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

Christopher Neale chris.neale at mail.utoronto.ca
Fri Sep 27 04:35:16 CEST 2013

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 
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,

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