AMBER Archive (2004)

Subject: Re: AMBER: PMEMD Built ? Wont run..

From: Amber admin (amber-admin_at_scripps.edu)
Date: Tue May 11 2004 - 12:25:03 CDT

From: "Robert Duke"
To: <amber_at_scripps.edu>
Subject: Re: AMBER: PMEMD Built ? Wont run..
Date: Tue, 11 May 2004 12:08:11 -0400

Gary -
Looks like an invalid variable in the namelist. What are the contents of
pmemd.in? Are all the variables things read by pmemd? Which version of
pmemd are you using? There can also be problems with the namelist
terminator on some systems, and variation in what f77 vs. f90 vs. f95
consider valid input. Thus some fortrans expect termination with &end,
others with /, and there can be different requirements for comments in the
namelists (you have to read the compiler manual). Here though, I think you
just have an invalid variable name.
Regards - Bob Duke

----- Original Message -----
From: "Gary Waters" <gwaters_at_paracel.com>
To: <amber_at_scripps.edu>
Sent: Tuesday, May 11, 2004 12:00 PM
Subject: AMBER: PMEMD Built ? Wont run..

> Hi Everyone,
>
> I believe I built pmemd correctly with mpich.
> On mpich I can do some of the example and test runs fine, with no
> errors. Then I go over to pmemd and run my script, and get these
> errors. I do not know what is going on, can someone shed some light on
> my dilemma ?
>
> forrtl: severe (19): invalid reference to variable in NAMELIST input,
> unit 5, file /export/bionumerik/pmemd.in
> Image PC Routine Line Source
> pmemd 0811333F Unknown Unknown Unknown
> pmemd 080DF9AB Unknown Unknown Unknown
>
> Stack trace terminated abnormally.
> p2_29314: p4_error: net_recv read: probable EOF on socket: 1
> p10_11492: p4_error: net_recv read: probable EOF on socket: 1
> bm_list_17110: (0.444700) wakeup_slave: unable to interrupt slave 0 pid
> 17109
> bm_list_17110: (0.444772) wakeup_slave: unable to interrupt slave 0 pid
> 17109
> p9_11334: p4_error: net_recv read: probable EOF on socket: 1
> p15_9668: p4_error: net_recv read: probable EOF on socket: 1
>
> --
> Thanks,
> Gary Waters
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