Re: AMBER: problem to compile PMEMD?

From: Robert Duke <>
Date: Tue, 29 Jan 2008 18:09:05 -0500

Not sure what you have done here. You configure for uniprocessor, and then
are getting errors over mpi stuff not being defined. Did you hand-edit the
config.h for pmemd to include -DMPI (not a good idea...)? Something else
nonstandard? Did you read the README under amber9/src/pmemd? If you send
your config.h with info about your machine, I'll look at it, but you are
really not providing much info here, and to do the parallel build, it really
helps to have somebody at your facility that knows how to build/test mpi.
Now, if you got parallel sander running okay, it should be relatively easy
to get pmemd running too...
Regards - Bob Duke

----- Original Message -----
From: <>
To: <>
Sent: Tuesday, January 29, 2008 5:45 PM
Subject: AMBER: problem to compile PMEMD?

> Dear Amber's users,
> I configured PMEMD but failed to install it !!
> I tried both nopar and mpich and got the same error
> any help !
> thanks
> fatima
> -------------------------------------------------------------
> ./configure linux64_opteron ifort nopar
> Intel ifort compiler found; version information:
> Version 9.0
> Use Intel MKL? (better performance) (answer yes or no):
> no
> File config_data/fft.pubfft being used...
> File config_data/linux64_opteron.ifort being used...
> File config_data/interconnect.nopar being used...
> PMEMD Configurate successfully completed.
> hamilton [x86_64.linux] 78% make install
> .....
> pmemd.f90:(.text+0x58): undefined reference to `mpi_init_'
> pmemd.f90:(.text+0x6e): undefined reference to `mpi_comm_rank_'
> pmemd.f90:(.text+0x84): undefined reference to `mpi_comm_size_'
> pmemd.f90:(.text+0x9a): undefined reference to `mpi_comm_group_'
> pmemd.f90:(.text+0x6ca): undefined reference to `mpi_bcast_'
> nmr_calls.o: In function `nmr_calls_mod_mp_bcast_nmr_dat_':
> nmr_calls.f90:(.text+0x37f): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0x3a6): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0x5f8): undefined reference to `mpi_bcast_'
> nmr_calls.f90:(.text+0x621): undefined reference to `mpi_bcast_'
> ene_frc_splines.o:ene_frc_splines.f90:(.text+0x1e0): more undefined
> references
> to `mpi_bcast_' follow
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory
> `/data/hamilton/dch1fc/amber/amber9/src/pmemd/src'
> make: *** [install] Error 2
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Received on Wed Jan 30 2008 - 06:07:31 PST
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