Re: AMBER: ambpdb segmentation fault

From: justin litchfield <>
Date: Sun, 21 Nov 2004 21:09:25 -0800

so, in my continuing saga of not having ambpdb, i got all the
compilers/whatever set up on my powerbook g4 (same version, 10.3, of
macosx) and installed everything. leap failed to compile
spectacularly, though i haven't looked into why yet, but more
importantly, ambpdb compiled fine. running it got the same
segmentation fault, and going into gdb to figure out got me the same
error as i reported below. so, that's two machines doing the same
thing. has anyone been able to get the ambpdb from amber8 to run an a
mac? or is there another way to look at the .inpcrd's or .rst's? i
have tried vmd, but it always makes anything i try to look at prior to
running MD, regardless of the minimisation look ridiculous. should i
be able to do that? thanks,

justin litchfield

On Nov 17, 2004, at 2:46 PM, justin litchfield wrote:

> Ross,
> 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 ()
> (gdb)
> thanks again for your help,
> justin
> 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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Received on Mon Nov 22 2004 - 05:53:01 PST
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