
errors to ensure the code compiles successfully.
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Actionable comments posted: 5
♻️ Duplicate comments (7)
src/amr/debugod.hpp (7)
40-40: Fix the singleton initialization logic.The
initmethod incorrectly creates a new instance of DEBUGOD within itself, breaking the singleton pattern.
52-52: Add missing return type declaration.The method declaration is missing the return type before
auto.
55-55: Fix syntax error with extra closing parenthesis.Remove the extra closing parenthesis in the for loop condition.
81-81: Return the populated data structure instead of empty one.The method should return the populated
god_valuesmap.
93-93: Fix parameter type mismatch in print method.The method expects
std::vector<GodValue>but should expectGodExtractwhich is the map type returned by inspect.
102-102: Fix missing assignment operator.Missing
=operator in variable assignment. Also, the variable name should beamr_indexnotloc_index.
144-147: Fix singleton design pattern implementation.The current design with a unique_ptr to itself breaks the singleton pattern. A proper singleton implementation is needed.
Apply this diff to implement a proper singleton pattern:
-DEBUGOD() {} -std::unique_ptr<DEBUGOD> god_; -std::shared_ptr<SAMRAI::hier::PatchHierarchy> hierarchy_; -std::array<double, dim> mesh_size_; +DEBUGOD() = default; +~DEBUGOD() = default; +DEBUGOD(const DEBUGOD&) = delete; +DEBUGOD& operator=(const DEBUGOD&) = delete; + +std::shared_ptr<SAMRAI::hier::PatchHierarchy> hierarchy_; +std::array<double, dim> mesh_size_;Additionally, implement the
INSTANCE()method in the corresponding.cppfile as:template<std::size_t dim> DEBUGOD<dim>& DEBUGOD<dim>::INSTANCE() { static DEBUGOD<dim> instance; return instance; }
🧹 Nitpick comments (1)
src/amr/debugod.hpp (1)
149-149: Remove extra semicolon after namespace closing brace.There's an unnecessary semicolon after the namespace closing brace.
-}; // namespace PHARE::amr +} // namespace PHARE::amr
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
src/amr/debugod.hpp
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src/amr/debugod.hpp
Outdated
| auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name) | ||
| { | ||
| auto db = SAMRAI::hier::VariableDatabase::getDatabase(); | ||
| auto var_id = db->getVariable(name); | ||
| // auto context = db->getContext("default"); | ||
| // auto patchdata = patch.getPatchData(var_id, context); | ||
| return FieldData::getPatchData(patch, var_id); | ||
| } |
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Complete the getField implementation and add missing include.
The method references FieldData which is not included or defined. Also, the return type is not specified.
Add the necessary include at the top of the file:
#include "amr/data/field/field_data.hpp" // or the appropriate headerAnd complete the implementation:
-auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name)
+auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name) const
{
auto db = SAMRAI::hier::VariableDatabase::getDatabase();
auto var_id = db->getVariable(name);
- // auto context = db->getContext("default");
- // auto patchdata = patch.getPatchData(var_id, context);
+ if (!var_id) {
+ throw std::runtime_error("Variable '" + name + "' not found in database");
+ }
return FieldData::getPatchData(patch, var_id);
}🤖 Prompt for AI Agents
In src/amr/debugod.hpp around lines 135 to 142, the getField method lacks a
specified return type and references FieldData without including its definition.
Add the include directive for "amr/data/field/field_data.hpp" at the top of the
file to provide FieldData's declaration. Then, specify the correct return type
for getField, likely a reference to the FieldData type returned by getPatchData,
and ensure the method implementation correctly returns that type.
src/amr/debugod.hpp
Outdated
| for () | ||
| { | ||
| GodValue gval; | ||
| gval.coords = {node[0], node[1], node[2]}; | ||
| } |
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Complete the incomplete node iteration loop.
The for loop at line 73 is incomplete - it lacks condition, iterator, and proper body implementation.
Apply this diff to complete the loop implementation:
-// loop on nodes
-for ()
-{
- GodValue gval;
- gval.coords = {node[0], node[1], node[2]};
-}
+// loop on nodes
+auto nodeIterator = field.getNodeIterator(intersected_box);
+for (nodeIterator.initialize(intersected_box); nodeIterator; nodeIterator++)
+{
+ auto node = nodeIterator();
+ GodValue gval;
+ gval.coords = {node[0], node[1], node[2]};
+ gval.loc_index = {nodeIterator.getNodeIndex()[0], nodeIterator.getNodeIndex()[1], nodeIterator.getNodeIndex()[2]};
+ gval.amr_index = {/* calculate AMR indices */};
+ gval.rank = PHARE::core::mpi::rank();
+ gval.patchID = patch.getPatchID();
+ god_values[ilvl].push_back(gval);
+}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| for () | |
| { | |
| GodValue gval; | |
| gval.coords = {node[0], node[1], node[2]}; | |
| } | |
| // loop on nodes | |
| auto nodeIterator = field.getNodeIterator(intersected_box); | |
| for (nodeIterator.initialize(intersected_box); nodeIterator; nodeIterator++) | |
| { | |
| auto node = nodeIterator(); | |
| GodValue gval; | |
| gval.coords = {node[0], node[1], node[2]}; | |
| gval.loc_index = { | |
| nodeIterator.getNodeIndex()[0], | |
| nodeIterator.getNodeIndex()[1], | |
| nodeIterator.getNodeIndex()[2] | |
| }; | |
| gval.amr_index = {/* calculate AMR indices */}; | |
| gval.rank = PHARE::core::mpi::rank(); | |
| gval.patchID = patch.getPatchID(); | |
| god_values[ilvl].push_back(gval); | |
| } |
🤖 Prompt for AI Agents
In src/amr/debugod.hpp around lines 73 to 77, the for loop is incomplete and
missing the iteration variable, condition, and increment. Complete the for loop
by specifying the loop variable, the range or container to iterate over (likely
the nodes collection), and the increment step. Also, ensure the loop body
correctly accesses each node and assigns its coordinates to gval.coords as
intended.
src/amr/debugod.hpp
Outdated
| auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) | ||
| { | ||
| auto db = SAMRAI::hier::VariableDatabase::getDatabase(); | ||
| auto var_id = db->getVariable(name); | ||
| auto context = db->getContext("default"); | ||
| return patch.getPatchData(var_id, context); | ||
| } |
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🛠️ Refactor suggestion
Add error handling for potential null returns.
The method should handle cases where the variable or context might not exist in the database.
Apply this diff to add error handling:
auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name)
{
auto db = SAMRAI::hier::VariableDatabase::getDatabase();
auto var_id = db->getVariable(name);
+ if (!var_id) {
+ throw std::runtime_error("Variable '" + name + "' not found in database");
+ }
auto context = db->getContext("default");
- return patch.getPatchData(var_id, context);
+ auto data = patch.getPatchData(var_id, context);
+ if (!data) {
+ throw std::runtime_error("Patch data not found for variable '" + name + "'");
+ }
+ return *data;
}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) | |
| { | |
| auto db = SAMRAI::hier::VariableDatabase::getDatabase(); | |
| auto var_id = db->getVariable(name); | |
| auto context = db->getContext("default"); | |
| return patch.getPatchData(var_id, context); | |
| } | |
| auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) | |
| { | |
| auto db = SAMRAI::hier::VariableDatabase::getDatabase(); | |
| auto var_id = db->getVariable(name); | |
| if (!var_id) { | |
| throw std::runtime_error("Variable '" + name + "' not found in database"); | |
| } | |
| auto context = db->getContext("default"); | |
| auto data = patch.getPatchData(var_id, context); | |
| if (!data) { | |
| throw std::runtime_error("Patch data not found for variable '" + name + "'"); | |
| } | |
| return *data; | |
| } |
🤖 Prompt for AI Agents
In src/amr/debugod.hpp around lines 127 to 133, the getPatchData function does
not handle cases where getVariable or getContext might return null pointers. Add
checks after retrieving var_id and context to verify they are not null. If
either is null, handle the error appropriately, such as throwing an exception or
returning an error indicator, to prevent undefined behavior when calling
patch.getPatchData.
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Actionable comments posted: 2
♻️ Duplicate comments (6)
src/amr/debugod.hpp (6)
39-42: Fix the singleton pattern implementation.The current design has fundamental issues:
- The class contains a
unique_ptrto itself (god_), which is not a proper singleton pattern- The
init()method tries to create a new instance without parameters, but the constructor is privateA proper singleton should use a static instance:
-NO_DISCARD static DEBUGOD& INSTANCE(); - -void init() { god_ = std::make_unique<DEBUGOD>(); } +NO_DISCARD static DEBUGOD& INSTANCE() +{ + static DEBUGOD instance; + return instance; +}And remove the self-referential member:
-DEBUGOD() {} -std::unique_ptr<DEBUGOD> god_; -std::shared_ptr<SAMRAI::hier::PatchHierarchy> hierarchy_; +DEBUGOD() = default; +std::shared_ptr<SAMRAI::hier::PatchHierarchy> hierarchy_;Also applies to: 179-181
61-64: Add missing Box type definition and phare_box_from function.The code uses
Box<double, dim>andphare_box_fromwhich are not defined or included.Add the necessary includes or type definitions:
#include "core/data/ndarray/ndarray_vector.hpp" // or wherever Box is defined #include "amr/utilities/box_utilities.hpp" // or wherever phare_box_from is defined
128-130: Fix parameter type in print method.The method should accept
GodExtract(the map type returned by inspect), notstd::vector<GodValue>.-void print(std::vector<GodValue> const& god_values) +void print(GodExtract const& god_values)
137-137: Fix missing assignment operator.Missing
=operator and wrong variable name in assignment.-auto& amr_idx v.loc_index; +auto& amr_idx = v.amr_index;
162-168: Add error handling and fix return type.The method should handle null returns and specify proper return type.
-auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) +auto getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) const { auto db = SAMRAI::hier::VariableDatabase::getDatabase(); auto var_id = db->getVariable(name); + if (!var_id) { + throw std::runtime_error("Variable '" + name + "' not found in database"); + } auto context = db->getContext("default"); - return patch.getPatchData(var_id, context); + auto data = patch.getPatchData(var_id, context); + if (!data) { + throw std::runtime_error("Patch data not found for variable '" + name + "'"); + } + return data; }
170-177: Complete getField implementation and add missing include.The method references undefined
FieldDataand needs proper implementation.Add the include at the top of the file:
#include "amr/data/field/field_data.hpp"And complete the implementation:
-auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name) +auto getField(SAMRAI::hier::Patch const& patch, std::string const& name) const { - auto db = SAMRAI::hier::VariableDatabase::getDatabase(); - auto var_id = db->getVariable(name); - // auto context = db->getContext("default"); - // auto patchdata = patch.getPatchData(var_id, context); - return FieldData::getPatchData(patch, var_id); + auto patchData = getPatchData(patch, name); + auto fieldData = std::dynamic_pointer_cast<FieldData<dim>>(patchData); + if (!fieldData) { + throw std::runtime_error("Failed to cast patch data to FieldData"); + } + return fieldData; }
🧹 Nitpick comments (1)
src/amr/debugod.hpp (1)
118-121: Add const qualifier to coord parameter.The parameter should be const as it's not modified.
-NO_DISCARD auto inspect(std::string name, Point_t& coord) +NO_DISCARD auto inspect(std::string name, Point_t const& coord)
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
**/*.hpp: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
src/amr/debugod.hpp
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src/amr/debugod.hpp (1)
183-183: Remove semicolon after namespace closing brace.Namespace declarations should not end with a semicolon.
-}; // namespace PHARE::amr +} // namespace PHARE::amrLikely an incorrect or invalid review comment.
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Actionable comments posted: 1
♻️ Duplicate comments (6)
src/amr/debugod.hpp (6)
43-43: Fix the broken singleton pattern implementation.The
init()method creates aunique_ptrto another instance of the same singleton class, which fundamentally breaks the singleton pattern and will cause memory management issues.Apply this diff to fix the singleton pattern:
-void init() { god_ = std::make_unique<DEBUGOD>(); } +void init(std::shared_ptr<SAMRAI::hier::PatchHierarchy> const& hier) +{ + hierarchy_ = hier; +}Also remove the
god_member variable from the private section (line 184).
73-73: Add missing getLayoutFromPatch function.The function
getLayoutFromPatchis called but not defined anywhere in the class or included headers, which will cause a compilation error.You need to either:
- Add the function definition to the class
- Include the appropriate header that defines it
- Use an alternative approach to get the layout
139-139: Fix incorrect field reference.The assignment uses
v.loc_indexbut should referencev.amr_indexfor the AMR index.Apply this diff:
- auto& amr_idx = v.loc_index; + auto& amr_idx = v.amr_index;
172-179: Complete the getField implementation and add missing include.The method references
FieldDatawhich is not included or defined, and lacks a return type specification.Add the necessary include at the top of the file:
#include "amr/data/field/field_data.hpp" // or the appropriate headerAnd specify the return type:
- auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name) + auto& getField(SAMRAI::hier::Patch const& patch, std::string const& name) const
164-170: Add error handling for potential null returns.The method should handle cases where the variable or context might not exist in the database.
Apply this diff to add error handling:
auto& getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) { auto db = SAMRAI::hier::VariableDatabase::getDatabase(); auto var_id = db->getVariable(name); + if (!var_id) { + throw std::runtime_error("Variable '" + name + "' not found in database"); + } auto context = db->getContext("default"); - return patch.getPatchData(var_id, context); + auto data = patch.getPatchData(var_id, context); + if (!data) { + throw std::runtime_error("Patch data not found for variable '" + name + "'"); + } + return *data; }
183-185: Fix singleton design pattern implementation.The current design has a
unique_ptrto itself which is problematic for a singleton. The singleton should not contain a pointer to another instance of itself.Apply this diff to fix the singleton pattern:
DEBUGOD() {} -std::unique_ptr<DEBUGOD> god_; std::shared_ptr<SAMRAI::hier::PatchHierarchy> hierarchy_;
🧹 Nitpick comments (1)
src/amr/debugod.hpp (1)
85-114: Complete the missing dimensional implementations.The 1D and 3D cases are not implemented, which limits the utility's functionality. Consider implementing these cases or documenting them as future work.
For the 1D case:
if constexpr (dim == 1) { auto& dl = layout.meshSize(); auto ixStart = intersected_box.lower(0) / dl[0] - layout.origin()[0]; auto ixEnd = intersected_box.upper(0) / dl[0] - layout.origin()[0]; for (auto ix = ixStart; ix <= ixEnd; ++ix) { GodValue gval; gval.coords = layout.fieldNodeCoordinates(field, layout.origin(), ix); gval.value = field(ix); gval.loc_index = {static_cast<int>(ix)}; gval.rank = PHARE::core::mpi::rank(); gval.patchID = patch.getPatchNumber(); god_values[ilvl].push_back(gval); } }
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
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src/amr/debugod.hpp
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Actionable comments posted: 1
♻️ Duplicate comments (2)
src/amr/debugod.hpp (2)
113-145: Critical: Fix data collection logic in 2D caseThe
gvalobject is declared outside the loops but only pushed once after all iterations, resulting in only the last data point being stored. Additionally, severalGodValuefields are never populated.Apply this fix:
- GodValue gval; auto box = *intersected_box; if constexpr (dimension == 1) { // } else if constexpr (dimension == 2) { auto& dl = layout.meshSize(); auto ixStart = static_cast<int>((box.lower[0] - layout.origin()[0]) / dl[0]); auto ixEnd = static_cast<int>((box.upper[0] - layout.origin()[0]) / dl[0]); auto iyStart = static_cast<int>((box.lower[1] - layout.origin()[1]) / dl[1]); auto iyEnd = static_cast<int>((box.upper[1] - layout.origin()[1]) / dl[1]); for (auto ix = ixStart; ix <= ixEnd; ++ix) { for (auto iy = iyStart; iy <= iyEnd; ++iy) { + GodValue gval; gval.coords = layout.fieldNodeCoordinates(field, layout.origin(), ix, iy); gval.value = field(ix, iy); + gval.loc_index = {ix, iy}; + gval.amr_index = {/* TODO: calculate AMR indices */}; + gval.rank = PHARE::core::mpi::rank(); + gval.patchID = patch->getPatchNumber(); + god_values[ilvl].push_back(gval); } } } else if constexpr (dimension == 3) { // for (auto& node : intersected_box) // { // } } - god_values[ilvl].push_back(gval);
169-169: Fix variable assignment errorThe variable
amr_idxshould be assigned fromv.amr_index, notv.loc_index.- auto& amr_idx = v.loc_index; + auto& amr_idx = v.amr_index;
🧹 Nitpick comments (2)
src/amr/debugod.hpp (2)
214-214: Fix namespace closing comment syntax-}; // namespace PHARE::amr +} // namespace PHARE::amr
116-119: Implement 1D and 3D casesThe 1D and 3D cases are currently unimplemented. Since this is marked as WIP, ensure these are completed before final review.
Would you like me to help implement the 1D and 3D iteration logic or open an issue to track this?
Also applies to: 139-144
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src/amr/utilities/box/amr_box.hppsrc/amr/debugod.hpp
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🔇 Additional comments (1)
src/amr/utilities/box/amr_box.hpp (1)
27-32: Good type safety improvement!The change from
std::array<Type, dim>tostd::array<int, dim>correctly reflects that SAMRAI boxes internally useintfor coordinates. The explicit casting via the generator lambda ensures type-safe conversion to the template parameterType.
| void print(GodExtract const& god_values) | ||
| { | ||
| for (auto& [ilvl, values] : god_values) | ||
| { | ||
| std::cout << "Level " << ilvl << ":\n"; | ||
| for (auto& v : values) | ||
| { | ||
| auto& coords = v.coords; | ||
| auto& loc_idx = v.loc_index; | ||
| auto& amr_idx = v.loc_index; | ||
| auto& rank = v.rank; | ||
| auto& patchID = v.patchID; | ||
|
|
||
| std::cout << "\n"; | ||
| } | ||
| } | ||
| } |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Complete the print implementation
The print method extracts variables but doesn't output them. Consider implementing proper output formatting.
void print(GodExtract const& god_values)
{
for (auto& [ilvl, values] : god_values)
{
std::cout << "Level " << ilvl << ":\n";
for (auto& v : values)
{
auto& coords = v.coords;
auto& loc_idx = v.loc_index;
- auto& amr_idx = v.loc_index;
+ auto& amr_idx = v.amr_index;
auto& rank = v.rank;
auto& patchID = v.patchID;
+ auto& value = v.value;
- std::cout << "\n";
+ std::cout << " Patch " << patchID << " (rank " << rank << "):\n";
+ std::cout << " Coords: (";
+ for (std::size_t d = 0; d < dimension; ++d) {
+ if (d > 0) std::cout << ", ";
+ std::cout << coords[d];
+ }
+ std::cout << ")\n";
+ std::cout << " Value: " << value << "\n";
+ std::cout << " Local index: (";
+ for (std::size_t d = 0; d < dimension; ++d) {
+ if (d > 0) std::cout << ", ";
+ std::cout << loc_idx[d];
+ }
+ std::cout << ")\n";
}
}
}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| void print(GodExtract const& god_values) | |
| { | |
| for (auto& [ilvl, values] : god_values) | |
| { | |
| std::cout << "Level " << ilvl << ":\n"; | |
| for (auto& v : values) | |
| { | |
| auto& coords = v.coords; | |
| auto& loc_idx = v.loc_index; | |
| auto& amr_idx = v.loc_index; | |
| auto& rank = v.rank; | |
| auto& patchID = v.patchID; | |
| std::cout << "\n"; | |
| } | |
| } | |
| } | |
| void print(GodExtract const& god_values) | |
| { | |
| for (auto& [ilvl, values] : god_values) | |
| { | |
| std::cout << "Level " << ilvl << ":\n"; | |
| for (auto& v : values) | |
| { | |
| auto& coords = v.coords; | |
| auto& loc_idx = v.loc_index; | |
| auto& amr_idx = v.amr_index; | |
| auto& rank = v.rank; | |
| auto& patchID = v.patchID; | |
| auto& value = v.value; | |
| std::cout << " Patch " << patchID << " (rank " << rank << "):\n"; | |
| std::cout << " Coords: ("; | |
| for (std::size_t d = 0; d < dimension; ++d) { | |
| if (d > 0) std::cout << ", "; | |
| std::cout << coords[d]; | |
| } | |
| std::cout << ")\n"; | |
| std::cout << " Value: " << value << "\n"; | |
| std::cout << " Local index: ("; | |
| for (std::size_t d = 0; d < dimension; ++d) { | |
| if (d > 0) std::cout << ", "; | |
| std::cout << loc_idx[d]; | |
| } | |
| std::cout << ")\n"; | |
| } | |
| } | |
| } |
🤖 Prompt for AI Agents
In src/amr/debugod.hpp between lines 160 and 176, the print method extracts
variables from god_values but does not output their contents. Complete the
implementation by adding std::cout statements to print the values of coords,
loc_index, amr_idx (correct the duplicate reference), rank, and patchID with
clear labels and formatting for readability.
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Actionable comments posted: 0
♻️ Duplicate comments (4)
src/amr/debugod.hpp (4)
171-171: Fix duplicate variable reference in print method.The line incorrectly references
v.loc_indextwice instead ofv.amr_indexfor the AMR index.Apply this diff to fix the variable reference:
- auto& amr_idx = v.loc_index; + auto& amr_idx = v.amr_index;
162-178: Complete the print method implementation.The print method extracts variables but doesn't output their values, making it ineffective for debugging purposes.
Apply this diff to complete the implementation:
void print(GodExtract const& god_values) { for (auto& [ilvl, values] : god_values) { std::cout << "Level " << ilvl << ":\n"; for (auto& v : values) { auto& coords = v.coords; auto& loc_idx = v.loc_index; - auto& amr_idx = v.loc_index; + auto& amr_idx = v.amr_index; auto& rank = v.rank; auto& patchID = v.patchID; + auto& value = v.value; - std::cout << "\n"; + std::cout << " Patch " << patchID << " (rank " << rank << "):\n"; + std::cout << " Coords: ("; + for (std::size_t d = 0; d < dimension; ++d) { + if (d > 0) std::cout << ", "; + std::cout << coords[d]; + } + std::cout << ")\n"; + std::cout << " Value: " << value << "\n"; + std::cout << " Local index: ("; + for (std::size_t d = 0; d < dimension; ++d) { + if (d > 0) std::cout << ", "; + std::cout << loc_idx[d]; + } + std::cout << ")\n"; } } }
202-208: Add error handling for potential null returns.The method should handle cases where
getVariableorgetContextmight return null pointers to prevent undefined behavior.Apply this diff to add error handling:
auto getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) const { auto db = SAMRAI::hier::VariableDatabase::getDatabase(); auto var_id = db->getVariable(name); + if (!var_id) { + throw std::runtime_error("Variable '" + name + "' not found in database"); + } auto context = db->getContext("default"); - return patch.getPatchData(var_id, context); + auto data = patch.getPatchData(var_id, context); + if (!data) { + throw std::runtime_error("Patch data not found for variable '" + name + "'"); + } + return data; }
113-147: Fix data collection logic - only last value is being stored.The
GodValue gvalis declared outside the nested loops and only pushed togod_values[ilvl]once after all iterations complete. This means only the last coordinate's data is stored, losing all other values.Apply this diff to fix the data collection:
- GodValue gval; auto box = *intersected_box; if constexpr (dimension == 1) { // } else if constexpr (dimension == 2) { auto& dl = layout.meshSize(); auto ixStart = static_cast<int>((box.lower[0] - layout.origin()[0]) / dl[0]); auto ixEnd = static_cast<int>((box.upper[0] - layout.origin()[0]) / dl[0]); auto iyStart = static_cast<int>((box.lower[1] - layout.origin()[1]) / dl[1]); auto iyEnd = static_cast<int>((box.upper[1] - layout.origin()[1]) / dl[1]); for (auto ix = ixStart; ix <= ixEnd; ++ix) { for (auto iy = iyStart; iy <= iyEnd; ++iy) { + GodValue gval; gval.coords = layout.fieldNodeCoordinates(field, layout.origin(), ix, iy); gval.value = field(ix, iy); gval.patchID = to_string(patch->getGlobalId()); gval.rank = get_rank(*patch); + gval.loc_index = {ix, iy}; + gval.amr_index = {/* calculate AMR indices */}; + god_values[ilvl].push_back(gval); } } } else if constexpr (dimension == 3) { // for (auto& node : intersected_box) // { // } } - god_values[ilvl].push_back(gval);
🧹 Nitpick comments (1)
src/amr/debugod.hpp (1)
116-119: Implement the 1D case for completeness.The 1D dimension case is left empty, making the debugging utility incomplete for 1D simulations.
Consider implementing the 1D case:
if constexpr (dimension == 1) { - // + auto& dl = layout.meshSize(); + auto ixStart = static_cast<int>((box.lower[0] - layout.origin()[0]) / dl[0]); + auto ixEnd = static_cast<int>((box.upper[0] - layout.origin()[0]) / dl[0]); + + for (auto ix = ixStart; ix <= ixEnd; ++ix) + { + GodValue gval; + gval.coords = layout.fieldNodeCoordinates(field, layout.origin(), ix); + gval.value = field(ix); + gval.patchID = to_string(patch->getGlobalId()); + gval.rank = get_rank(*patch); + gval.loc_index = {ix}; + gval.amr_index = {/* calculate AMR indices */}; + god_values[ilvl].push_back(gval); + } }
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
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src/amr/debugod.hpp
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🔇 Additional comments (1)
src/amr/debugod.hpp (1)
24-32: Well-structured template class design.The template design with PHARE_TYPES parameter and extracted type aliases provides good flexibility and readability for different dimension and interpolation order configurations.
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Actionable comments posted: 1
♻️ Duplicate comments (3)
src/amr/debugod.hpp (3)
129-148: Fix data collection logic and missing closing brace.The nested loops populate
gvalfor each coordinate, butgvalis only added togod_values[ilvl]once outside the loops (line 148). This results in only the last iteration's data being stored. Additionally, the closing brace for the inner loop is missing.Apply this diff to fix both issues:
for (auto ix = ixStart; ix <= ixEnd; ++ix) { for (auto iy = iyStart; iy <= iyEnd; ++iy) { gval.coords = layout.fieldNodeCoordinates(field, layout.origin(), ix, iy); gval.value = field(ix, iy); gval.patchID = to_string(patch->getGlobalId()); gval.rank = get_rank(*patch); gval.loc_index = {ix, iy}; + god_values[ilvl].push_back(gval); } } - } - else if constexpr (dimension == 3) + } + else if constexpr (dimension == 3)
172-172: Fix incorrect variable reference.Line 172 incorrectly references
v.loc_indexinstead ofv.amr_index.Apply this diff:
- auto& amr_idx = v.loc_index; + auto& amr_idx = v.amr_index;
203-209: Add error handling for potential null returns.The method should handle cases where the variable or context might not exist in the database.
Apply this diff to add error handling:
auto getPatchData(SAMRAI::hier::Patch const& patch, std::string const& name) const { auto db = SAMRAI::hier::VariableDatabase::getDatabase(); auto var_id = db->getVariable(name); + if (!var_id) { + throw std::runtime_error("Variable '" + name + "' not found in database"); + } auto context = db->getContext("default"); - return patch.getPatchData(var_id, context); + auto data = patch.getPatchData(var_id, context); + if (!data) { + throw std::runtime_error("Patch data not found for variable '" + name + "'"); + } + return data; }
🧹 Nitpick comments (2)
src/amr/debugod.hpp (2)
223-223: Remove unnecessary semicolon after namespace closing brace.Namespaces don't require semicolons after the closing brace.
-}; // namespace PHARE::amr +} // namespace PHARE::amr
116-119: Complete the implementation for 1D and 3D cases.The 1D and 3D cases are not implemented. Consider completing these implementations or adding TODO comments explaining the plan.
Would you like me to help implement the 1D and 3D cases based on the 2D pattern?
Also applies to: 142-147
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`**/*.hpp`: Review the C++ code, point out issues relative to principles of clean code, expressiveness, and performance.
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src/amr/debugod.hpp
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| = phare_box_from<dimension, double>(getPatchData(*patch, name)->getGhostBox()); | ||
|
|
||
| auto& field = getField(*patch, name); | ||
| auto layout = layoutFromPatch<GridLayout_t>(*patch); |
There was a problem hiding this comment.
Missing function definition for layoutFromPatch.
The function layoutFromPatch is used but not defined or included. This will cause a compilation error.
You need to either:
- Include the header that defines
layoutFromPatch - Add the function definition to this file or another appropriate location
🤖 Prompt for AI Agents
In src/amr/debugod.hpp at line 87, the function layoutFromPatch is used but not
defined or included, causing a compilation error. To fix this, either include
the header file where layoutFromPatch is defined or provide its function
definition in this file or another appropriate source file to ensure it is
available during compilation.
WIP
This idea is to have some god singleton made at the very beginning of the execution from the top level dict once the hierarchy is made.
Knowing the hierarchy and the root mesh resolution (from the top level dict), we can interrogate this singleton from anywhere in the code to get values of specific fields at specific node coordinates or range of coordinates.
We should be able to get values on every level and even in the given coordinate range spans several patches per level.
All meta-data that could be useful should be accessible....
field value, local patch data index, amr index, MPI rank ID, etc.
Attention is needed in parallel since ranks have only certain patchdatas.