Dear Ross,
Thank you very much for your help. Sorry to bother you again!
These are the files in exe directory:
am1bcc bondtype cpinutil.pl espgen makeDIP_RST.dna
makeSHF_RST molsurf prepgen senergy teLeap
antechamber calcpka.pl crdgrow makeANG_RST makeDIP_RST.protein
mm_pbsa.pl parmcal README sviol tleap
atomtype CPin.pm database makeCHIR_RST makeDIST_RST
mm_pbsa_statistics.pl 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
libraries.
-mmtsb Request building sander for MMTSB.
-static Static linking, i.e., prevent linking with shared
libraries.
-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 $AMBERHOME/test and
make test. However, it leads to the error message below.
What should I do next? Based on the inforamtion about, do I need to buy a
compiler, if yes, could you mind to recommend a compiler that is compatible
with amber8 and could solve the problems I raised above?
Many thanks in advanced.
Annie
>From: "Ross Walker" <ross.rosswalker.co.uk>
>Reply-To: amber.scripps.edu
>To: <amber.scripps.edu>
>Subject: RE: AMBER: Amber install on RedHat Linux
>Date: Wed, 3 May 2006 19:36:45 -0700
>
>Dear Annie,
>
> > I am a new user to Amber, and I am trying to install the
> > Amber 9 with a
> > fortan compiler 77 on our Redhat linux system.
>
>Which compiler are you using? Note Amber 9 requires a Fortran 95 compiler.
>
> > can I next so as to get the installation done?
> > [PATH]$ 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 $AMBERHOME/exe/ and see what files are in there. Also
>take a look at the messages that came up after you typed make in
>$AMBERHOME/src/
>
>All the best
>Ross
>
>
>/\
>\/
>|\oss Walker
>
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
>Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>be read every day, and should not be used for urgent or sensitive issues.
>
>
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Received on Thu May 04 2006 - 17:10:40 PDT
