RE: [AMBER] PMEMD compiling errors

From: Ross Walker <>
Date: Fri, 23 Apr 2010 12:09:19 -0700

Hi Dian,

> ifort: command line warning #10120: overriding '-O2' with '-O3'
> fortcom: Error: charmm.f90, line 275: Declaration of module
> conflicts with a previous declaration
> module charmm_mod
> -------^
> fortcom: Error: charmm.f90, line 275: Declaration of routine
> conflicts with a previous declaration
> module charmm_mod
> -------^
> compilation aborted for charmm.f90 (code 1)

This makes no sense at all. It is complaining that line 275 of charmm.f90
conflicts with itself. I suspect you did not do a make clean here. Try
starting from a completely new Amber10.tar.bz2. Untar it and apply
bugfix.all from - download it fresh
because there have been some recent changes. Then try compiling again. Edit
the config.h file. Replace ifort with mpif90, icc with mpicc. Also remove
the contents of the F90_OPT_HI line and replace it with '-fast'

Also change the MPI_LIBS and MPI_LIBDIR entries to be blank. (Note all of
these complexities building AMBER 10 pmemd are finally gone in the upcoming
AMBER 11). Also remove and -DSLOW_NONBLOCKING_MPI if it is there.

Then try again. If you still have problems try a newer version of the Intel
compiler. I can confirm that ifort v10.1.018 works great.

> similar thing by adding "-DCHARMM" at the end of same line, but it
> didn't
> help.

There is no ifdef CHARMM option.
> Actually, I don't need CHARMM at all, so I deleted object files that
> related
> to charmm, including charmm.o charmm_gold.o, from the the Makefile, but
> still got the same error.

The issue is much deeper than a simple issue with CHARMM here. The compiler
looks to be very confused, either because of old module files hanging around
or a broken version of the Intel compiler (not uncommen). Starting from a
completely clean tree and applying the latest bugfix.all will likely go a
long way to helping.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Fri Apr 23 2010 - 12:30:02 PDT
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