AMBER Archive (2004)

Subject: Re: AMBER: amber compilation

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Mon Jul 26 2004 - 15:47:33 CDT

Dear Lucian,

the following page on the amber website provides more details for
compiling amber8 (amber7) on PC linux machines:
http://amber.scripps.edu/cluster_info/index.html#compile_a8
I'd suggest to compile amber8 with Intel compilers (get at least intel
fortran compiler). Also, you don't say which version of Suse or other
linux distributions you tried on those other machines...

Cheers,
-Viktor

Livadaru, Lucian wrote:
> Hello,
>
> I need help with compiling AMBER. Following the instructions in the
> amber manual, I have tried to compile amber7 and amber8 on 3 different
> machines and the compilation failed on all attempts. Note that I
> followed exactly the instructions in the amber manual.
>
> Besides, it is very unclear to me what goes wrong or how could I get a
> constructive response from the compilation process. I could use some
> support in that direction.
>
> On my last attempt, I tried to compile amber7 on a Suse linux machine
> with g77 compiler suite. Following the manual I set the AMBERHOME
> variable and then typed (from src directory):
>
> ln -s -f Machines/Machine.g77 MACHINE
>
> then
>
> make install
>
> The compilation went on for a while and then stopped with the message:
>
> cd gibbs; make install
> make[1]: Entering directory `/usr/local/amber7/src/gibbs'
> ../Compile L2 -P -DNOEWALD connrg.f
> cat connrg.f | cpp -traditional -P -DNOEWALD -DLinux >
> _connrg_.f
> g77 -c -O3 -fno-globals -ff90 -funix-intrinsics-hide _connrg_.f
> _connrg_.f: In subroutine `torccs':
> _connrg_.f:852: internal compiler error: in get_loop_body, at
> cfgloop.c:1026
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <URL:http://www.suse.de/feedback> for instructions.
> make[1]: *** [connrg.o] Error 1
> make[1]: Leaving directory `/usr/local/amber7/src/gibbs'
> make: *** [install] Error 2
> nanows10:/usr/local/amber7/src #
>
>
>
>
>
> If I comment the line corresponding to GIBBS in the Makefile, there is
> an error for leap:
>
> cd leap; make World
> make[1]: Entering directory `/usr/local/amber7/src/leap'
>
> Building LEaP for the X Window System Release 604
>
> Mon Jul 26 10:52:29 CDT 2004
> make Makefile
> make[2]: Entering directory `/usr/local/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 `/usr/local/amber7/src/leap'
> make Makefiles
> make[2]: Entering directory `/usr/local/amber7/src/leap'
> making Makefiles in src/Wc...
> mv -f Makefile Makefile.bak
> make[3]: Entering directory `/usr/local/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 `/usr/local/amber7/src/leap'
> make[2]: [Makefiles] Error 2 (ignored)
> make[2]: Leaving directory `/usr/local/amber7/src/leap'
> make cleandir
> make[2]: Entering directory `/usr/local/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 `/usr/local/amber7/src/leap'
> make includes
> make[2]: Entering directory `/usr/local/amber7/src/leap'
> mkdir ./src/X11
> including in ./src/Wc...
> make[3]: Entering directory `/usr/local/amber7/src/leap/src/Wc'
> Makefile:8: *** missing separator. Stop.
> make[3]: Leaving directory `/usr/local/amber7/src/leap/src/Wc'
> make[2]: *** [includes] Error 2
> make[2]: Leaving directory `/usr/local/amber7/src/leap'
> make[1]: *** [World] Error 2
> make[1]: Leaving directory `/usr/local/amber7/src/leap'
> make: *** [install] Error 2
> nanows10:/usr/local/amber7/src #
>
>
> Thanks, sincerely,
> Lucian Livadaru
>
>
>
> 

-- 
===================================================================
Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail: viktor.hornak_at_sunysb.edu
===================================================================
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