RE: AMBER: Amber install on RedHat Linux

From: a a <>
Date: Thu, 04 May 2006 15:37:34 +0800

Dear Ross,

Thank you very much for your help. Sorry to bother you again!

These are the files in exe directory:
am1bcc bondtype espgen makeDIP_RST.dna
makeSHF_RST molsurf prepgen senergy teLeap
antechamber crdgrow makeANG_RST makeDIP_RST.protein parmcal README sviol tleap
atomtype database makeCHIR_RST makeDIST_RST parmchk respgen sviol2 xleap

Did anything is missing?

In fact, before I type the "make -i" commands, and leads to the error
message that I mentioned earlier. It was what did I do:
[PATH bin]$ cd $AMBERHOME/src
[PATH src]$ ls
addles anal arpack carnal configure etc lapack lib
Makefile nmode pbsa protonate README resp
amber8 antechamber blas config.h divcon gibbs leap lmod
mm_pbsa nmr_aux pmemd ptraj README_EXE sander
[PATH src]$ /configure -help
bash: /configure: No such file or directory
[PATH src]$ ./configure -help

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

    where <compiler/architecture> is one of:

        absoft, compaqf90, efc7, hpf90, ifc7, ifort, ia64_ifort,
        pgf90, sgi_altix, sgi_mips, sparc, xlf90_aix, xlf90_suse.

    If not specified then the compiler is guessed.

    Parallel option flags:
      -lam Use LAM/MPI (LAM_HOME must be set)
      -mpi Use native MPI
      -mpich Use MPICH (MPICH_HOME must be set)
      -mplite Use MP_Lite (MPLITE_HOME must be set)
      -nopar Explicit request of no MPI, the default
      -scali Use SCALI (SCALI_HOME must be set)

    Platform option flags:
      -athlon Optimize for Athlon processor (intel,pgf90).
      -gnucompat Add a second underscore to some symbols to maintain
                    GNU compatibility (pgf90).
      -opteron Optimize for Opteron processor (pgf90).
      -p4 Optimize for Pentium 4 processor (intel,pgf90).
      -cygwin Add CygWin flags for Windows (absoft).

    General flags:
      -big Big systems support, ie, 8 byte integers and pointers.
      -fpp_prefix= Define the prefix for FPP preprocessing; default is "_".
      -lmod Request linking sander with Istvan Kolossvary's LMOD
      -mmtsb Request building sander for MMTSB.
      -static Static linking, i.e., prevent linking with shared
      -verbose Add verbose compiler comment and warning flags.

    Other environment variables:
      AMBERHOME Root directory of the Amber tree.
      MKL_HOME Root directory of the Intel Math Kernel Library
                     (intel,sgi_altix); for example, /opt/intel/mkl61.
                     The MKL is recommended for optimal performance.

[PATH src]$ ./configure -p4 ifort
AMBERHOME is set to /home/cmche/amber8/amber8
Setting up Amber configuration file for architecture: ifort
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
    The MKL is recommended for optimal performance.

The configuration file, config.h, was successfully created.


Then, I type the make serial command as follows:

PATH src]$ make serial
Starting installation of Amber8 (serial) at Thu May 4 15:04:30 HKT 2006.
mkdir ../exe
mkdir: cannot create directory `../exe': File exists
make: [serial] Error 1 (ignored)
cd lib; make install
make[1]: Entering directory `/PATH/src/lib'
cpp -traditional -P -I/PATH/src/include new2oldparm.f > _new2oldparm.f
ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
make[1]: ifort: Command not found
make[1]: *** [new2oldparm.o] Error 127
make[1]: Leaving directory `/PATH/src/lib'
make: *** [serial] Error 2
[PATH src]$


Since I suspect no compilation has done, I type "make -i" instead. It seems
compiling for several min, and then stop. So, I type cd $AMBERHOME/test and
make test. However, it leads to the error message below.

What should I do next? Based on the inforamtion about, do I need to buy a
compiler, if yes, could you mind to recommend a compiler that is compatible
with amber8 and could solve the problems I raised above?

Many thanks in advanced.


>From: "Ross Walker" <>
>To: <>
>Subject: RE: AMBER: Amber install on RedHat Linux
>Date: Wed, 3 May 2006 19:36:45 -0700
>Dear Annie,
> > I am a new user to Amber, and I am trying to install the
> > Amber 9 with a
> > fortan compiler 77 on our Redhat linux system.
>Which compiler are you using? Note Amber 9 requires a Fortran 95 compiler.
> > can I next so as to get the installation done?
> > [PATH]$ cd $AMBERHOME/test
> > [PATH]$ make test
> > cd dmp; ./Run.dmp
> > ../../exe/sander: Command not found.
>So the command was not found. Did the compilation complete okay? I doubt
>that it did. Check $AMBERHOME/exe/ and see what files are in there. Also
>take a look at the messages that came up after you typed make in
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
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Received on Thu May 04 2006 - 17:10:40 PDT
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