AMBER Archive (2006)

Subject: AMBER: Problem Installing Amber in SGI Irix 6.5

From: trudy_at_uoguelph.ca
Date: Mon Nov 27 2006 - 14:29:53 CST

Hello All:

I am new to Amber, and I am having some trouble installing Amber 9 on
an Irix 6.5 SGI machine. I have been trying to do the installation
with g95 and gcc compilers.
  I downloaded the gcc front-end from the SGI website and installed
the Irix Development CDs and libraries to obtain the SGI assembler and
linker. So, gcc seems to be installed alright. I also installed g95
and that seems to be fine.

I tried compiling Amber at that point, and got the following error messages:

# make serial
Starting installation of Amber9 (serial) at Wed Nov 8 15:46:50 EST 2006.
         cd lib; make install
         cpp -traditional -P -xassembler-with-cpp new2oldparm.f >
_new2oldparm.f

         g95 -c -O0 -fno-second-underscore -o new2oldparm.o _new2oldparm.f
as ERROR: --traditional-format not allowed in non XPG4 environment
as ERROR parsing --traditional-format: unknown flag
as ERROR parsing -no-mdebug: unknown flag
as ERROR parsing -mabi=n32: unknown flag
*** Error code 1 (bu21)
*** Error code 1 (bu21)

I thought that perhaps g95 does not like the SGI assembler and linker.
  So, I decided to try the GNU assembler and linker in the Binutils
2.17.2 package, but I cannot get that package to compile either.

The error messages are:

gcc -c -DHAVE_CONFIG_H -g -O2 -I. -I.././libiberty/../include -W
-Wall -pedantic -Wwrite-strings -Wstrict-prototypes
.././libiberty/lrealpath.c -o lrealpath.o
../libiberty/lrealpath.c: In function `lrealpath':
../libiberty/lrealpath.c:85: warning: implicit declaration of function
`realpath'
../libiberty/lrealpath.c:85: warning: initialization makes pointer
from integer without a cast
../libiberty/lrealpath.c:115: warning: implicit declaration of
function `pathconf'
../libiberty/lrealpath.c:115: error: `_PC_PATH_MAX' undeclared (first
use in this function)
../libiberty/lrealpath.c:115: error: (Each undeclared identifier is
reported only once
../libiberty/lrealpath.c:115: error: for each function it appears in.)
../libiberty/lrealpath.c:120: warning: implicit declaration of
function `malloc'
../libiberty/lrealpath.c:123: warning: assignment makes pointer from
integer without a cast
../libiberty/lrealpath.c:125: warning: implicit declaration of function `free'
gmake[2]: *** [lrealpath.o] Error 1
gmake[2]: Leaving directory `/usr/local/Binutils/binutils-2.17/libiberty'
gmake[1]: *** [all-libiberty] Error 2
gmake[1]: Leaving directory `/usr/local/Binutils/binutils-2.17'
gmake: *** [all] Error 2

I think that I might be missing some libraries, but I am not sure
which ones, where to find them or how to include them once I find them.

I notice that in a previous post someone suggested using gfortran to
compile Amber 9 but it’s not included in the version of gcc that I
downloaded from the SGI website. I also have not been able to find
that compiler on it’s own outside of gcc, and, in any case, I am not
sure if Amber will recognize it during the compilation.

So, my questions are:

1. Does anyone know how to “fix” the errors that I am getting?
2. If I am not on the right track, could someone tell me how to go
about installing Amber9 in Irix 6.5 using the GNU compilers?

Thanks in advance,

Trudy

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