[AMBER] installation of ambertools-- help

From: Nyla Zaman <nyla.zaman.hotmail.com>
Date: Thu, 14 Jul 2011 22:20:15 +1030

specs of my system are :

OS information
OS: Linux i686
System: openSUSE 11.4 (i586)
KDE: 4.6.00 (4.6.0) "release 6"

CPU Information
Processor (CPU): Intel(R) Core(TM)2 Duo CPU E8600 . 3.33GHz
Speed: 2,000.00 MHz
Cores: 2

I followed the following procedure to install amber 10 on my system whose specs have been given above:

COMMAND on terminal
cd usr/local/amber10/src

./configure_at --help

Usage: ./configure_at [flags] compiler

    where compiler is one of:

        gcc, icc, solaris_cc, irix_cc, osf1_cc

    If not specified then gcc is used.

    Option flags:

      -mpi use MPI for parallelization
      -scalapack use ScaLAPACK for linear algebra (utilizes MPI)
      -openmp Use OpenMP pragmas for parallelization (icc, solaris_cc,gcc(>4.2))
      -opteron options for solaris/opteron
      -ultra2 options for solaris/ultra2
      -ultra3 options for solaris/ultra3
      -ultra4 options for solaris/ultra4
      -bit64 64-bit compilation for solaris
      -perflib Use solaris performance library in lieu of LAPACK and BLAS
      -cygwin modifications for cygwin/windows
      -p4 use optimizations specific for the Intel Pentium4 processor
      -altix use optimizations specific for the SGI Altix with icc
      -static create statically linked executables
      -noX11 Do not build programs that require X11 libraries, e.g. xleap.
      -nobintraj Delete support for binary (netCDF) trajectory files
      -nosleap Do not build sleap, which requires unantiquated compilers.

    Environment variables:
      MKL_HOME If present, will link in Intel's MKL libraries (icc,gcc)
      GOTO If present, and MKL_HOME is not set, will use this location
                  for the Goto BLAS routines


./configure_at gcc

Setting AMBERHOME to /usr/local/amber10
Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On Fedora Core 5 install an xorg-x11-devel package.
    On RedHat8 install an XFree86-devel package.
    For the moment Amber will be configured not to build XLEaP.

Testing the C compiler:
      gcc -m32 -o testp testp.c

Obtaining the C++ compiler version:
      g++ -v
The version is
./configure_at: line 509: [: too many arguments

Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
./configure_at: line 538: g77: command not found
./configure_at: line 539: ./testp: No such file or directory
Unable to compile a Fortran program using g77 -O2 -fno-automatic -finit-local-zero

Testing the gfortran compiler:
     gfortran -O1 -fno-automatic -o testp testp.f

Testing flex:
./configure_at: line 583: flex: command not found
Unable to run flex; this is recommended for NAB
Please check your PATH, or install the program

We will try to solider on with precompiled files

cp: cannot stat `lex.*.c': No such file or directory

Configuring netcdf; (may be time-consuming)

netcdf configure returned 127
NETCDF configure failed! Check the netcdf_config.log file

i would nee help in this regard that what should i do to resolve this problem? either flex was not installed on the system correctly or what steps should i follow to install it correctly on my system?

looking forward for you’re response:

Nyla Zaman
M.phil student Bioinformatics

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Received on Thu Jul 14 2011 - 05:00:03 PDT
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