AMBER Archive (2008)

Subject: RE: AMBER: The list-directed or NAMELIST READ statement cannot be completed

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 17 2008 - 11:55:22 CDT

Hi Rebecca,

> I am trying to do replica exchange calculation using Amber 9.
> First of all I am trying to do an equilibration using this input for each
> one of my 10 replicas (I only change the temperature from one to another
> one):

I hope you are also changing the random number seed (ig) for each replica. This is extremely important when running Langevin dynamics.

> Equilibration
> &cntrl
> nstlim = 100000, dt = 0.002,
> ntx = 1, temp0 = 300.00, ig=28615,
----^^^^^^
|
Are these tabs? This could cause a problem if they are tabs.

> gamma_ln = 1.0, ntt = 3,
> ntc = 2, ntf = 2, ntb = 0, nmropt = 1,
> ntwx = 500, ntwr =100000, ntpr = 500,
> cut = 999.0, rgbmax = 999.0,
> nscm = 1000, igb = 5, irest=0,
> &end

This should probably be a / and not &end. &end works on some compilers but not others - I don't know what happens if you mix &end and / in the same file as you are doing.

> &wt TYPE= END
> /
> DISANG=1ftg_dry_chir.dat

I assume this file exists and is in the same directory as the mdin file and available on all nodes. The same with the mdin file - I assume all nodes can see the mdin file in the same path?

> As a groupfile I use:
>
> -O -rem 0 -i equilibrate.mdin.001 -o equilibrate.mdout.001 -c min.rst -r
> equilibrate.rst.001 -x equilibrate.mdcrd.001 -inf equilibrate.mdinfo.001 -
> p
> 1ftg.dry.top

This looks fine as long as your input files all have the correct names here and this running from the correct path.

> I get this error from the calculation, writen a lot of times in the error
> file:
>
> 1525-049 The list-directed or NAMELIST READ statement cannot be completed
> because the input data did not specify a valid delimited character string.
> The program will recover by ignoring the item in the READ statement.
> (...)
> 525-049 The list-directed or NAMELIST READ statement cannot be completed
> because the input data did not specify a valid delimited character string.
> The program will recover by ignoring the item in the READ statement.
> [6] MPI Abort by user Aborting program !
> [6] Aborting program!
> srun: error: s11c4b09: task[0,2]: Exited with exit code 255
> srun: error: s11c4b09: task[1,3]: Killed
> srun: Job Failed

Another thing to check, make sure your input file is in UNIX text format, I.e. just has a carriage return at the end of each line and not a carriage return + line feed. Some instances of Linux include a tool called dos2unix that you could run on the input file to force it to be Unix format.

> In the output file I can see:
>
> Could anyone help me to find the reason of this error, please?
> Thank you very much in advance for you help.

What about the mdout files that are produced do you see anything in those? If there are namelist read problems this is where they will likely show up.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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