Re: [AMBER] Problem with pmed installation: Amber 10

From: Jason Swails <>
Date: Mon, 21 Jun 2010 10:18:19 -0400


On Mon, Jun 21, 2010 at 6:53 AM, Devlina Chakravarty <> wrote:

> Hi! I am trying to get pmed working for 8 node blade server with Red Hat
> Enterprise 5, my machine doesn't have a ifort or Compaq Fortran 90 or any
> other mentioned in the config_data directory, it has gfortran. To make the
> installation work I had defined other platform/compiler/parallel option/fft
> option combinations by creating a file:
> config_data/linux_em64t.gfortran.lam, the contents of the file are given
> below:
> CPP = /lib/cpp
> CPPFLAGS = -traditional -P
> F90 = gfortran
> F90FLAGS = -c -auto
> F90_OPT_DBG = -g -traceback
> F90_OPT_LO = -tpp7 -O0
> F90_OPT_MED = -tpp7 -O2
> F90_OPT_HI = -tpp7 -xP -ip -O3
> F90_OPT_DFLT = $(F90_OPT_HI)

Some of the optimization flags look like they may be ifort-specific (i.e.
-xP and/or -ip, and I've never seen -tpp7).

> CC = gcc
> LOAD = gfortran

I would suggest using mpif90 instead of gfortran, just make sure that mpif90
comes from the (working) MPI you want to use, and that it wraps the gfortran
compiler (mpif90 -show will help you here).

> LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)

-lsvml is, I'm quite sure, an intel compiler specific library. As is -limf.
 And IFORT_RPATH basically confirms that you attempted to hijack the ifort
config_data file and didn't really make any changes. Different compilers
have different flags that they use.

> Somehow I can't get it working. Does pmem support gfortran,if not what
> would
> be the fortran compilier for my machine specification?

I would not imagine the above would work, but you have to be more specific.
 First of all, you created the file with .lam on the end, but didn't define
any MPI variables (i.e. MPI_DEFINES), etc. Also, like I said, it looks like
you just changed ifort to gfortran and didn't change any of the
ifort-specific flags.

I've attached a config.h file that you can use (so you do not need to run
the configure script). This should work as long as you have a working MPI
in which the mpif90 works. Place this in $AMBERHOME/src/pmemd and make sure
that $MPI_HOME is set appropriately, then run make install in that

All the best,

> Thanks in advance!
> --
> Devlina Chakravarty
> Bose Institute
> Kolkata
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student

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Received on Mon Jun 21 2010 - 07:30:14 PDT
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