AMBER Archive (2004)

Subject: RE: RE: AMBER: Amber 8 installation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 25 2004 - 12:27:23 CDT

Hi Fangyu,

Try compiling amber with static linking:

cd $AMBERHOME/exe
rm -f *
cd ../src
make clean
rm -f config.h
./configure -p4 -nopar -static ifort
make

After recompiling this problem should go away. It is most probably caused by
your LD_LIBRARY_PATH environment variable being set wrong. You should really
try and fix this but compiling amber as static means you won't have to worry
and you can move the executables onto other similar machines without having
to install all the intel compiler libraries on those machines.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of fangyu liang
> Sent: 25 June 2004 00:35
> To: amber_at_scripps.edu
> Subject: Re: RE: AMBER: Amber 8 installation
>
> Hi,
>
> I downloaded and installed all the necessary development
> tools. The crt1.o problem went away. But I got another
> problem. When I run 'make test', I got this:
>
> cd dmp; ./Run.dmp
>
> ../../exe/sander: error while loading shared libraries:
> libcxa.so.5: cannot open shared object file: No such file or diectory
>
> ./Run.dmp: Program error
>
> make: ***[test.sander.no_lmod]Error 1
>
> I searched the Amber email archives and didn't find a
> solution. Please tell me what is wrong. Thank you very much!
>
> Sincerely,
>
> Fangyu
> P.S Ross/Spookie: Thank you very much!
>
> ----- Original Message -----
> From: Ross Walker <ross_at_rosswalker.co.uk>
> Date: Thursday, June 24, 2004 3:38 pm
> Subject: RE: AMBER: Amber 8 installation
>
> > Hi Fangyu,
> >
> > This is a problem with the linux installation on your
> machine. Once again
> > the fountain of all knowledge (www.google.com) comes through:
> >
> http://www.google.com/search?sourceid=navclient&ie=UTF-8&oe=UT
> F-8&q=%2Fusr%2
> > Fbin%2Fld%3A+%2Fusr%2Flib%2Fcrt1%2Eo
> >
> > Note the second entry:
> >
> >
> http://softwareforums.intel.com/ids/board/message?board.id=11&
> message.id=119
> > 6&jump=true
> >
> > It seems that you may have a corrupted or missing installation of
> > glibc-devel.
> >
> > In fact I suspect you are missing all of the development
> libraries for your
> > system. If you intend to compile any programs these are
> essential. It is
> > probably best for you to contact the person in charge of
> your system and ask
> > them to install the development RPM's for you. You should
> then have another
> > go at compiling Amber 8.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk/ | PGP Key available on request |
> >
> >
> > > -----Original Message-----
> > > From: owner-amber_at_scripps.edu
> > > [owner-amber_at_scripps.edu] On Behalf Of fangyu liang
> > > Sent: 24 June 2004 15:25
> > > To: amber_at_scripps.edu
> > > Subject: AMBER: Amber 8 installation
> > >
> > > Hi,
> > >
> > > I am installing Amber 8 on a PC with latest Linux (SuSe 9.1)
> > > and Intel f90 compiler. Everything is fine until I run 'make
> > > serial'. Here is the entire message:
> > >
> > > Starting installation of Amber8 (serial) at Thu Jun 24
> > > 14:31:44 PDT 2004.
> > >
> > > mkdir ../exe
> > >
> > > mkdir: cannot create directory '../exe': File exists
> > >
> > > make: [serial] Error 1 (ignored)
> > >
> > > cd lib; make install
> > >
> > > make[1]: Entering directory '/home/owner/Desktop/amber8/src/lib'
> > >
> > > ifort -o new2oldparm new2oldparm.o nxtsec.o
> > >
> > > /usr/bin/ld: /usr/lib/crt1.o: No such file: No such file
> or directory
> > >
> > > make[1]: *** [new2oldparm] Error 1
> > >
> > > make[1]: Leaving directory '/home/owner/Desktop/amber8/src/lib'
> > >
> > > make: *** [serial] Error 2
> > >
> > > I used 'make serial -i' later on and tested it in the
> > > $AMBERHOME/test directory. Here is the message:
> > >
> > > cd dmp; ./Run.dmp
> > > .../../exe/sander: Command not found.
> > > ./Run.dmp: Program error
> > > make: *** [test.sander.no_lmod] Error 1
> > >
> > > Can someone please tell me what I did wrong? So I can have
> > > Amber8 working properly. Thank you very much!
> > >
> > > Sincerely,
> > >
> > > Fangyu Liang
> > >
> > >
> > > --------------------------------------------------------------
> > > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> >
> >
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> >
>
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