[gmx-users] Re: md.log i/o error in futil.c +459

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 11 08:46:45 CEST 2012

On 10/06/2012 5:50 PM, Inon Sharony wrote:
>  Hi Mark! Thanks for the response. Just to follow up, the problem was
>  that another program was deleting md.log before it could be accessed.
>  This is entirely not the fault of GROMACS, however a more descriptive
>  error message could have saved us some time (e.g. "md.log not found"
>  as opposed to "md.log could not be opened" instead of "file i/o
>  error"). Also, I still don't understand under which directory futil.c
>  is located. I would check whether this file outdated and change the
>  error message accordingly if it is.

Thanks for the thought.

One problem is that there are a wide range of circumstances that can 
provoke the conditions that mdrun detected in your case, e.g. missing 
file, network file system unavailability, invalid file permissions. At 
least some of those can be transient, also, so any detective work mdrun 
might do subsequent to an I/O failure might be inaccurate, or depend on 
details of the OS and file system in use. Unfortunately, GROMACS 
developers don't have the time to write and test code that can deal with 
all possible such contingencies, so the burden of solving the problem is 
pushed to those who know the most about their local conditions. This 
lets the GROMACS devs spend more time doing what they do best :-) Free 
software will be imperfect - and software for which you paid money is 
rarely fully satisfactory either!

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