AMBER Archive (2004)

Subject: Re: AMBER: ambpdb segmentation fault

From: justin litchfield (
Date: Wed Nov 17 2004 - 16:46:01 CST

Thanks for the help. I am also using xlf90 v8.1. slight modifications
to your config.h file were necessary (my AMB_SRC was not
/nfs/auts/users/crowley/amber9/osx/src but was /usr/local/amber8/src )
;) and the SYSDIR pointed at a non-existent folder on my machine,
though pointing it to /lib made the compiling go smoothly.
unfortunately, then the make test failed for sander, though it worked
for leap. going back to my previous config.h file allowed the make
test to work again.

i compiled ambpdb with my config with -g and then looked at the crash
with gdb.

here's what it told me:
(gdb) run ambpdb
Starting program: /usr/local/amber8/exe/ambpdb ambpdb
Reading symbols for shared libraries .+++....... done

Program received signal EXC_BAD_ACCESS, Could not access memory.
0x00002b94 in main ()
(gdb) bt
#0 0x00002b94 in main ()
#1 0x8fe1a558 in __dyld__dyld_start ()
#2 0x8fe1a558 in __dyld__dyld_start ()

thanks again for your help,


On Nov 17, 2004, at 1:35 PM, Ross Walker wrote:

> Hi Justin,
> I have tried this out on our G5 and can't reproduce the problem you are
> seeing. We are using xlf90 v8.1. I have attached the config.h file I
> used
> for this. Try using this instead of your config.h file. Make sure you
> do
> "make clean" in $AMBERHOME/src before recompiling.
> All the best
> Ross
> /\
> \/
> |\oss Walker
>> -----Original Message-----
>> From:
>> [] On Behalf Of justin litchfield
>> Sent: 15 November 2004 18:57
>> To:
>> Subject: AMBER: ambpdb segmentation fault
>> I've just recently installed amber8 on a G5 powermac (dual 1.8GHz),
>> which seems to have worked fine. all the modules i've used so far
>> (nucgen, sander, xleap) work fine, but while working through
>> the first
>> DNA tutorial, i found that ambpdb returns a segmentation fault every
>> time i call it, regardless of the input (even none). this is
>> the input
>> i was trying to get to work:
>> ambpdb -p polyAT_vac.prmtop < polyAT_vac_init_min.rst >
>> polyAT_vac_init_min.pdb
>> and i made sure that the input files were all valid, matched the
>> tutorial, etc.
>> i applied the patch bugfix.all and recompiled, and am now at
>> a loss as
>> to what to do. i'm really new to unix systems and compiling and
>> whatnot, so your help is definitely appreciated. thanks,
>> justin litchfield

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