AMBER Archive (2008)

Subject: AMBER: Installation Problem of AMBER10

From: bhargav patel (
Date: Thu Jun 19 2008 - 05:57:26 CDT

at 4:10 PM
Subject: Installation Problem of AMBER10

I am trying to install AMBER10 on my Sun Ultra 40 workstation with

with ./configure_amber -help i get the following message.

# ./configure_amber -help

Usage: ./configure [flags] [compiler/architecture]

where <compiler/architecture> is one of:

compaqf90, hpf90, ifort, pgf90, sgi_altix, sgi_mips,

sparc, xlf90_aix, xlf90_suse, xlf90_macosx, xlf90_bluegene,

ifort_macosx, g95, gfortran, pathscale

Parallel option flags:

-mpi Use native MPI (assumes that the proper path will be searched)

-mpi2 Like -mpi, but assumes mpi2 compatibility

-nopar Explicit request of no MPI, the default

-lamsource Use LAM/MPI (compile from source code)

-lam Use (existing) LAM/MPI (MPI_HOME must be set)

-mpich Use MPICH (MPI_HOME must be set)

-mpich2 Use MPICH2 (MPI_HOME must be set)

-openmpi Use OpenMPI (MPI_HOME must be set)

-intelmpi Use Intel MPI (MPI_HOME must be set,

e.g. to /opt/intel/mpi/2.0)

-scali Use scali MPI (MPI_HOME must be set, e.g. to /opt/scali)

Platform option flags:

-gnucompat Add a second underscore to some symbols to maintain

GNU link compatibility (g95, gfortran, pgf90).

-p4 Optimize for Pentium 4 processor (pgf90,g95,

gfortran, pathscale). Adds SSE1, SSE2 vectorisation

where available.

-cygwin Add CygWin flags for Windows (g95, gfortran).

General flags:

-mmtsb Request building sander for MMTSB.

-static Static linking, i.e., prevent linking with shared libraries.

-verbose Add verbose compiler comment and warning flags.

-nobintraj Do not include support for binary (netCDF) trajectory files

-nolfs Remove compile flags for Large File Support

-nosanderidc Do not include support for IDC>0 in Sander.

Environment variables:

MKL_HOME Root directory of the Intel Math Kernel Library

for example, /opt/intel/mkl/8.0.

The MKL helps some with performance, but it is generally

not a big deal if you leave this variable empty.

GOTO Location for the "Goto" optimized blas library; this is

used if MKL_HOME is *not* defined.


Can anyone tell me which flag and compiler I shuold use for my system for my

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