[gmx-users] "Illegal instruction" error from alchemical-gromacs.py

Michael Shirts mrshirts at gmail.com
Fri Sep 27 04:53:22 CEST 2013

Hi, Chris-

The best place to file this issue is the SimTK pymbar page, rather
than alchemistry.org, since it's a pymbar problem.

We have collaborators that may have updated the pymbar.py recently.
I'll try to get this stabilized in the very near future.

Testing quickly, my best guess is that it's not alchemical-gromacs.py
(latest version seems to work fine for me), but the pymbar
installation that is causing problems.  Give the illegal instruction
calculations, the helper C++ code is probably causing a problem;
perhaps it compiled using headers from the wrong version of numpy.

In most cases, the best way is to explicitly force it to use the pure
python. If you just delete the compiled _pymbar.so, then it will
default to pure Python.   It may be slower (5-10x) but it should still
finish in a minute or two.

I'm working on getting instructions for g_bar up there in
alchemistry.org as well, but there are some bugs in g_bar that I am
dealing with.

On Thu, Sep 26, 2013 at 10:35 PM, Christopher Neale
<chris.neale at mail.utoronto.ca> wrote:
> Dear Users:
> I'm having difficulty running MBAR after some free energy calculations (MBAR via alchemical-gromacs.py obtained from alchemistry.org).
> The input options to alchemical-gromacs.py have obviously changed since the site at
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy
> was updated, but I've taken a look at the python source and it seems as if my invocation below should work.
> Nevertheless, I get an "Illegal instruction" error (See below).
> gpc-logindm02-$ ls ANALYSIS/
> ethanol.0.dhdl.xvg  ethanol.2.dhdl.xvg  ethanol.4.dhdl.xvg  ethanol.6.dhdl.xvg  ethanol.8.dhdl.xvg
> ethanol.1.dhdl.xvg  ethanol.3.dhdl.xvg  ethanol.5.dhdl.xvg  ethanol.7.dhdl.xvg
> gpc-logindm02-$ python /project/p/pomes/cneale/GPC/exe/pymbar/trunk/examples/alchemical-free-energy/alchemical-gromacs.py -d ANALYSIS -p ethanol. -t 300 -s 1000 -v
> Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate.  The estimate presumes the use of many statistically independent samples.  Tests should be performed to assess whether this condition is satisfied.   Be cautious in the interpretation of the data.
> Started on Thu Sep 26 22:32:05 2013
> Illegal instruction
> (omitting the -t -s and -v flags yields the same error).
> I realize that I'm hijacking the gromacs list a little bit here but there is no mailing list for http://www.alchemistry.org/
> and it seems like a good idea to have these Q&A's archived.
> Thank you,
> Chris.
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