Re: [AMBER] Could not read velocities from restart file

From: Ross Walker <>
Date: Tue, 10 Apr 2012 11:41:49 -0700

> -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/1.rst
> -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/2.rst
> -rw-r--r-- 1 dave dave 252901 2012-04-10 08:33 New/3.rst
> -rw-r--r-- 1 dave dave 245309 2012-04-10 12:59 New/4.rst

This is the problem - 4.rst is shorter than the rest of the restart files.
This is a problem that has only appeared recently - this code has worked
fine for many years. Something has changed in the way certain versions of
Linux uses write buffers - It is extremely dangerous and I am bewildered why
specific versions of Linux would choose to do this - It seems the buffer is
only ever flushed if the file is closed.

I would like to start documenting specifically which versions of Linux do
this. Also does the same thing happen with mdcrd and output files (which
also aren't closed during a run). It seems to me there are dangerous write
buffer settings being set by default.

There are two options to fix this:

1) Have pmemd (and probably sander too) open and close all files on every
write. This is undesirable since it will hurt performance a lot.

2) Find out what setting is being, rather foolishly set, on specific new
linux configs and then figuring out what /proc setting needs to be updated
to disable this. Then document that this needs to be set startup / login
scripts that have permission to edit /proc.

We can fix the restart issue with an open and close since one typically only
writes this every hundred thousand steps or so but I suspect a similar issue
is occurring with the mdcrd and mdout files that mean these might not match
where the restart file is in some cases. So it is not a very satisfying fix.

Can everybody who has seen this issue please post the specific version of
Linux they are running and we can try to see if there is a correlation.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Apr 10 2012 - 12:00:05 PDT
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