Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7

From: David A Case <>
Date: Wed, 22 May 2019 08:03:30 -0400

On Wed, May 22, 2019, Rajarshi Roy wrote:

>I am facing an issue regarding the installation of the parallel version of
>AMBER 18 in our centos 7 workstations.
>after doing ./configure -mpi gnu
>I am getting;
>Warning: Could not link to boost. Ensure boost-thread, boost-system and
>boost headers are installed.

If you wish to run packmol_memgen, you should upgrade to AmberTools19:

   cd $AMBERHOME; ./update_amber --upgrade

(You should do this for reasons beyond improved boost compatibility.)

>MPITypeCast.c: In function ‘DefineMPITypes’:
>MPITypeCast.c:43:18: error: call to ‘MPI_Type_struct’ declared with
>attribute error: MPI_Type_struct was removed in MPI-3.0. Use
>MPI_Type_create_struct instead.

Looks like you are trying to use openmpi version 4: is that correct?
You can do this by compiling it yourself: go to AMBERHOME/AmberTools/src
and run the "configure_openmpi" command there. This will be build
openmpi and place the executables and libraries inside your AMBERHOME
folder where programs can find them.

Right now, AmberTools cannot be compiled with standard distributions of
openMPI version 4, because we still use deprecated calls like the one
listed above. (That particular one is fixed in AmberTools19, but there
is a remaining problem with CHARMM-related code in sander--developers
are encouraged to jump in and figure this one out.)

You should be fine with openMPI versions before 4.0, or with other MPI
stacks, like mpich.

...good luck...dac

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Received on Wed May 22 2019 - 05:30:02 PDT
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