Frequently Asked Questions

Q. Why am I getting a segmentation fault after my code runs?

A. Do you have amrex::Initialize(); { and } amrex::Finalize(); at the beginning and end of your code? For all AMReX commands to function properly, including to release resources, they need to be contained between these two curly braces or in a separate function. In the Initialize and Finalize section, these commands are discussed further detail.


Q. I want to use a different compiler with GNU Make to compile AMReX. How do I do this?

A. In the file amrex/Tools/GNUMake/Make.local you can specify your own compile commands by setting the variables CXX, CC, FC, and F90. An example can be found at Specifying your own compiler . Additional customizations are described in the file, amrex/Tools/GNUMake/Make.local.template. In the same directory, amrex/Tools/GNUMake/README.md contains detailed information on compiler commands.


Q. I’m having trouble compiling my code.

A. AMReX developers have found that running the command make clean can resolve many compilation issues.

If you are working in an environment that uses a module system, please ensure you have the correct modules loaded. Typically, to do this, type module list at the command prompt.


Q. When I profile my code that uses GPUs with TINY_PROFILE=TRUE or PROFILE=TRUE my timings are inconsistent.

A. Due to the asynchronous nature of GPU execution, profilers might only measure the run time on CPU, if there is no explicit synchronization. For TINY_PROFILE, one could use ParmParse parameter tiny_profiler.device_synchronize_around_region=1 to add synchronization. Note that this may degrade performance.


Q. How do I know I am getting the right answer?

A. AMReX provides support for verifying output with several tools. To briefly mention a few:

  • The print_state function can be used to output the data of a single cell.

  • VisMF::Write can be used to write MultiFab data to disk that can be viewed with Amrvis.

  • amrex::Print() and amrex::AllPrint() are useful for printing output when using multiple processes or threads as it prevents messages from getting mixed up.

  • fcompare compares two plotfiles and reports absolute and relative error.

Additional tools and discussion on this topic is contained in the section Debugging.


Q. What’s the difference between Copy and ParallelCopy for MultiFab data?

A. MultiFab::Copy is for two MultiFabs built with the same BoxArray and DistributionMapping, whereas ParallelCopy is for parallel communication of two MultiFabs with different BoxArray and/or DistributionMapping.


Q. How do I fill ghost cells?

A. See Ghost Cells in the AMReX Source Documentation.


Q. What’s the difference between AmrCore and AmrLevel? How do I decide which to use?

A. The AmrLevel class is an abstract base class that holds data for a single AMR level. A vector of AmrLevel is stored in the Amr class, which is derived from AmrCore. An application code can derive from AmrLevel and override functions. AmrCore contains the meta-data for the AMR hierarchy, but it does not contain any floating point mesh data. Instead of using Amr/AmrLevel, an application can also derive from AmrCore. If you want flexibility, you might choose the AmrCore approach, otherwise the AmrLevel approach might be easier because it already has a lot of built-in capabilities that are common for AMR applications.


Q. For GPU usage, how can I perform explicit host to device and device to host copies without relying on managed memory?

A. Use The_Pinned_Arena() (See Memory Allocation in the AMReX Source Documentation.) and

void htod_memcpy (void* p_d, const void* p_h, const std::size_t sz);
void dtoh_memcpy (void* p_h, const void* p_d, const std::size_t sz);
void dtoh_memcpy (FabArray<FAB>& dst, FabArray<FAB> const& src, int scomp, int dcomp, int ncomp);
void htod_memcpy (FabArray<FAB>& dst, FabArray<FAB> const& src, int scomp, int dcomp, int ncomp);

Q. How do I generate random numbers with AMReX? Can I set the seed? Are they thread safe with MPI and OpenMP?

A. (Thread safe) Yes, amrex::Random() is thread safe. When OpenMP is on, each thread will have its own dedicated Random Number Generator that is totally independent of the others.


Q. Is Dirichlet boundary condition data loaded into cell-centered, or face-centered containers? How is it used in AMReX-based codes like MLMG and the advection routines in AMReX-Hydro?

A. In the cell-centered MLMG solver, the Dirichlet boundary data are stored in containers that have the information of the location of the data.


Q. How does coarse-grained OpenMP parallelism work in AMReX? How is it different from the fine-grained approach?

A. Our OpenMP strategy is explained in this paper, https://arxiv.org/abs/1604.03570.



More Questions

If your question was not addressed here, you are encouraged to search and ask for help on the AMReX GitHub Discussions page.