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 - 11:30:03 PDT
