RE: AMBER: A question on AMBER8 installation

From: Ross Walker <>
Date: Thu, 14 Oct 2004 09:50:25 -0700

Dear Hwankyu,

> ./configure -p4 -nopar -ifort

You definitely did ./configure -p4 -nopar ifort here yes (I.e no - before
the ifort)?

> icc -c -O2 -o makeDIST_RST.o makeDIST_RST.c
> makeDIST_RST.c(338): warning #266: function declared implicitly
> if ( !lookuprtyp(atma.rnum,atma.nrtyp) ||

Don't worry about these. They are just warnings. The compiler thinks the
routines are declared implicitly because the call to the routine comes
earlier in the file than the actual routine and the function is not
prototyped at the beginning of the file. This occurs because icc is not
really smart enough to scan through the file twice before reporting
warnings. This sort of error is only a problem if it occurs at the link
stage (when all routines must have been declared in the object files or

> bondtype.o(.eh_frame+0x12): undefined reference to
> `__gxx_personality_v0'

Are you certain you did:

cd $AMBERHOME/src/
make clean

Before you did the make?

The reason I ask is because the __ in front of gxx_peronality_v0 looks like
the naming convention used by gcc. As far as I am aware icc only expects one
underscore. Hence it looks like all the object files were not cleaned from
the directory before you ran the make again.

If you have not done it, I would suggest the following:

Remove your existing amber8 directory tree.

1) Get hold of the original tar file from the amber8 cd (so you know it is
2) Untar this to a folder on your machine.
3) set AMBERHOME to this directory setenv AMBERHOME /path_to_inst/amber8
3) Obtain the latest bugfixes from here: - save it in the amber8
directory the untaring created.
4) Patch your amber8 copy with these bugfixes:
   patch -p0 -N -r patch_rejects < bugfix.all
5) cd into the src directory
   cd $AMBERHOME/src
6) Create the configure script
   ./configure -p4 -static -nopar ifort
7) Edit config.h and change all gcc and g++ to icc
8) clean everything
   make clean
9) make
10) cd $AMBEROME/test
11) make

See how you get on. The important thing is to make sure you are starting
from a clean un-aulterated copy of amber8.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Oct 14 2004 - 17:53:00 PDT
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