Hi!
I checked the patched, gnu-compiled version of AmberTools16 and I didn't
get any failures. I also checked the unpatched version and I got the same
job failures with the unpatched, intel-compiled version, apart from
fluorescein.mol2.dif and Results.dat.dif which were not produced failures
with the unpatched, gnu compiled version. To be clear, these 'make tests'
were all done without my modifications.
My modified version behaves the same as the unmodified version, so I think
my modifications are not interfere with the original code. Therefore I
would also like to ask that who should I contact with from the Amber
development team if I would like to have my changes to be included in the
official AmberTools version?
Thank you for your help!
Bence
On Tue, Aug 30, 2016 at 7:07 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> ah, make sure to apply all the updates
>
> cd $AMBERHOME
> ./update_amber --update
>
> Hai
>
> On Tue, Aug 30, 2016 at 12:30 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Hi,
> >
> > I've checked amber testing log before releasing and we indeed got trouble
> > compiling LES sander interface with intel compiler.
> > (I am not sure about other failures).
> >
> > Can you try GNU compiler? (be sure to make clean first)
> >
> > Hai
> >
> >
> > On Tue, Aug 30, 2016 at 10:37 AM, Bence Hégely <hoemberr.gmail.com>
> wrote:
> >
> >> Hi!
> >> I got the failures with the original distribution.
> >> (and I also got the same failures with my modified version)
> >>
> >> Bence
> >>
> >> On Mon, Aug 29, 2016 at 7:09 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >> > Hi,
> >> >
> >> > so did you get the failure (1st post) with original distribution or
> with
> >> > your change?
> >> >
> >> > Hai
> >> >
> >> > On Fri, Aug 26, 2016 at 10:19 AM, Bence Hégely <hoemberr.gmail.com>
> >> wrote:
> >> >
> >> > > Thank you for your reply!
> >> > > The libcpptraj.so is only linked to the
> $AMBERHOME/lib/libcpptraj.so,
> >> > > however, I installed other Amber versions earlier as well. Can these
> >> > > versions interfere somehow?
> >> > >
> >> > > On ignoring the job fails: i didn't mention in my previous letter
> >> that I
> >> > > made some modifications to the QM/MM, so my aim is to be 100% sure
> >> that i
> >> > > didn't mess up the original code. The first step of this process is
> to
> >> > test
> >> > > the unmodified version.
> >> > >
> >> > > Bence
> >> > >
> >> > > On Thu, Aug 25, 2016 at 9:45 PM, Hai Nguyen <nhai.qn.gmail.com>
> >> wrote:
> >> > >
> >> > > > Hi,
> >> > > >
> >> > > > per pytraj issue:
> >> > > >
> >> > > > Did you install it somewhere else too?
> >> > > >
> >> > > > Can you try
> >> > > >
> >> > > > ldd
> >> > > > /export/home/hegely/Programz/amber16/lib/python2.7/site-
> >> > > > packages/pytraj/cpp_options.so
> >> > > > | grep cpptraj
> >> > > >
> >> > > > to see which libcpptraj.so library that pytraj linked to. If that
> >> > library
> >> > > > is not in $AMBERHOM/lib, you might want to remove the old
> installed.
> >> > > >
> >> > > > PS: Otherwise you can ignore pytraj (binding to cpptraj) if you
> >> don't
> >> > > want
> >> > > > to use cpptraj Python interface. It does not affect your QM job.
> >> > > >
> >> > > > Per other issues, I will let others to give comments. Cheers
> >> > > >
> >> > > > Hai
> >> > > >
> >> > > > On Thu, Aug 25, 2016 at 2:53 PM, Bence Hégely <hoemberr.gmail.com
> >
> >> > > wrote:
> >> > > >
> >> > > > > Dear Amber users and developers,
> >> > > > >
> >> > > > > Apparently, I successfully installed AmberTool16, however, i
> >> wanted
> >> > to
> >> > > > > check my installation by doing the test jobs with the "make
> test"
> >> > > command
> >> > > > > and I got the the following results:
> >> > > > >
> >> > > > > 1864 file comparisons passed
> >> > > > > 8 file comparisons failed
> >> > > > > 3 tests experienced errors
> >> > > > >
> >> > > > > The manual says that a failed test job does not necessary mean
> >> that
> >> > the
> >> > > > > installed Amber version is wrong due to the differences in the
> >> > > > > implementation of arithmetic operations, however, it also states
> >> that
> >> > > the
> >> > > > > reported integers, and the results of the 1st step should be
> >> > > identical. I
> >> > > > > checked the failed test jobs and it seems to me that reported
> >> > integers
> >> > > > are
> >> > > > > not the same and also the real numbers are not only differ in
> >> their
> >> > > last
> >> > > > > digit. The possible job fails can be traced back to the leap and
> >> > > > > antechamber programs and the errors apparent in Python LES API,
> C
> >> LES
> >> > > > API,
> >> > > > > and pytraj. tests but I don't know if I can "live" with these
> >> errors
> >> > > if I
> >> > > > > want to do some QM/MM calculations, so I would like to ask for
> >> some
> >> > > help.
> >> > > > >
> >> > > > > I don't really know how you can reproduce these results of mine,
> >> but
> >> > I
> >> > > > > attached some program specifications and the summary of my
> >> results.
> >> > > > >
> >> > > > > Any suggestion would be greatly appreciated.
> >> > > > >
> >> > > > > Sincerely yours,
> >> > > > > Bence Hégely
> >> > > > >
> >> > > > > _______________________________________________
> >> > > > > AMBER mailing list
> >> > > > > AMBER.ambermd.org
> >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > >
> >> > > > >
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
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> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
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> >>
> >
> >
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Received on Tue Sep 06 2016 - 05:30:02 PDT
