Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10

From: Nathalie Godbout <>
Date: Mon 22 Jan 2001 16:31:45 -0500

Margaret Doll wrote:
> Dear Sirs,
> I emailed one of your technical groups last week concerning a
> problem I am having in compiling amber 6.0 on our Indy. The compilation
> bombs out with
> f77 -mips2 -o sander_classic sander.o cshf.o ...
> ...
> ...
> ../lib/malloc.o /usr/local/amber6/src/Machines/sgi/sys.a -lblas
> -lcompib.sgimath -lfastm
> ld: FATAL 12: Expecting o32 objects: ../lib/malloc.o is n32.
> *** Error code 1 (bu21)
> *** Error code 1 (bu21).
> We had tried to get this software running last semester on the Indy
> when it was running 5.3., but we were unsuccessful. We invested in a new
> 9 Gb system disk, and paid for an upgrade in the system software. Please
> help us get you software running on our system.
> Margaret Doll (401-863-1982)
> (401) 745-7306 (beeper)

Hi Margaret,

I'm attaching a text file below with the suggestions I had made last
week. What were the results? Let me know if I can help further.


Nathalie Godbout, Ph.D.       SGI        Chemistry and Biology Applications Group
(978)567-2147                 One Cabot Road, Hudson
(978)562-4755 fax             MA 01749, USA
--------------------------------------------------------------------------Hi Margaret,
You are using -mips2 flag and default with that is -o32. It looks like
you have an n32 object in ../lib named malloc.o. Could it have been
there from a previous compilation? You need to remove it and recompile
this file the same way the other objects were compiled. The makefile
output indicates that you have been able to compile sander, sander.MC
and sander.LES. The problem you are having is with sander_classic. Which
version of sander were you interested in? Finally, on a R4k machine, you
should be using -mips3 which will create n32 objects. You can do that by
changing the following lines in the MACHINE file from:
 # R4k machines
if ( $WHICHIP >= 17 ) then
   set MIPSFLAG = '-mips2'
# R4k machines
if ( $WHICHIP >= 17 ) then
   set MIPSFLAG = '-mips3'
Before you recompile, make sure you have removed all the o32 objects. 
Let me know if you have more problems or questions,
Received on Mon Jan 22 2001 - 13:31:45 PST
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