AMBER Archive (2004)

Subject: Re: AMBER: Additional note on vs. LD_LIBRARY_PATH

From: David E. Konerding DSD Staff (
Date: Tue Apr 27 2004 - 17:11:33 CDT

Robert Duke wrote:

>Folks -
>I should have included this in my previous posting. All my comments about
>the caveats assume that you are set up to use rsh or ssh as your mechanism
>of starting processes (what I do using ch_p4 and mpirun on my machines). If
>you use ch_p4mpd and the mpd demon on your systems, then environments should
>not be inherited, and it is definitely preferable to use as
>opposed to LD_LIBRARY_PATH. Dave K. did not report problems with limits.
>Regards - Bob Duke

Actually, I did have the problem with stack size limits, and they
magically disappeared when I stopped using -static. But, the program
crashes for another reason (obscure one,
not easy to debug because IFC8's -g flag causes PMEMD to fail to
compile. Bob- have you seen this as well?) if I compile with -static.

For those of you using mpd, if you do not want to modify
/etc/, use an mpirun command line like:

 mpirun -wdir `pwd` -m machines.all -np 8 -g 2 ./pmemd -O -i mdin -p
prmtop -c inpcrd.equil -o mdout -MPDENV-

The -MPDENV- part at the end sets the LD_LIBRARY_PATH in the child
pmemds running within the MPI environment.

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