Frequently Asked Questions (FAQ)

This page may be outdated, the most recent list of FAQs are available here:


  • How can I cleanly shutdown a simulation (without corrupting the h5 file)?

It is generally safe to shutdown a WESTPA simulation by simply canceling the job through your queue management. However, to ensure data integrity in the h5 file, you should wait until the WESTPA log indicates that an iteration has begun or is occurring; canceling a job too quickly after submission can result in the absolute corruption of the h5 file and should be avoided.

  • Storage of Large Files

During a normal WESTPA run, many small files are created and it is convenient to tar these into a larger file (one tarball per iteration, for instance). It is generally best to do this ‘offline’. An important aspect to consider is that some disk systems, such as LUSTRE, will suffer impaired performance if very large files are created. On Stampede, for instance, any file larger than 200 GB must be ‘striped’ properly (such that its individual bits are spread across numerous disks).

Within the user guide for such systems, there is generally a section on how to handle large files. Some computers have special versions of tar which stripe appropriately; others do not (such as Stampede). For those that do not, it may be necessary to contact the sysadmin, and/or create a directory where you can place your tarball with a different stripe level than the default.

  • H5py Inflate() Failed error

While running or analyzing a simulation, you may run into an error such as IOError: Can't write data (Inflate() failed). These errors may be related to an open bug in H5py. However, the following tips may help you to find a workaround.

WESTPA may present you with such an error when unable to read or write a data set. In the case that a simulation gives this error when you attempt to run it, it may be helpful to check if a data set may be read or written to using an interactive Python session. Restarting the simulation may require deleting and remaking the data set. Also, this error may be related to compression and other storage options. Thus, it may be helpful to disable compression and chunked storage. Note that existing datasets will retain compression and other options given to them at the time of their creation, so it may be necessary to truncate an iteration (for example, using w_truncate) in order for changes to take effect.

This error may also occur during repeated opening (e.g., 1000s of times) of an HDF5 data set. Thus, this error may occur while running analysis scripts. In this case, it may be helpful to cache data sets in physical memory (RAM) as numpy arrays when they are read, so that the script loads the dataset a minimal number of times.

  • Dynamics Packages

WESTPA was designed to work cleanly with any dynamics package available (using the executable propagator); however, many of the tips and tricks available on the web or the user manual for these packages make the (reasonable) assumption that you will be running a set of brute force trajectories. As such, some of their guidelines for handling periodic boundary conditions may not be applicable.

  • How can I restart a WESTPA simulation?

In general restarting a westpa simulation will restart an incomplete iteration, retaining data from segments that have completed and re-running segments that were incomplete (or never started).

In case that the iteration data got corrupted or you want to go back to an specific iteration and change something, you need to delete all the trajectory segments and other files related to that iteration and run w_truncate on that iteration. This will delete westpa’s information about the nth iteration, which includes which segments have run and which have not. Then restarting your westpa simulation will restart that iteration afresh.


  • Periodic Boundary Conditions

While many of the built in tools now handle periodic boundary conditions cleanly (such as g_dist) with relatively little user interaction, others, such as g_rms, do not. If your simulation analysis protocol requires you to run such a tool, you must correct for the periodic boundary conditions before running it. While there are guidelines available to help you correct for whatever conditions your system may have here, there is an implicit assumption that you have one long running trajectory.

It will be necessary, within your executable propagator (usually to run trjconv (typically, two or three times, depending on your needs: once to remove the periodic boundary conditions, then to make molecules whole, then to remove any jumps). If no extra input is supplied (the -s flag in GROMACS 4.X), GROMACS uses the first frame of your segment trajectory as a reference state to remove jumps. If your segment’s parent ended the previous iteration having jumped across the box barrier, trjconv will erroneously assume this is the correct state and ‘correct’ any jump back across the barrier. This can result in unusually high RMSD values for one segment for one or more iterations, and can show as discontinuities on the probability distribution. It is important to note that a lack of discontinuities does not imply a lack of imaging problems.

To fix this, simply pass in the last frame of the imaged parent trajectory and use that as the reference structure for trjconv. This will ensure that trjconv is aware if your segment has crossed the barrier at time 0 and will make the appropriate corrections.


  • I’m trying to profile a parallel script using the –profile

    option of bin/west. I get a PicklingError. What gives?

When executing a script using –profile, the following error may crop up:

PicklingError: Can't pickle <type 'function'>: attribute lookup __builtin__.function failed

The cProfile module used by the –profile option modifies function definitions such that they are no longer pickleable, meaning that they cannot be passed through the work manager to other processes. If you absolutely must profile a parallel script, use the threads work manager.