Re: AMBER: recompiling amber8

From: Carsten Detering <>
Date: Tue, 03 Aug 2004 17:55:04 +0200

Dear David and Robert,

I didnt imply a connection between the bugfix of pbsa and the
unsuccessful recompilation. Sorry if it sounded that way.

I had actually used the setenv command, I guess I wanted to say that I
had set the variable, and then wanted to write the command, apologies
for the confusion.

Meanwhile I solved the problem by pointing to the correct mpich dir.
Thanks for pointing that out. One question here: is it necessary to
point to the .../mpich/ch_p4 respectively the .../mpich/ch_p4mpd dir, so
  that it finds the libraries there? Or is .../mpich sufficient?

Do the MKL libraries come with the intel compiler? I dont have the mkl61
dir in my /opt/intel/ directory.

Thanks a lot again for your help.


David A. Case wrote:

> On Mon, Aug 02, 2004, Carsten Detering wrote:
>>after fixing a bug in pbsa (#4 in amber8) I needed to recompile amber,
>>which worked ok for the serial version. For parallel however, the
>>compilation interrupted with an error:
> First: the fix to pbsa has nothing to do with problems you may have compiling
> sander. The two codes are unrelated, and sander does not use any of the
> files in $AMBERHOME/src/pbsa.
>>ew_dipole_recip.o: In function `do_pmesh_dipole_kspace_':
>>ew_dipole_recip.o(.text+0x5c8): undefined reference to `mpi_barrier_'
>>ew_dipole_recip.o(.text+0x74e): undefined reference to `mpi_barrier_'
>>ew_dipole_recip.o(.text+0xa64): undefined reference to `mpi_barrier_'
> You should check your $LOADLIB variable in config.h: is it actually pointing
> to the correct place to find the mpich libraries? Have you previously
> compiled a parallel sander?
> There are detailed instructions for setting up mpich here:
>>set AMBERHOME /usr/local/amber8
>>set MPICH_HOME /usr/local/mpich
> I suspect that each of the above should use "setenv" rather than "set". It
> may be that AMBERHOME and MPICH_HOME are not really in your environment, so
> that the Makefile may not see them.
>>Also, I am missing the MKL libraries. When I configure, I get
>># ./configure -mpich ifc7
>>AMBERHOME is set to /usr/local/amber8
>>Setting up Amber configuration file for architecture: ifc7
>>Using parallel communications library: mpich
>>MPICH_HOME is set to /usr/local/mpich
>>The MKL_HOME environment variable is not defined.
> Again, you need to "setenv" (not just "set") MKL_HOME to point to the
> location of the MKL libraries on your machine. This is typically (but not
> always) in a place like /opt/intel/mkl61.
> ...good luck...dac
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Received on Tue Aug 03 2004 - 17:53:01 PDT
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