AMBER Archive (2009)

Subject: Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi

From: Alan (alanwilter_at_gmail.com)
Date: Wed Jun 10 2009 - 11:26:13 CDT

Thanks David.
Indeed, I tried many options and I put here the one that I guess it can be a
starter:

make clean

./configure_amber -nosanderidc -mpi -p4 gfortran

make -e AMBERBUILDFLAGS="-I/sw/include" -j 2 parallel

I got:

[snip]

Undefined symbols:

  "_mpi_reduce_", referenced from:

      ___decomp_MOD_collect_dec in decomp.o

    ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o

[long snip]

      ___ncsu_sander_hooks_MOD_rem_preinit in ncsu-sander-hooks.o

  "_mpi_isend_", referenced from:

      _zx_xy_transpose_ in ew_fft.o

      _xy_zx_transpose_ in ew_fft.o

      ___fft_MOD_transpose in spatial_fft.o

      ___fft_MOD_ftranspose in spatial_fft.o

ld: symbol(s) not found

collect2: ld returned 1 exit status

make[1]: *** [sander.MPI] Error 1

make: *** [parallel] Error 2

I was hoping that someone here in the list would have done it for mac intel
already and could share his/her recipe.

Cheers,
Alan

On Wed, Jun 10, 2009 at 16:34, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Wed, Jun 10, 2009, Alan wrote:
>
> > I am using a mac intel (old macbook pro 32 bit only), with Fink (openmpi)
> > and intel compilers.
> >
> > Does anyone have a suggestion of how to do this? I have tried:
> >
> > make clean
> >
> > ./configure_amber -mpi ifort_macosx
> >
> > make -j 2 parallel
> >
> > for no avail.
>
> What does "no avail" mean??? Without knowing the error(s), it's hard to
> be of much help. You could certainly try to leave out the "-j 2" flag:
> there
> may be glitches with parallel *compilation* (as opposed to parallel
> execution
> of the resulting executable). But I'm just guessing here...
>
> ...dac
>
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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