AMBER Archive (2007)

Subject: RE: AMBER: amber 9

From: Sophie Barbe (sbarbe_at_insa-toulouse.fr)
Date: Wed Jan 10 2007 - 12:28:51 CST

Dear Ross,

I tried but then I have the following error :
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
                                          e.c
gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2
gcc -m32 -static -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getli
                                          tf.o pdb_sscanf.o pdb_write.o
vector.o zMatrix.o sort.o bag.o hash.o dictionar
            rtran.o displayer.o assoc.o atom.o byteArray.o collection.o
container.o interna teger.o oString.o
objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUti
                        rary.o chirality.o minimizer.o model.o parmLib.o
pdbFile.o tools.o variables.o p .o
mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLe
                                        o XrawRegistr.o xaCommand.o xaTools.o
xaAtomParmTable.o xaBondParmTable.o xaA
   mTable.o xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a
../Wc/libWcL r/X11R6/lib -lXt -lXext
-lSM -lICE -lX11 -lm -lpthread
/usr/bin/ld: cannot find -lXt
collect2: ld returned 1 exit status
make[2]: *** [xaLeap] Error 1
make[2]: Leaving directory `/home/sbarbe/AMBER9/amber9/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/sbarbe/AMBER9/amber9/src/leap'
make: *** [serial] Error 2

Sincerely,

Sophie

Selon Ross Walker <ross_at_rosswalker.co.uk>:

> Dear Sophie,
>
> This seems to be an issue with Fedora Core 5. Try implementing what is
> suggested in:
>
> http://amber.ch.ic.ac.uk/archive/200605/0054.html
>
> Then recompile - making sure that you do make clean before hand just to be
> sure.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_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.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of Sophie Barbe
> > Sent: Wednesday, January 10, 2007 09:55
> > To: amber_at_scripps.edu
> > Subject: RE: AMBER: amber 9
> >
> >
> > Dear Ross,
> >
> > The error at the end of make.log is :
> > gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64
> > -D_LARGEFILE_SOURCE -O2
> > -o Repeater.o Repeater.c
> > gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64
> > -D_LARGEFILE_SOURCE -O2
> > -o Scrollbar.o Scrollbar.c
> > gcc -m32 -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64
> > -D_LARGEFILE_SOURCE -O2
> > -o ScrolledTable.o ScrolledTable.c
> > ScrolledTable.c:1167: error: conflicting types for
> > ‘XawScrolledTableSetLocation’
> > ScrolledTable.h:99: error: previous declaration of
> > ‘XawScrolledTableSetLocation’
> > was here
> > make[2]: *** [ScrolledTable.o] Error 1
> > make[2]: Leaving directory
> > `/home/sbarbe/AMBER9/amber9/src/leap/src/Xraw'
> > make[1]: *** [install] Error 2
> > make[1]: Leaving directory `/home/sbarbe/AMBER9/amber9/src/leap'
> > make: *** [serial] Error 2
> >
> >
> > Could you help me please?
> >
> > Thank
> >
> > Sincerely,
> > Sophie
> >
> >
> > Selon Ross Walker <ross_at_rosswalker.co.uk>:
> >
> > > Dear Sophie,
> > >
> > > > I have a problem with xleap in amber 9.
> > > > To compile amber 9 under fedora, I made :
> > > > ./configure ifort_ia32
> > > > make -i serial
> > >
> > > Why use the -i? Who advised you to do this? This simply
> > means ignore errors
> > > but the errors are there for a reason, if you just ignore
> > them you end up
> > > wasting yours and everyone elses time trying to wade
> > through log files to
> > > find out where the original error occured.
> > >
> > > Do the following. Download
> > http://amber.scripps.edu/bugfixes/9.0/bugfix.all
> > > and save it in your home directory.
> > >
> > > Then
> > >
> > > cd $AMBERHOME
> > > patch -p0 -N -r patch_rejects < ~/bugfix.all
> > > cd src
> > > ./configure -static ifort_ia32 (assuming this is a 32
> > bit machine)
> > > make clean
> > > make >& make.log
> > >
> > > You can then watch the progress with
> > >
> > > tail -f make.log
> > >
> > > If it ends with an error take a look at the error and see
> > if you can work
> > > out what it means. Cutting and pasting the error into the
> > search box on
> > > http://amber.ch.ic.ac.uk/archive/ can help.
> > >
> > > Then if you still can't work it out please post back to the
> > amber list but
> > > this time attach the make.log file so people can see what
> > the error is and
> > > then they might be able to help.
> > >
> > > It is also useful to know the version of fedora core. Show
> > the results of:
> > >
> > > uname -a
> > > cat /proc/cpuinfo
> > > ifort -V
> > > gcc -v
> > >
> > > This can really help with troubleshooting.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | HPC Consultant and Staff Scientist |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross_at_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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> > > 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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Chercheur Post-doctoral
Institut National des Sciences Appliquées
Groupe Ingénierie Enzymatique Moléculaire
Laboratoire Biotechnologie-Bioprocédés (UMR CNRS 5504/ INRA 792)
135, Avenue de Rangueil
31077 TOULOUSE Cedex 4
Tel: +33 (0) 561 559 963
     +33 (0) 561 559 273
Fax: +33 (0) 561 559 400
E-mail: sbarbe_at_insa-toulouse.fr
http://www.insa-toulouse.fr/lbb
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