AMBER Archive (2009)

Subject: Re: [AMBER] ambertools and Snow Leopard 64 bits kernel

From: gilbert_at_bluemarble.net
Date: Tue Sep 22 2009 - 21:18:12 CDT

  I don't know how you have modified your makefile but I found (when compiling
some 32 bit code on a 64 bit linux system) that I needed -m32 on both the
compile and linker lines (CFLAGS, FFLAGS and LDFLAGS all had the -m32 option).
That may be of help trying to compile 64 bit code on a 32 bit OS. But I have
compiled ambertools on my 64 bit linux machine with nothing other that the
standard configure and make.

Kevin Gilbert
Serena Software

Quoting Tom Joseph <ttjoseph_at_gmail.com>:

> I was able to reproduce these failures.
>
> In the nab testcase, strange object code that nukes pointers returned
> from functions is generated, causing the segfault. I suspect it has
> something to do with 32 vs 64 bit linking, but I don't know enough
> about Apple's linker to know what's going on here. For the antechamber
> failure...not sure what's going on there; perhaps some antechamber
> expert can comment?
>
> For the time being perhaps it's best to use nab and antechamber on
> another platform.
>
> --Tom
>
> 2009/9/22 Alan <alanwilter_at_gmail.com>:
> > Thanks Tom, it did help.
> >
> > However, nab still fails and from antechamber the last test failed with:
> > ==============================================================
> > cd antechamber/chemokine && ./Run.1b2t
> > make: *** [test.antechamber] Error 1
> >
> > [DETAILED]
> >
> > ../../../exe/antechamber -fi pdb -fo ac -i 1b2t.pdb -o 1b2t.ac -at amber \
> >>    -s 2 -pf yes
> >
> > The atom number exceeds the MAXATOM, reallocate memory
> > Info: the bond number exceeds MAXBOND, reallocate memory automatically
> > Running: /Users/alan/Programmes/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > Info: the atom number exceeds the MAXATOM, reallocate memory automatically
> > ---Judge bond type for Residue 1 with ID of 0 and Name of MET ---
> >
> > [snip]
> >
> > ---Judge bond type for Residue 15 with ID of 14 and Name of LYS ---
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> > (aromatic double)Error: cannot run
> > "/Users/alan/Programmes/amber10/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > judgebondtype() of antechamber.c properly, exit
> >
> > Many thanks,
> >
> > Alan
> >
> > On Tue, Sep 22, 2009 at 19:12, Tom Joseph <ttjoseph_at_gmail.com> wrote:
> >> When you compiled antechamber, did you get warnings such as the
> following?
> >>
> >> alc.c:155: warning: call to __builtin___strcpy_chk will always
> >> overflow destination buffer
> >>
> >> If so, this is a bug in antechamber - there are several instances
> >> where a string is copied into a char array that is too small. Please
> >> try the attached patch.
> >>
> >> --Tom
> >>
> >> 2009/9/22 Alan <alanwilter_at_gmail.com>:
> >>> Hi there,
> >>>
> >>> I would like to know if there's other already using (or trying to use)
> >>> AmberTools with Snow Leopard in 64 bits kernel.
> >>>
> >>> I did a try and although I had a nice compilation (gcc/gfortran with
> >>> -m64), running tests failed for:
> >>>
> >>> nab, antechamber (some cases)
> >>>
> >>> For example:
> >>>
> >>> make -f Makefile_at test.nab
> >>> ( cd nab; make test )
> >>> =====================================================
> >>> Running test to make dna duplex:
> >>>
> >>> /bin/sh: line 1: 21844 Segmentation fault      ./duplex < duplex.in
> >>> make[1]: *** [duplex_test] Error 139
> >>> make: *** [test.nab] Error 2
> >>>
> >>> make -f Makefile_at test.antechamber
> >>> cd antechamber/top2mol2 && ./Run.top2mol2
> >>> diffing sustiva.mol2.save with sustiva.mol2
> >>> PASSED
> >>> ==============================================================
> >>> [snip]
> >>> ==============================================================
> >>> diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
> >>> possible FAILURE:  check fluorescein_f2.mol2.dif
> >>> ==============================================================
> >>> cd antechamber/c60 && ./Run.c60
> >>> Abort
> >>>  ./Run.c60:  Program error
> >>> make: *** [test.antechamber] Error 1
> >>>
> >>> Many thanks in advance,
> >>>
> >>> Alan
> >>>
> >>> _______________________________________________
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> >>>
> >>
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