It's ParmEd.... That is where the issue is...
I did "clean installs" on 2 nearly identical machines. One worked, one
didn't work. how can I trouble shoot that?
On Fri, Mar 13, 2015 at 2:14 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, 2015-03-13 at 13:52 -0400, Jonathan Gough wrote:
> > Hi everyone,
> >
> > I am getting 26 errors when I compile AmberTool14:
> >
> >
> > possible FAILURE: check prmtop.new_type.dif
> > possible FAILURE: check prmtop.NBFIX.dif
> > possible FAILURE: check prmtop.new_chg.dif
> > possible FAILURE: check final.prmtop.dif
> > possible FAILURE: check md3_cpout.pH_4.50.dif
> > possible FAILURE: check pH_2.00.calcpka.dif
> > possible FAILURE: check pH_2.50.calcpka.dif
> > possible FAILURE: check pH_3.00.calcpka.dif
> > possible FAILURE: check pH_3.50.calcpka.dif
> > possible FAILURE: check pH_4.00.calcpka.dif
> > possible FAILURE: check pH_4.50.calcpka.dif
> > possible FAILURE: check pH_6.00.calcpka.dif
> > possible FAILURE: check pH_7.50.calcpka.dif
> > possible FAILURE: check pH_2.00.calcpka.dif
> > possible FAILURE: check running_avgs.dat.dif
> > possible FAILURE: check running_avg.dat.dif
> > possible FAILURE: check running_pKa.dat.dif
> > possible FAILURE: check chunk.dat.dif
> > possible FAILURE: check chunk_deprot.dat.dif
> > possible FAILURE: check chunk_pka.dat.dif
> > possible FAILURE: check cumulative.dat.dif
> > possible FAILURE: check cumulative_deprot.dat.dif
> > possible FAILURE: check cumulative_pka.dat.dif
> > possible FAILURE: check pop.dat.dif
> > possible FAILURE: check conditional.dat.dif
> > possible FAILURE: check conditional_chunks.dat.dif
>
> Hey! Look at that! All of those are from my programs... :).
>
> These represent errors with two different programs. The first is ParmEd
> (the first 4 tests). The rest are from cphstats (a program for
> analyzing the output of constant pH simulations).
>
> The cphstats issue is a segfault, or something of the like -- whatever
> it was that was crashing the test cases on some machines has been fixed
> in the master branch and will be released in about a month. This
> program doesn't always encounter the bug, but when it does the result is
> a crash rather than wrong answers. The fixed version is available on
> Github (http://github.com/swails/cphmd_tools) if you need a version with
> the fixes.
>
> The ParmEd issues are potentially more confusing. If you are using the
> version from AmberTools 14, then none of those tests should be failing.
> However, if you have downloaded the version from Github (presumably to
> use the 'chamber' functionality, or some other newer feature), then it's
> possible the test cases are being run with this "new" version. In that
> case, the errors you're seeing are the result of changes in the way that
> ParmEd orders atom references in the pointer sections (but the energies
> and forces you get from prmtops using either version are identical).
>
> Long story short, the ParmEd failures are most likely versioning issues
> that don't reflect an actual problem, and cphstats is known to be broken
> in some cases. If you don't need either of these programs, you can
> safely ignore them.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Mar 13 2015 - 12:00:02 PDT
