Dear Sir,
Thank you, sir, for your helpful response. OpenMPI version 4 is not working
with amber18. we successfully install amber18 with OpenMPI 3.1.4.
On Wed, May 22, 2019 at 5:36 PM David A Case <david.case.rutgers.edu> wrote:
> 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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>
--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Thu May 23 2019 - 07:00:02 PDT
