Debugging GCHP

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Introduction

As a researcher at JPL, debugging complex models like GCHP is crucial for advancing our understanding of the Earth's system. However, debugging GCHP can be a daunting task, especially when using the gdb debugger on high-performance computing systems like Pleiades. In this article, we will explore the challenges of debugging GCHP with gdb and provide solutions for setting breakpoints and halting execution at specific lines in the code. We will also discuss how to run GCHP on a single CPU for easier debugging.

Compiling GCHP with Debugging Options

To debug GCHP using gdb, it is essential to compile the code with debugging options enabled. The -DCMAKE_BUILD_TYPE=Debug option is a good starting point, but it may not be sufficient for all debugging scenarios. When compiling GCHP with CMake, you can add additional flags to enable more comprehensive debugging.

cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS=-g3 -DCMAKE_C_FLAGS=-g3 ..

In the above command, we added the -g3 flag to enable full debugging information. The -g3 flag tells the compiler to include all debugging information, including symbol tables and line number information.

Setting Breakpoints with GDB

Once you have compiled GCHP with debugging options enabled, you can set breakpoints using gdb. To set a breakpoint at a specific line in the code, you can use the break command followed by the line number.

gdb ./gchp
(gdb) break 1234

In the above example, we set a breakpoint at line 1234. You can also set breakpoints at specific functions or labels using the break command.

(gdb) break my_function

Running GCHP on a Single CPU

Running GCHP on a single CPU can be helpful for debugging, as it allows you to focus on a specific part of the code without the complexity of multi-CPU execution. To run GCHP on a single CPU, you can use the mpirun command with the -np option to specify the number of processes.

mpirun -np 1 ./gchp

However, this may not work as expected, as GCHP is designed to run on multiple CPUs. To run GCHP on a single CPU, you can modify the gchp.run file to set the NUM_CORES variable to 1.

NUM_CORES=1

You can also use the GCHP_NPROC environment variable to set the number of processes to 1.

export GCHP_NPROC=1

Additional Debugging Options

In addition to the -DCMAKE_BUILD_TYPE=Debug option, you can use other flags to enable more comprehensive debugging. Some additional flags include:

  • -DCMAKE_CXX_FLAGS=-O0: This flag tells the compiler to disable optimization, which can help with debugging.
  • -DCMAKE_C_FLAGS=-O0: This flag tells the compiler to disable optimization for C code.
  • -DCMAKE_CXX_FLAGS=-gline-tables-only: This flag tells the compiler to include only line number information in the debugging symbols.
  • -DCMAKE_C_FLAGS=-gline-tables-only: This flag tells the compiler to include only line number information in the debugging symbols for C code.

Conclusion

Debugging GCHP can be a challenging task, but with the right tools and options, you can overcome common obstacles. By compiling GCHP with debugging options enabled and using gdb to set breakpoints, you can gain a deeper understanding of the code and identify issues more efficiently. Additionally, running GCHP on a single CPU can be helpful for debugging, and modifying the gchp.run file or using environment variables can achieve this. By following the tips and tricks outlined in this article, you can become a more effective GCHP debugger and contribute to the advancement of our understanding of the Earth's system.

References

Introduction

Debugging GCHP can be a complex and challenging task, especially for those new to the model. In this article, we will provide a Q&A guide to help you overcome common obstacles and become a more effective GCHP debugger.

Q: What are the most common issues when debugging GCHP?

A: Some of the most common issues when debugging GCHP include:

  • Crashes upon execution: GCHP may crash when run with debugging options enabled.
  • Difficulty setting breakpoints: Breakpoints may not be set correctly or may not be triggered.
  • Trouble running GCHP on a single CPU: GCHP may not run on a single CPU as expected.

Q: How do I compile GCHP with debugging options enabled?

A: To compile GCHP with debugging options enabled, you can use the following command:

cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS=-g3 -DCMAKE_C_FLAGS=-g3 ..

This command tells CMake to compile GCHP with the -DCMAKE_BUILD_TYPE=Debug option, which enables debugging information. The -g3 flag tells the compiler to include all debugging information, including symbol tables and line number information.

Q: How do I set breakpoints in GCHP using gdb?

A: To set breakpoints in GCHP using gdb, you can use the break command followed by the line number or function name.

gdb ./gchp
(gdb) break 1234

This command sets a breakpoint at line 1234. You can also set breakpoints at specific functions or labels using the break command.

Q: How do I run GCHP on a single CPU?

A: To run GCHP on a single CPU, you can use the mpirun command with the -np option to specify the number of processes.

mpirun -np 1 ./gchp

However, this may not work as expected, as GCHP is designed to run on multiple CPUs. To run GCHP on a single CPU, you can modify the gchp.run file to set the NUM_CORES variable to 1.

NUM_CORES=1

You can also use the GCHP_NPROC environment variable to set the number of processes to 1.

export GCHP_NPROC=1

Q: What are some additional debugging options I can use?

A: Some additional debugging options you can use include:

  • -DCMAKE_CXX_FLAGS=-O0: This flag tells the compiler to disable optimization, which can help with debugging.
  • -DCMAKE_C_FLAGS=-O0: This flag tells the compiler to disable optimization for C code.
  • -DCMAKE_CXX_FLAGS=-gline-tables-only: This flag tells the compiler to include only line number information in the debugging symbols.
  • -DCMAKE_C_FLAGS=-gline-tables-only: This flag tells the compiler to include only line number information in the debugging symbols for C code.

Q: Where can I find more information on debugging GCHP?

A: You can find more information on debugging GCHP in the following resources:

Conclusion

Debugging GCHP can be a complex and challenging task, but with the right tools and options, you can overcome common obstacles and become a more effective GCHP debugger. By following the tips and tricks outlined in this article, you can gain a deeper understanding of the code and identify issues more efficiently.