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
>> > > > >
>> > > > > _______________________________________________
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>> > > > > AMBER.ambermd.org
>> > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > >
>> > > > >
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Received on Tue Aug 30 2016 - 10:30:03 PDT
