I suggest sending the ptraj output to a file for each case and diffing them.
On Thu, Mar 11, 2010 at 1:55 PM, Ganesh Krishnan <hereisganesh.yahoo.com>wrote:
> It is indeed the same executable.
>
> In fact, I just found out that I don't even have to submit it to LSF to
> reproduce the error. If I run a shell script on the local node, the same
> thing happens (pdb files are messed up). Executing the exact same command on
> the command line works perfectly.
>
> Additionally, ptraj seems to be reading frames that don't exist when run
> from the shell script. My trajin command is:
>
> trajin 1 40000 100
>
> In some cases my trajectory has less than 40000 frames. When run in shell
> script mode, it generates snapshots upto 40000 even though those frames
> don't exist. This problem doesn't occur when run from the command line.
>
> --- On Thu, 3/11/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> From: Bill Ross <ross.cgl.ucsf.edu>
> Subject: Re: [AMBER] Ptraj problems
> To: amber.ambermd.org
> Date: Thursday, March 11, 2010, 10:27 AM
>
> > I am trying to generate pdb snapshots using ptraj. I am running
> > into a very strange issue. When I try to generate the snapshots
> > by submitting a ptraj job to LSF (using bsub), I have very weird
> > snapshots (the bonds are messed up). But when I use the exact same
> > command and run it on the local node, it works perfectly.
>
> Is it the same executable? If so, it sounds like you are mixing
> up your files, maybe because of different path interpretation in
> the batch environment. This could still be the case if the executable
> is different, but there is an added possibility of a bug in the one
> used in the batch env.
>
> Bill
>
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Received on Thu Mar 11 2010 - 11:00:04 PST
