On Thu, Feb 02, 2006, Andreas Svrcek-Seiler wrote:
Hi Andreas:
Thanks for your tests. You should consider posting results like these to
the Amber wiki: http://amber.scripps.edu/pmwiki/pmwiki.php. Go to the
"test
failures" page.
> 1) The 'core' Makefile in $AMBERHOME/src should contain a
> mkdir ../exe or something like that.
This has to do with the flags you use to check out the CVS tree; you are
not getting empty directories. It will not be a problem with what users
see.
>
> make faile for ptraj due to a missing include statement
> (../netcdf/src/libsrc).
This is a bug in CVS and is Tom's fault: he needs to check in the code
that
protects the netCDF code with ifdef BINTRAJ statements.
>
>
> {t,x}leap don't build as 32bit programs on a 64 it machine, since LOADCC
> misses a '-m32' and gcc defaults to 64 bit mode during the linking
stage.
I don't understand this. Is it supposed to build 32-bit programs? On my
em64t machine, I get 64 bit versions of these programs with the default
configure output. Same on SGI-altix. So, I'm not sure I know what the
real
"error" is here.
Does "it" stand for Itanium? I think we have only tested SGI-altix (which
uses icc not gcc) for itanium. Can you propose a patch to configure?
>
> Several further divcon test quit with something like
> "Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c
properly,
> exit"
Please check your stacksize limits, as discussed here:
http://amber.scripps.edu/pmwiki/pmwiki.php/Main/Amber9tf
Also, we need to know your exact configuration: compiler, OS, version of
MKL.
It looks like there are problems with divcon when MKL is not defined.
>
> Now on to ifort 9.0.032. Since updating from 9.0.031,
> I get error messages like:
> fortcom: Error: _amoeba_runmd.f, line 118: Syntax error, found '.' when
> expecting one of: ( <IDENTIFIER> <CHAR_CON_KIND_PARAM>
> <CHAR_NAM_KIND_PARAM> <CHARACTER_CONSTANT> <INTEGER_CONSTANT> ...
> allocate(acceleration(3,num_atoms),stat=ier);
if(.not.(ier==0))call
> Aass('ier==0',"amoeba_runmd.f",27)
> -------------------------------------------------------^
> I can't tell whether the code above is bad fortran or the current
compiler
> is "wrong" (?).
Weird. We have been using this for a long time. Try changing this line
(about line 27 of amoeba_runmd.f) from:
allocate(acceleration(3,num_atoms),stat=ier); REQUIRE(ier==0)
to
allocate(acceleration(3,num_atoms),stat=ier)
REQUIRE(ier==0)
That is, I wonder if the semicolon is messing things up -- this is the
only
place where this syntax is used, so there may be an easy fix.
>
> Baseline: with the latest ifort (9.0.032 ia32) compiler,
> the routine nonbond_list seems segfault-prone and even disabling all
> optimizations doesn't help.
On clue about this one.
>
>
> a) it's o.k. to send this to the list
It is, but using the wiki is the preferred method, since things can be
removed
from there when they are fixed, and people's e-mail boxes are not so
crowded.
...thanks again...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Wed Apr 05 2006 - 23:49:43 PDT
