AMBER Archive (2003)

Subject: Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Nov 03 2003 - 13:31:34 CST

David -
Did you check if maybe you need to use icc (the intel c compiler) as your c
compiler? If so, define CC as icc in the machine file. I by default define
CC as gcc (the GNU c compiler, of course) because most folks have that, and
it interoperates fine with ifc. Perhaps it is out on your systems as
/usr/bin/cc? Or perhaps you do have the c compiler, but there is a problem
with the make being used? I have not checked a bunch of makes out, but the
Makefile structure and Compile script are pretty much "stock amber".
Regarding erfc(), I know that is available in the c math lib on a lot of
systems; I have just always used the amber defaults to get the code in the
system-specific diretories under Machines, avoiding any potential
compatibility issues. I don't know what the speed or precisions issues, if
any, are (but once you find the c compiler, you can use whichever you
prefer).
Regards - Bob

----- Original Message -----
From: "David E. Konerding" <dekonerding_at_lbl.gov>
To: <amber_at_scripps.edu>
Sent: Monday, November 03, 2003 1:41 PM
Subject: Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD

> Hi Robert,
>
> A couple thing I noticed trying to compile on an MPICH/GM cluster w/
> Intel 7 compiler
> 1) pmemd_clib.c doesn't get compiled so the link fails
> 2) erfcfun.o doesn't seem to be necessary; I added HAS_FTN_ERFC to the
> MACHINE file and it seems to work OK.
>
> Dave
>
>
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