Great!
I'm forwarding this solution to the Amber mailing list for the sake of
record keeping ...
Ray
---------- Forwarded message ----------
From: HIromichi Tsurui <tsurui.juntendo.ac.jp>
Date: Thu, Aug 18, 2011 at 3:36 PM
Subject: Re: [AMBER] _mmpbsa_py_energy error durint PB calculations
To: "Ray Luo, Ph.D." <ray.luo.uci.edu>, MengJuei Hsieh <mengjueh.uci.edu>
Thank you Ray, MengJuei;
I should have make link from intel64 to em64t in $MKL_HOME. Fortran
seeks for libraries in $MKL_HOME/lib/em64t, and , and originally, intel
generated the directory intel64. I recompiled after making the link,
MMPBSA worked properly.
Many many thanks.
Hiromichi
2011-08-17 (水) の 16:18 -0700 に Ray Luo, Ph.D. さんは書きました:
> Thaks a lot for looking into this!
>
> Ray
>
> On Wednesday, August 17, 2011, MengJuei Hsieh <mengjueh.uci.edu>
> wrote:
> > Dear Ray,
> >
> > No, not really, I only know SciLinux is a RHEL clone. I'll let you
> know if I
> > can reproduce those errors in my virtualbox.
> >
> > Best,
> > --
> > Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California
> Irvine.
> >
> >
> >> From: "Ray Luo, Ph.D." <ray.luo.uci.edu>
> >> Date: Wed, 17 Aug 2011 03:54:15 -0700
> >> To: MengJuei Hsieh <mengjueh.uci.edu>
> >> Cc: <tsurui.juntendo.ac.jp>, <jason.swails.gmail.com>
> >> Subject: Fwd: [AMBER] _mmpbsa_py_energy error durint PB
> calculations
> >>
> >> MJ,
> >>
> >> Do you know anything about this combination of OS and compiler?
> >>
> >> All the best,
> >> Ray
> >>
> >>
> >> ---------- Forwarded message ----------
> >> From: 鶴井博理 <tsurui.juntendo.ac.jp>
> >> Date: 2011/8/17
> >> Subject: Re: [AMBER] _mmpbsa_py_energy error durint PB calculations
> >> To: AMBER Mailing List <amber.ambermd.org>
> >>
> >>
> >> Thank you Jason.
> >>
> >> I ran AT15_Amber11.py. Errors reported in Amber 11 test.log but not
> included
> >> in the result of AT15_Amber11.py are as follows;
> >> Run.dmp.min, Run laz6.min, Run.ion.min, and Run.pbsa_decpw.
> >> Test.log for AmberTools report some more errors. Those are
> >> Run.IIM.min, Run.t4bnz.min., and Run.mb., not included in
> >> AT15_Amber11.py-result.
> >>
> >> My OS is Scientific Linux 6.0 and I compiled Amber11 and AmberTools
> with
> >> Intel compiler 12.0.2.137 for 64bit.
> >>
> >> Hiromichi
> >>
> >>
> >> 2011/8/16 Jason Swails <jason.swails.gmail.com>
> >>
> >>> Run AT15_Amber11.py. At the bottom of that, it should give a
> summary about
> >>> which tests are *expected* to fail, specifically using sander and
> PBSA.
> >>> The
> >>> reason this occurs is because the pbsa program was updated and the
> user
> >>> interface slightly changed (for instance, with different input
> namelist
> >>> variables), which causes some tests to quit in error (like you
> saw) and
> >>> other tests to fail with what appear to be non-trivial roundoff
> error, but
> >>> the numbers are fairly close regardless.
> >>>
> >>> As long as all of the AmberTools tests pass and *only* those tests
> listed
> >>> by
> >>> AT15_Amber11.py fail, you should be fine.
> >>>
> >>> Hope this helps,
> >>> Jason
> >>>
> >>> On Tue, Aug 16, 2011 at 12:36 AM, Ray Luo, Ph.D. <ray.luo.uci.edu>
> wrote:
> >>>
> >>>> Interesting ... is there any other error messages when you run
> rest of
> >>>> the test cases? There is a makefile to run all these test cases
> under
> >>>> the test directory. It is crucial that all test cases pass after
> your
> >>>> installation.
> >>>>
> >>>> All the best,
> >>>> Ray
> >>>>
> >>>> 2011/8/15 鶴井博理 <tsurui.juntendo.ac.jp>:
> >>>>> Thank you Jason.
> >>>>>
> >>>>> I noticed that sander_pbsa was also occurred in test.
> >>>>> Below is the output of the test log.
> >>>>> I found *Dmitry Osolodkin in 19, April 2011 also suffered form
> this
> >>>> error,
> >>>>> and I tired to obtain informations about this issue*, but the
> link in
> >>>> this
> >>>>> thread did not work.
> >>>>> Could you give me any suggestion?
> >>>>>
> >>>>>
> >>>>> ======cd sander_pbsa_dmp && ./Run.dmp.min
> >>>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >>>>> Image PC Routine Line
> >>>>> Source
> >>>>> sander 00000000008241E3 Unknown
> Unknown
> >>>> Unknown
> >>>>> sander 00000000004C81A4 Unknown
> Unknown
> >>>> Unknown
> >>>>> sander 00000000004918C0 Unknown
> Unknown
> >>>> Unknown
> >>>>> sander 0000000000490528 Unknown
> Unknown
> >>>> Unknown
> >>>>> sander 00000000004030BC Unknown
> Unknown
> >>>> Unknown
> >>>>> libc.so.6 00007F8F9DFADC5D Unknown
> Unknown
> >>>>
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Received on Thu Aug 18 2011 - 18:00:05 PDT
