Re: [AMBER] Problem during parallel installation

From: Pratul Agarwal <>
Date: Tue, 19 Feb 2019 13:45:39 +0000


Amber12 is an fairly outdated version of AMBER, while Openmpi 4.0.0 is much newer. The two versions may have compatibility issues, as you are seeing.

Possible solution is for you to upgrade to Amber 18, a lot has been updated and changed since Amber12 was released.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 2/19/2019 10:05 AM, Sunita Patel wrote:

Dear amber-users,

I am trying to install amber12 to extend my earlier ran simulations. I am
having problem during parallel installation. Pls have a look on the error

Openmpi-4.0.0 is installed and path is already set.

Your suggestion will be highly appreciated.

With best regards,
MPITypeCast.o: In function `DefineMPITypes':
MPITypeCast.c:(.text+0x81): undefined reference to `MPI_Type_struct'
MPITypeCast.c:(.text+0xde): undefined reference to `MPI_Type_struct'
MPITypeCast.c:(.text+0x128): undefined reference to `MPI_Type_struct'
MPITypeCast.c:(.text+0x172): undefined reference to `MPI_Type_struct'
MPITypeCast.c:(.text+0x1fb): undefined reference to `MPI_Type_struct'
collect2: error: ld returned 1 exit status
Makefile:147: recipe for target
'/home/sunita/softwares/amber12/bin/mdgx.MPI' failed
make[2]: *** [/home/sunita/softwares/amber12/bin/mdgx.MPI] Error 1
make[2]: Leaving directory
Makefile:117: recipe for target 'parallel' failed
make[1]: *** [parallel] Error 2
make[1]: Leaving directory '/home/sunita/softwares/amber12/AmberTools/src'
Makefile:7: recipe for target 'install' failed
make: *** [install] Error 2
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Received on Tue Feb 19 2019 - 06:00:02 PST
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