AMBER Archive (2007)

Subject: RE: AMBER: Parallel Amber compilation problems !!

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 13 2007 - 12:33:25 CST


Dear Sampath,

I suspect that when you installed mpich in your home directory you did not
explicitly tell it to use the Intel ifort compiler. You should clean the
mpich installation and then rebuild it telling it to use ifort - something
like export FCC=ifort, F90=ifort - although you will need to chekc the mpich
documentation for the correct way of doing this.

Also check that you MPI_HOME and path variables are set to point to the
correct mpi installation. Do:

which mpirun

if you get /usr/bin/mpirun or something else which is not your new mpich
installation then you need to edit your path, likely in .bashrc/.cshrc to
make sure the mpich bin directory precedes /usr/bin etc.

Good luck,

Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Sampath Koppole
> Sent: Tuesday, November 13, 2007 06:05
> To: amber_at_scripps.edu
> Subject: AMBER: Parallel Amber compilation problems !!
>
> Hello,
> I am trying to compile Amber in parallel (after
> successfully compiling the serial version !!). I have
> tried to follow the instructions in the INSTALL file
> as closely as I can.
>
> To give you a little background:
>
> I installed (successfully) MPICH-1.2.7 (in my home
> directory) and set MPI_HOME to this directory by :
> setenv MPI_HOME $HOME/mpich-1.2.7p1/
>
> I then configured with "./configure -mpich -p4
> ifort_ia32"
>
> and did a "make clean" after which I ran "make
> parallel" but this crashes very early with the
> following:
>
> ---------------------------------------------------------
> evb_init.o(.text+0x741): In function `evb_init_':
> : undefined reference to `mpi_bcast_'
> evb_init.o(.text+0x77a): In function `evb_init_':
> : undefined reference to `mpi_bcast_'
> evb_init.o(.text+0x107e): In function `evb_init_':
> : undefined reference to `mpi_bcast_'
> evb_init.o(.text+0x141f): In function `evb_init_':
> : undefined reference to `mpi_bcast_'
> evb_init.o(.text+0x1970): In function `evb_init_':
> : undefined reference to `mpi_bcast_'
> .
> .
> .
> .
> goes on ...
> .
> .
> .
> .
> .
> .
> force.o(.text+0x80e3): In function `force_.A':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x810b): In function `force_.A':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x8132): In function `force_.A':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x8170): In function `force_.A':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x8198): more undefined references to
> `mpi_bcast_' follow
> make[1]: *** [sander.MPI] Error 1
> make[1]: Leaving directory
> `/netfs/people/camm/kopposa1/amber9/src/sander'
> make: *** [parallel] Error 2
> ------------------------------------------------------
>
> Is there something I have missed doing ??
>
> Thanks a lot for your help.
>
> With best regards,
> Sampath.
>
>
>
>
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