Merge pull request #109 from cindytsai/Pre-v0.1

Prepare for release v0.1

doc/in-situ-python-analysis/jupyter-notebook/jupyter-notebook-access.md

@@ -39,7 +39,7 @@ We need another process to start Jupyter Notebook/JupyterLab and connect to liby
 4. Launch Jupyter Notebook/JupyterLab
    ```bash
    jupyter notebook # launch Jupyter Notebook
-   jupyter-lab      # launch JupyterLab
+   jupyter lab      # launch JupyterLab
    ```
 5. Click `Libyt` to connect to libyt kernel once the simulation is running and libyt kernel is activated.
 

doc/in-situ-python-analysis/jupyter-notebook/remote-cluster.md

@@ -47,7 +47,7 @@ Please go through [Login Node](#login-node) before going through [Local Laptop](
 2. Launch Jupyter Notebook / JupyterLab in no-browser mode with port `XXXX` and allowing access from other IP address (`--ip="0.0.0.0"`):
    ```bash
    jupyter notebook --no-browser --port=XXXX --ip="0.0.0.0"
-   jupyter-lab --no-browser --port=XXXX --ip="0.0.0.0"
+   jupyter lab --no-browser --port=XXXX --ip="0.0.0.0"
    ```
    Change `XXXX` to some unused port on login node, this is just a placeholder.
 3. You should see something like:

example/amr-example/example.cpp

@@ -208,6 +208,10 @@ int main(int argc, char* argv[]) {
         yt_set_UserParameterInt("mhd", 1, &mhd);
         const int srhd = 0;
         yt_set_UserParameterInt("srhd", 1, &srhd);
+        const int opt_unit = 0;
+        yt_set_UserParameterInt("opt_unit", 1, &opt_unit);
+        const float mu = 0.6;
+        yt_set_UserParameterFloat("mu", 1, &mu);
 
         // demo of some other parameters we can add
         const int user_int = 1;

example/quick-start/quick-start.cpp

@@ -43,15 +43,18 @@ int main(int argc, char* argv[]) {
     // Execute Python functions and activate Python entry points
     // ==========================================================
     if (yt_run_Function("print_hello_world") != YT_SUCCESS) {
+        fprintf(stderr, "ERROR: yt_run_Function failed!\n");
         exit(EXIT_FAILURE);
     }
 
     if (yt_run_FunctionArguments("print_args", 3, "\'1\'", "2", "3.0") != YT_SUCCESS) {
+        fprintf(stderr, "ERROR: yt_run_FunctionArguments failed!\n");
         exit(EXIT_FAILURE);
     }
 
     // Activate Python prompt
     if (yt_run_InteractiveMode("LIBYT_STOP") != YT_SUCCESS) {
+        fprintf(stderr, "ERROR: yt_run_InteractiveMode failed!\n");
         exit(EXIT_FAILURE);
     }
 
@@ -67,6 +70,12 @@ int main(int argc, char* argv[]) {
         exit(EXIT_FAILURE);
     }
 
+    // Free and reset the state
+    if (yt_free() != YT_SUCCESS) {
+        fprintf(stderr, "ERROR: yt_free() failed!\n");
+        exit(EXIT_FAILURE);
+    }
+
     // =======================================
     // Finalize libyt
     // =======================================

src/append_grid.cpp

@@ -23,8 +23,6 @@ static int set_particle_data(yt_grid* grid);
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int append_grid(yt_grid* grid) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     // export grid info to libyt.hierarchy
     PyArrayObject* py_array_obj;
 
@@ -76,8 +74,6 @@ int append_grid(yt_grid* grid) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 static int set_field_data(yt_grid* grid) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     yt_field* field_list = LibytProcessControl::Get().field_list;
 
     PyObject *py_grid_id, *py_field_labels, *py_field_data;
@@ -179,8 +175,6 @@ static int set_field_data(yt_grid* grid) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 static int set_particle_data(yt_grid* grid) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     yt_particle* particle_list = LibytProcessControl::Get().particle_list;
 
     PyObject *py_grid_id, *py_ptype_labels, *py_attributes, *py_data;

src/get_dtype_property.cpp

@@ -25,8 +25,6 @@
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_npy_dtype(yt_dtype data_type, int* npy_dtype) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (data_type) {
         case YT_FLOAT:
             *npy_dtype = NPY_FLOAT;
@@ -103,8 +101,6 @@ int get_npy_dtype(yt_dtype data_type, int* npy_dtype) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_yt_dtype_from_npy(int npy_dtype, yt_dtype* data_dtype) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (npy_dtype) {
         case NPY_FLOAT:
             *data_dtype = YT_FLOAT;
@@ -173,8 +169,6 @@ int get_yt_dtype_from_npy(int npy_dtype, yt_dtype* data_dtype) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_mpi_dtype(yt_dtype data_type, MPI_Datatype* mpi_dtype) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (data_type) {
         case YT_FLOAT:
             *mpi_dtype = MPI_FLOAT;
@@ -258,8 +252,6 @@ int get_mpi_dtype(yt_dtype data_type, MPI_Datatype* mpi_dtype) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_dtype_size(yt_dtype data_type, int* dtype_size) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (data_type) {
         case YT_FLOAT:
             *dtype_size = sizeof(float);
@@ -343,8 +335,6 @@ int get_dtype_size(yt_dtype data_type, int* dtype_size) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_dtype_typeid(yt_dtype data_type, const std::type_info** dtype_id) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (data_type) {
         case YT_FLOAT:
             *dtype_id = &typeid(float);
@@ -430,8 +420,6 @@ int get_dtype_typeid(yt_dtype data_type, const std::type_info** dtype_id) {
 // Return      :  YT_SUCCESS or YT_FAIL
 //-------------------------------------------------------------------------------------------------------
 int get_dtype_allocation(yt_dtype data_type, unsigned long length, void** data_ptr) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (data_type) {
         case YT_FLOAT:
             *data_ptr = malloc(length * sizeof(float));
@@ -532,8 +520,6 @@ int get_dtype_allocation(yt_dtype data_type, unsigned long length, void** data_p
 //-------------------------------------------------------------------------------------------------------
 int big_MPI_Get_dtype(void* recv_buff, long data_len, yt_dtype* data_dtype, MPI_Datatype* mpi_dtype, int get_rank,
                       MPI_Aint base_address, MPI_Win* window) {
-    SET_TIMER(__PRETTY_FUNCTION__);
-
     switch (*data_dtype) {
         case YT_FLOAT:
             return big_MPI_Get<float>(recv_buff, data_len, mpi_dtype, get_rank, base_address, window);

src/libyt_kernel.cpp

@@ -32,8 +32,8 @@ void LibytKernel::configure_impl() {
 
     PyObject* py_module_jedi = PyImport_ImportModule("jedi");
     if (py_module_jedi == NULL) {
-        log_info("Unable to import jedi, jedi auto-completion library is disabled\n");
-        log_info("See https://jedi.readthedocs.io/ \n");
+        log_info(
+            "Unable to import jedi, jedi auto-completion library is disabled (See https://jedi.readthedocs.io/)\n");
         m_py_jedi_interpreter = NULL;
     } else {
         m_py_jedi_interpreter = PyObject_GetAttrString(py_module_jedi, "Interpreter");
@@ -68,7 +68,7 @@ nl::json LibytKernel::execute_request_impl(int execution_counter, const std::str
                                            bool store_history, nl::json user_expressions, bool allow_stdin) {
     SET_TIMER(__PRETTY_FUNCTION__);
 
-    std::string cell_name = std::string("In [") + std::to_string(execution_counter) + std::string("]");
+    std::string cell_name = std::string("<In [") + std::to_string(execution_counter) + std::string("]>");
 
     // Find if '%' is the first non-space character, if so, redirect jobs to define command
     std::size_t found = code.find_first_not_of("\t\n\v\f\r ");
@@ -187,8 +187,8 @@ nl::json LibytKernel::complete_request_impl(const std::string& code, int cursor_
 
     // Check if jedi has successfully import
     if (m_py_jedi_interpreter == NULL) {
-        log_info("Unable to import jedi, jedi auto-completion library is disabled\n");
-        log_info("See https://jedi.readthedocs.io/ \n");
+        log_info(
+            "Unable to import jedi, jedi auto-completion library is disabled (See https://jedi.readthedocs.io/)\n");
         return xeus::create_complete_reply({}, cursor_pos, cursor_pos);
     }
 
@@ -325,7 +325,7 @@ nl::json LibytKernel::kernel_info_request_impl() {
     // helper
     libyt_kernel_info["help_links"] = nl::json::array();
     libyt_kernel_info["help_links"][0] =
-        nl::json::object({{"text", "libyt Kernel Documents"}, {"url", "https://yt-project.github.io/libyt/"}});
+        nl::json::object({{"text", "libyt Kernel Documents"}, {"url", "https://libyt.readthedocs.io/en/latest/"}});
 
     // status
     libyt_kernel_info["status"] = "ok";

src/libyt_python_shell.cpp

@@ -469,6 +469,8 @@ CodeValidity LibytPythonShell::check_code_validity(const std::string& code, bool
 
     CodeValidity code_validity;
 
+    // clear error buffer before redirecting stderr
+    PyErr_Clear();
     PyRun_SimpleString("import sys, io\n");
     PyRun_SimpleString("sys.OUTPUT_STDERR=''\nstderr_buf=io.StringIO()\nsys.stderr=stderr_buf\n");
 
@@ -561,6 +563,7 @@ std::array<AccumulatedOutputString, 2> LibytPythonShell::execute_cell(const std:
 #endif
 
     // Clear the template buffer and redirect stdout, stderr
+    PyErr_Clear();
     PyRun_SimpleString("import sys, io\n");
     PyRun_SimpleString("sys.OUTPUT_STDOUT=''\nstdout_buf=io.StringIO()\nsys.stdout=stdout_buf\n");
     PyRun_SimpleString("sys.OUTPUT_STDERR=''\nstderr_buf=io.StringIO()\nsys.stderr=stderr_buf\n");