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Additional settings

The BLUPF90 programs may use a large amount of memory, especially when the dataset is large and a genomic model is applied. Heavy memory consumption often leads to a program crash with a segmentation fault (or bus error). A segmentation fault occurs when a program attempts to access memory in an inappropriate way or location. Note that this error can happen even if your computer has a lot of free memory. This is because the operating system (Linux, macOS, or Windows) imposes limitations on the memory usage of each program. More specifically, the system limits the amount of memory called the stack, and our programs use a large stack memory to achieve maximum performance.

This is a common issue with large datasets. You may encounter it when updating to a newer version of the program while using the same input files. Even a small code change can affect memory usage behavior.

You can either remove the limitation or increase the stack size. The following settings are recommended even if you haven’t encountered this problem yet. More details are available on our website: http://nce.ads.uga.edu/wiki/doku.php?id=faq.segfault.

Increase stack size

This setting is required on Linux and macOS. First, type the following command in your shell (terminal):

ulimit

If it shows unlimited, the configuration is fine. If you see a number (like 8192), it is likely to be a problem. This number represents the stack size and it should be unlimited. To change the stack size, type the following command before running our programs:

ulimit -s unlimited

You can also add this command at the end of your .bash_profile in your home directory. This way, the setting will be applied automatically every time you log in.

Increase stack size for OpenMP

There is a separate setting to define the stack size for OpenMP. This value is independent of the system stack size explained above. You can set it using an environment variable.

Linux and macOS

To check the current value, type the following command in your shell:

echo $OMP_STACKSIZE

If it shows nothing, or a small value like 4M, it might be too small. The default value is usually 4M, which is likely insufficient. Before running the program, set it using the following command (no spaces around =):

export OMP_STACKSIZE=64M

This sets the stack size to 64 megabytes. If the program still fails with the same error, increase the size gradually (e.g., to 128M, 192M, etc.). However, a large value can lead to high memory usage, because each thread can allocate this much stack. There is no universally appropriate value — it depends on your system, so adjust empirically.

For a one-time setting, you can add the variable inline when you run the program (no export):

OMP_STACKSIZE=64M ./blupf90

As with ulimit, you can save this setting permanently in your .bash_profile.

Windows

On Windows, you can set the OMP_STACKSIZE environment variable either temporarily via the Command Prompt or permanently via the system settings in Control Panel.

To check the current value, type:

set %OMP_STACKSIZE%

To set a value (e.g., 64 megabytes), type:

set OMP_STACKSIZE=64M

This setting lasts only for the current session, so you must run the BLUPF90 programs in the same session after setting it. To make it permanent, use the Control Panel. For instructions, search for keywords like windows environment variable using a search engine.

The value should include a number and unit, such as 64M for 64 megabytes. Start with 64M, and if the problem persists, increase the value (e.g., 128M or more). As with other systems, a value that is too large will result in high memory consumption because each thread may use that much memory. You will need to determine an appropriate value based on your computer’s resources.

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