AMBER Archive (2006)

Subject: AMBER: Compiling Amber 9 on SGI with gcc

From: Shin, John Y CONTRACTOR WRAIR-Wash DC (John.Shin_at_AMEDD.ARMY.MIL)
Date: Fri Dec 08 2006 - 12:46:32 CST

Hi all,

I'm trying to compile Amber 9 on an Octane 2 SGI machine running IRIX
6.5.25f using gcc 4.0.3, binutils 2.17, and g95 0.9. I use the
following commands to compile:

1. ./configure g95
2. make serial

It proceeds fine until the first instance that gcc is invoked, and the
following occurs:

make[1]: entering directory
'/usr/people/jshin/Amber_Files/amber9/src/sander'
./checkserconf
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -02 -m32 -o
mmtsb_client.o mmtsb_client.c
cc1: error: invalid option '32'
make[1]: *** [mmtsb_client.o] Error 1
make[1]: Leaving directory
'/usr/people/jshin/Amber_Files/amber9/src/sander'
make: *** [serial] Error 2

I read elsewhere in the mail archives that some people who had a similar
problem were able to make Amber compile by deleting the "-m32" flag from
config.h. In my case, deleting the flag does allow compilation to
proceed further, but it runs into another error down the road and gives
the following message:

ld32: FATAL 2 : Internal: at ../../ld/multigot.c lgot_local_got_offset()
seg_ndx exceeds per_seg_lgot_table
ld32: INFO 152: Output file removed because of error.
make[1]: *** [sander] Error 1
make[1]: Leaving directory
'/usr/people/jshin/Amber_Files/amber9/src/sander'
make: *** [serial] Error 2

According to the GCC 4.0.3 manual it seems -m32 is a valid flag for some
architectures, although I didn't see the SGI listed as one of them. If
the flag is not valid for SGIs, what would be the SGI equivalent I need
to use? Any help would be greatly appreciated!

John Shin

Walter Reed Army Institute of Research
Division of Molecular Pharmacology
Department of Biochemistry
503 Robert Grant Ave.
Silver Spring, MD 20910
Tel: 301-319-9054
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