Okay,
I am going to defer to the xleap experts (Scott?) on this one; it could be
something else about the C build not being quite right, and you would pick
up C problems big time in xleap. I would note that THE big problem I have
ever had with xleap is trying to build it on a system that does not have all
the X Window development pieces (rpms or whatever) installed. Installing
the X dev environment has always fixed my xleap problems on 6, 7, or 8, but
others may know other gotcha's. I suppose there could be some version
sensitivity, but once again I defer. I would note that if you use redhat,
and have fully updated a RHEL3 system but did not originally install all of
X development, then you will not be able to install it from the original
CD's (real cool feature, that). I tried picking up the individual rpm's
from the redhat network site, and they were corrupted. I then picked up the
updated RHEL cd's, and they were okay. Very frustrating, though.
Good Luck - Bob
----- Original Message -----
From: "Stephen P. Molnar, Ph.D." <s.molnar.sbcglobal.net>
To: "Amber" <amber.scripps.edu>
Sent: Wednesday, September 15, 2004 12:23 PM
Subject: Re: AMBER: Intel Fortran Compiler Problem
> Thanks for your reply to my messages.
>
>
> On Wed, 2004-09-15 at 11:30, Robert Duke wrote:
> > Hmmm. I am not at ptraj expert. However, I note that LOADCC here is
> > mapping to ifort, whereas it would normally map to gcc, even if you are
> > using ifort. Did you maybe whack config.h, changing this value?. You
are
> > having trouble with two "main" routines, one from rdparm.c, and one from
the
> > fortran libraries. You want the one from rdparm.c, which was
gcc-compiled,
> > presumably, and when linked with gcc, gcc will use the main() in
rdparm.c.
> > This is all guesswork; I happen to compile the ptraj project (which
includes
> > rdparm) with g77 currently (no reason other than convenience).
> > Regards - Bob Duke
>
> I decided to try the g77 compiler and got quite a bit furnter before it
> bombed.
>
> Here is the end of the log file:
>
> cd leap; xmkmf
> imake -DUseInstalled -I/usr/X11R6/lib/X11/config
> cd leap; make World
> make[1]: Entering directory `/home/computation/amber7/src/leap'
>
> Building LEaP for the X Window System Release 604
>
> Wed Sep 15 12:18:29 EDT 2004
> make Makefile
> make[2]: Entering directory `/home/computation/amber7/src/leap'
> + rm -f Makefile.bak
> + mv -f Makefile Makefile.bak
> imake -DUseInstalled -I/usr/X11R6/lib/X11/config -DDoNormalLib=1
> -DDoProfileLib=0 -DDoDebugLib=0 -DDoSharedLib=0 -DLEAP_CONFIG=0x0000
> -Wundef -DTOPDIR=. -DCURDIR=.
> make[2]: Leaving directory `/home/computation/amber7/src/leap'
> make Makefiles
> make[2]: Entering directory `/home/computation/amber7/src/leap'
> making Makefiles in src/Wc...
> make[3]: Entering directory `/home/computation/amber7/src/leap'
> In file included from Imakefile:26,
> from /usr/X11R6/lib/X11/config/Imake.tmpl:2030,
> from Imakefile.c:35:
> ../Leap_lib.tmpl:10: warning: "NormalLibX" redefined
> ../Leap_lib.tmpl:6: warning: this is the location of the previous
> definition
> In file included from /usr/X11R6/lib/X11/config/Imake.tmpl:2030,
> from Imakefile.c:35:
> Imakefile:28: invalid preprocessing directive ###
> Imakefile:29: invalid preprocessing directive ##
> Imakefile:47: invalid preprocessing directive #CREATE_DEFS
> Imakefile:63: invalid preprocessing directive ###
> Imakefile:64: invalid preprocessing directive ##
> Imakefile:168: invalid preprocessing directive ###
> Imakefile:196: invalid preprocessing directive ###
> imake: Exit code 1.
> Stop.
> make[3]: *** [src/Wc/Makefile] Error 1
> make[3]: Leaving directory `/home/computation/amber7/src/leap'
> make[2]: [Makefiles] Error 2 (ignored)
> make[2]: Leaving directory `/home/computation/amber7/src/leap'
> make cleandir
> make[2]: Entering directory `/home/computation/amber7/src/leap'
> rm -f -rf ./src/X11
> rm -f *.CKP *.ln *.BAK *.bak *.o core errs ,* *~ *.a .emacs_* tags TAGS
> make.log MakeOut "#"*
> make[2]: Leaving directory `/home/computation/amber7/src/leap'
> make includes
> make[2]: Entering directory `/home/computation/amber7/src/leap'
> mkdir ./src/X11
> including in ./src/Wc...
> make[3]: Entering directory `/home/computation/amber7/src/leap/src/Wc'
> Makefile:8: *** missing separator. Stop.
> make[3]: Leaving directory `/home/computation/amber7/src/leap/src/Wc'
> make[2]: *** [includes] Error 2
> make[2]: Leaving directory `/home/computation/amber7/src/leap'
> make[1]: *** [World] Error 2
> make[1]: Leaving directory `/home/computation/amber7/src/leap'
> make: *** [install] Error 2
>
> Suggestions?
>
> Thanks in advance.
> >
> > ----- Original Message -----
> > From: "Stephen P. Molnar, Ph.D." <s.molnar.sbcglobal.net>
> > To: "Amber" <amber.scripps.edu>
> > Sent: Wednesday, September 15, 2004 11:38 AM
> > Subject: Re: AMBER: Intel Fortran Compiler Problem
> >
> >
> > > Thanks for the reply. That took care of the first error.
> > >
> > > I got quite a bit further before:
> > >
> > > ar cru libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o
> > > pdb_write.o ms.o
> > > : libpdb.a
> > > make[2]: Leaving directory `/home/computation/amber7/src/ptraj/pdb'
> > > ../Compile LOADCC -o rdparm main.o rdparm.o dispatch.o help.o
utility.o
> > > io.o trajectory.o torsion.o rms.o display.o interface.o energy.o
> > > experimental.o ptraj.o actions.o analyze.o pdb/libpdb.a -lm
> > > /opt/intel_fc_80/bin/ifort -o rdparm main.o rdparm.o dispatch.o help.o
> > > utility.o io.o trajectory.o torsion.o rms.o display.o interface.o
> > > energy.o experimental.o ptraj.o actions.o analyze.o pdb/libpdb.a -lm
> > > main.o(.text+0x68): In function `main':
> > > : multiple definition of `main'
> > > /opt/intel_fc_80/lib/for_main.o(.text+0x0): first defined here
> > > ld: Warning: size of symbol `main' changed from 42 in
> > > /opt/intel_fc_80/lib/for_main.o to 271 in main.o
> > > /opt/intel_fc_80/lib/for_main.o(.text+0x1c): In function `main':
> > > : undefined reference to `MAIN__'
> > > make[1]: *** [rdparm] Error 1
> > > make[1]: Leaving directory `/home/computation/amber7/src/ptraj'
> > > make: *** [install] Error 2
> > >
> > >
> > > On Wed, 2004-09-15 at 10:52, Robert Duke wrote:
> > > > Maybe leave LOADLIB defined as nothing in the MACHINE file?
> > > > ----- Original Message -----
> > > > From: "Stephen P. Molnar, Ph.D." <s.molnar.sbcglobal.net>
> > > > To: "Amber" <amber.scripps.edu>
> > > > Sent: Wednesday, September 15, 2004 11:13 AM
> > > > Subject: Re: AMBER: Intel Fortran Compiler Problem
> > > >
> > > >
> > > > > Thanks for your reply.
> > > > >
> > > > > On Wed, 2004-09-15 at 10:33, Viktor Hornak wrote:
> > > > > > Stephen P. Molnar, Ph.D. wrote:
> > > > > > > I am attempting to compile Amber v7 for my SuSE9.0 linux
partition
> > > > using
> > > > > > > the Inter Fortran Compiler v8.
> > > > > > >
> > > > > > > Unfortunately, I got the following error early on:
> > > > > > >
> > > > > > > /opt/intel_fc_80/bin/ifort -o new2oldparm new2oldparm.o
nxtsec.o
> > > > > > > -lPEPCF90
> > > > > > > ld: cannot find -lPEPCF90
> > > > > > >
> > > > > > > Now, according, to the locate command PEPCF90 is part of the
v7
> > Intel
> > > > > > > compiler, and is not to be found in v8.
> > > > > > >
> > > > > > > What is the solution to this problem.
> > > > > >
> > > > > > removing the -lPEPCF90 from the MACHINE file should do it...
> > > > > >
> > > > > Good suggestion! Unfortunately, it generated a new error:
> > > > > mkdir ../exe
> > > > > cd lib; make install
> > > > > make[1]: Entering directory `/home/computation/amber7/src/lib'
> > > > > ../Compile L0 -P -DNEWPARM nxtsec.f
> > > > > cat nxtsec.f | /lib/cpp -traditional -P -DNEWPARM -DLinux
> > > > > -DMEM_ALLOC > _nxtsec_.f
> > > > > /opt/intel_fc_80/bin/ifort -c -w -O2 _nxtsec_.f
> > > > > ../Compile LOAD -o new2oldparm new2oldparm.o nxtsec.o
> > > > > LOADLIB: Undefined variable.
> > > > > make[1]: *** [new2oldparm] Error 1
> > > > > make[1]: Leaving directory `/home/computation/amber7/src/lib'
> > > > > make: *** [install] Error 2
> > > > >
> > > > >
> > > > > > Cheers,
> > > > > > -Viktor
> > > > > --
> > > > > Stephen P. Molnar, Ph.D. Life is a fuzzy set
> > > > > Foundation for Chemistry Stochastic and multibariant
> > > > > http://www.geocities.com/FoundationForChemistry
> > > > >
> > > >
> >
> -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
> > > > > To post, send mail to amber.scripps.edu
> > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > > > >
> > > >
> > > >
> > >
> -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber.scripps.edu
> > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> >
> -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> --
> Stephen P. Molnar, Ph.D. Life is a fuzzy set
> Foundation for Chemistry Stochastic and multibariant
> http://www.geocities.com/FoundationForChemistry
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
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Received on Wed Sep 15 2004 - 17:53:00 PDT
