FAQs¶

When Installing¶

Get errors when using CMake¶

Make sure the folder where CMake generates build files is empty or not exist yet by removing the folder:

cd libyt
rm -rf <build-folder>
cmake -S . -B <build-folder>

Get errors when linking shared library libyt.so¶

If we compile Python from source, and we get errors like this when compiling libyt:

ld: <some-path-to-python-library>: relocation R_X86_64_32S against symbol `_Py_FalseStruct' can not be used when making a shared object; recompile with -fPIC
ld: failed to set dynamic section sizes: bad value

We need to re-compile and install Python and add --enable-shared when configuring.

The simplest way to avoid this is to install Python from package manager.

Unable to link to dependencies fetched by libyt after installation¶

Keep libyt project repo after installation. libyt fetches and stores dependencies under libyt/vendor folder, so that the content can be reused in different builds.

When Running Applications¶

How does libyt run Python script?¶

libyt runs Python script synchronously, which means every MPI process runs the same piece of Python code. They do the job together under the process space of MPI tasks using mpi4py.

Have problems when running libyt in parallel mode¶

If we happen to get errors related to one-sided MPI, for example:

*** An error occurred in MPI_Win_attach
*** reported by process [3353411585,1]
*** on win rdma window 3
*** MPI_ERR_RMA_ATTACH: Could not attach RMA segment
*** MPI_ERRORS_ARE_FATAL (processes in this win will now abort,
***    and potentially your MPI job)
3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Remember to set OMPI_MCA_osc=sm,pt2pt before running the application. It is for one-sided MPI communication. For example:

OMPI_MCA_osc=sm,pt2pt mpirun -np 3 ./example

Why does my program hang and how do I solve it?¶

Though libyt can execute any Python module, when it comes to reading simulation data, it requires every MPI process to participate. The program hanging problem is due to only some MPI processes are accessing the data, but not all of them.

Please do:

Check if there is an if statements that makes MPI processes non-symmetric. For example, only root process runs the statement:
```
def func():
    if yt.is_root():
        ...  # <-- This statement only executes in MPI root rank
```
Move the statement out of if yt.is_root() (for the case here).

When accessing simulation data, libyt requires every process to participate. We are working on this in both yt and libyt.

Have Problems when Using Interactive Prompt¶

Why can’t I find the prompt `>>>`?¶

>>> is probably immersed inside the output. We can hit enter again, which is to provide an empty statement, and it will come out.

We can make prompt more smoothly by setting YT_VERBOSE to YT_VERBOSE_INFO.

Where can I use interactive mode?¶

libyt interactive Python prompt only works on local machine or submit the job to HPC platforms using interactive jobs like qsub -I in PBS scheduler. The reason is that the user interface is exposed in the terminal.