The programs Prep, Link, Edit and Parm are no longer
supported. Also Amber 4.1 was never tested under
any form of Linux that I know of. We can't offer
any support. Please upgrade to Amber6.
jim
On Wed, 21 Nov 2001, Fabrice YERLY wrote:
> Dear Amber users,
>
> I try to compile Amber 4.1 with gcc 2.95.4 under
> Debian Linux 2.2.19 on a AMD monoprocessor 1.4 GHz.
> Compilation seems to work.
>
> PREP works OK
> LINK return segmentation faults and empty output files
> EDIT return program error
> PARM return program error
> SANDER seems to work
>
> Here is a copy of the MACHINE file i used for
> compilation:
> --------------------------------------------------------------------------------
> #
> setenv MACHINE "linux"
> setenv MACH Linux
> setenv MACHINEFLAGS "-DISTAR2 -DREGNML "
>
> # CPP is the cpp for this machine
> setenv CPP "/lib/cpp -traditional "
> setenv CC gcc
>
> # SYSDIR is the name of the system-specific source directory relative to
> src/*/
> setenv SYSDIR Machine/g77
>
> # COMPILER ALIASES:
>
> # LOADER/LINKER:
> setenv LOAD "g77 -O6"
> setenv LOADLIB "-lm"
>
> setenv G77_COMPAT "-fno-globals -ff90 -funix-intrinsics-hide"
> #
> # following seems to actually slow down code, though it works well on
> CHARMM:
> #setenv G77_OPT "-O6 -m486 -malign-double -ffast-math -fomit-frame-pointer
> -funroll-loops -funroll-all-loops
> -mcpu=pentiumpro -march=pentiumpro -ffloat-store -fforce-mem
> -frerun-cse-after-loop -fexpensive-optimizations
> -fugly-complex"
> # following appears to be the best we have found so far:
> setenv G77_OPT "-O3 -m486 -malign-double -ffast-math -fomit-frame-pointer"
>
> # little or no optimization:
> setenv L0 "g77 -c -g"
>
> # modest optimization (local scalar):
> setenv L1 "g77 -c $G77_OPT $G77_COMPAT"
>
> # high scalar optimization (but not vectorization):
> setenv L2 "g77 -c $G77_OPT $G77_COMPAT"
>
> # high optimization (may be vectorization, not parallelization):
> setenv L3 "g77 -c $G77_OPT $G77_COMPAT"
>
> # ranlib, if it exists
> setenv RANLIB ranlib
> --------------------------------------------------------------------------------
>
> If somebody could help me ...
>
> Thanks in advance
>
> Fabrice
>
>
>
> ============================================
> Fabrice YERLY
> Institut de Chimie Minerale & Analytique
> EPFL-BCH CH-1015 Lausanne
> Phone +41 21 693 9881
> Fax +41 21 693 9855
> Fabrice.Yerly_at_epfl.ch
> http://pcbch3207h.unil.ch/~fyerly/index.html
> ============================================
>
>
----------------------------------------------------------------------------
James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue
University of California
San Francisco, CA 94143-0446
----------------------------------------------------------------------------
Received on Wed Nov 21 2001 - 09:02:48 PST
