Re: [AMBER] question about failures

From: peker milas <>
Date: Tue, 8 Dec 2009 00:31:06 -0500

Hi again,

you have no idea how i m grateful for this quick reply, so thank you
again. What i understand from your email, this is an important
problem because i would like to use this program with all of its
features. Now, it looks like being more explicit about the situation
is needed. First of all this machine has 2 intel nehalem cpu s (8
physical cores and 16 logical cores) on it, with 8Gb ram. It also has
ubuntu 9.10 (kermic i believe) as its operating system. Its compiler
set is gcc 4.4.1. I installed AmberTools1.2 using gcc. There was some
bugs in configuration script and in fortran.cpp file which i fixed.
And then, probably more than 10 times i tried to install Amber10
parallel. While i was installing i believe i used all relevant
paralellizations (mpich,openmpi, even lam which was the default
parallelization method, so that comes with amber ). Every single trial
failed when i run tests. What i meant is the program started doing
either the first or the second test but it could never finish. This
was frustrating enough and i decided to install it first serially.
When i did that i got those errors. What i m trying to say here i
really lost in this installation process and i will definitely need
help for both types of installation. Again if somebody wants to help
it will be appreciated deeply...

thank you so much...

On Mon, Dec 7, 2009 at 11:51 PM, Jason Swails <> wrote:
> All but one of these differences seem benign.  The tip5p test, however, is
> slightly disconcerting since it doesn't appear that any output was created
> by the test run comparable to that blip that's printed in
> TEST_FAILURES.dif.  If you plan on using that solvent model, I'd check out
> that test case a little more carefully.
> Good luck!
> Jason
> On Mon, Dec 7, 2009 at 10:37 PM, peker milas <> wrote:
>> Dear Amber users,
>> I recently installed AmberTools 1.2 and Amber 10 to a pc. Just for now
>> it is serial but i m planning to make it parallel in a very near
>> future. At the same time i had some test failures. I will attach my
>> test failures file to this email. My question is about those failures.
>> If anybody can explain me whether they are crucial or not also whether
>> i should fix them  i will be very happy.
>> Thank you so much
>> peker
>> _______________________________________________
>> AMBER mailing list
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list

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Received on Mon Dec 07 2009 - 22:00:02 PST
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