[Wien] WIEN2k on Xeon 5500 Series

Laurence Marks L-marks at northwestern.edu
Thu Nov 24 14:35:36 CET 2011 

Neither the heap array idea (a bad one, look up what it really does) or
ulimit are relevant. In fact the key codes in Wien2k now set ulimit
themselves due to some issues with openmpi.

SIGSEV errors mean in most cases that the code has got corrupted by an
array going out of bounds or an illegal instruction. Almost certainly Intel
has overoptimized something so the machine level code is doing something
wrong. Sometimes turning on every possible debug option then running inside
a debugger (ddd) can work to find it. It is not easy, which is why you do
not have people rushing forward with answers. (I do not have that compiler.)
On Nov 23, 2011 7:20 PM, "Aaron Sutton" <asutton at physics.utoronto.ca> wrote:

> Hi,
> I also tried the -heap-arrays suggestion from intel to no avail. I
> believe the two packages you've mentioned, including revision 3 of the
> 2011 intel fortran compiler, should be all you need. As for the C
> compiler, I'm using gcc 4.6.1, which I believe is the standard version
> on Ubuntu 11.10.
>
> ----------------------------------------------------------------------------
> Aaron Sutton
> Ph.D. Candidate | University of Toronto
> Office: McLennan MP090 | Phone: +1 416 946 3639
> Email: asutton at physics.utoronto.ca
>
>
>
> 2011/11/23 Paul Fons <paul-fons at aist.go.jp>:
> > I am trying to compile Wien2K as well with the latest intel compilers.
>  At
> > first I thought it might be a stack overflow problem (of course limit
> > stacksize was set to unlimited) and I tried the suggestion -heap-arrays
> from
> > intel
> > (
> http://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors/
> )
> > but it did not help either.
> > Has any progress been made in tracking down the source of this error?
>  The
> > traceback is essentially worthless.  Has anyone corresponded with intel
> with
> > regards to the problem?
> >
> > I am now in the process of downloading an older version of the compiler.
>  I
> > am a little worried about downloading having different versions of the
> > compiler as there is also C code in Wien2K.  Exactly which versions of
> the
> > C, Fortran, and MKL libraries should be used.  I have a copy of a Intel
> > Parallel Studio XE for Linux and don't typically download the individual
> > packages hence my confusion.
> > From what I understand, update 3 is the
> >  I am downloading currently:
> > Fortran
> > l_fcompxe_2011.3.174.tgz
> > ]MKL
> > l_mkl_10.3.3.174.tgz
> >
> >
> > On Nov 11, 2011, at 6:04 AM, Aaron Sutton wrote:
> >
> > Great, thank you I will try this. I haven't seen this as I'm new to
> > the mailing list. I actually eliminated the the segmentation fault by
> > linking to libmkl_mc.so explicitly, this however has caused an error
> > in SECLR4. Don't think I'm further along, but at least the error is
> > different.
> >
> >
> ----------------------------------------------------------------------------
> > Aaron Sutton
> > Ph.D. Candidate | University of Toronto
> > Office: McLennan MP090 | Phone: +1 416 946 3639
> > Email: asutton at physics.utoronto.ca
> >
> >
> >
> > On Thu, Nov 10, 2011 at 15:48, Gavin Abo <gsabo at crimson.ua.edu> wrote:
> >
> > Hi Aaron,
> >
> > If you have been following some of the recent mailing list posts, I think
> >
> > this error is because of the intel compiler.  I had the same or similar
> >
> > error with update 6.  I never tried update 7, but it sounds like the
> >
> > compiler does not seem to be compiling the Wien2k code correctly like
> update
> >
> > 6.  Try update 3 of Intel FORTRAN compiler & MKL
> >
> > library, which should be composerxe-2011.3.174.
> >
> > Gavin
> >
> > On 11/10/2011 2:31 PM, Aaron Sutton wrote:
> >
> > Hi,
> >
> > I am experiencing a segmentation fault when running WIEN2k compiled
> >
> > using the most recent version of the Intel FORTRAN compiler&  MKL
> >
> > library (composer_xe_2011_sp1.7.256). The computer it's being run on
> >
> > is a 2009 Mac Pro with 2 quad core intel xeon 5500 series processors
> >
> > at 2.93GHz and 8GB RAM. The computer is natively running Ubuntu Linux
> >
> > 11.10 (though the same issue occurred while running 11.04). WIEN2k is
> >
> > compiled using the default flags and links provided by the Linux with
> >
> > Intel FORTRAN v12.0 + MKL option of siteconfig_lapw, no modifications.
> >
> > The software compiles without error. Upon running the software, either
> >
> > through the web interface or using run_lapw in the case directory,
> >
> > lapw0 completes successfully and then I receive:
> >
> > LAPW0 END
> >
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >
> > IMAGE                           PC
> >
> >    ROUTINE                              LINE
> >
> >      SOURCE
> >
> > libmkl_mc3.so                 00002B0321624A30               Unknown
> >
> >                             Unknown                          Unknown
> >
> > stop error
> >
> > According to the intel compiler documentation, the libmkl_mc3 library
> >
> > is a kernel library specifically for core i7 type processors, which
> >
> > the Xeon 5500s are. I do not link specifically to libmkl_mc3.so
> >
> > anywhere as I am using the default options. I can report that this
> >
> > error does not occur on i3 or i5 processors. Any thoughts on how to
> >
> > remedy this situation?
> >
> > Thank you.
> >
> >
> ----------------------------------------------------------------------------
> >
> > Aaron Sutton
> >
> > Ph.D. Candidate | University of Toronto
> >
> > Office: McLennan MP090 | Phone: +1 416 946 3639
> >
> > Email: asutton at physics.utoronto.ca
> >
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> >
> > Dr. Paul Fons
> > Functional Nano-phase-change Research Team
> > Team Leader
> > Nanodevice Innovation Research Center (NIRC)
> > National Institute for Advanced Industrial Science & Technology
> > METI
> > AIST Central 4, Higashi 1-1-1
> > Tsukuba, Ibaraki JAPAN 305-8568
> > tel. +81-298-61-5636
> > fax. +81-298-61-2939
> > email: paul-fons at aist.go.jp
> > The following lines are in a Japanese font
> > 〒305-8562 茨城県つくば市つくば中央東 1-1-1
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