Re: [AMBER] Fwd: parallel amber installation failed

From: Fabian Gmail <>
Date: Tue, 7 Oct 2014 21:14:39 +0300

Jason, Dac,

Thanks a lot for your suggestions we will try to follow and report if still having problems.

Our clusters experts will take a good look and report.



Sent from my iPhone

> On 7 באוק 2014, at 20:58, Jason Swails <> wrote:
>> On Tue, 2014-10-07 at 13:53 -0400, David A Case wrote:
>>> On Tue, Oct 07, 2014, Fabian Glaser wrote:
>>> Thanks for your quick reply here there is a link to both files with the
>>> configure and make outputs, please let me know if you can access them.
>> Several things to look at:
>> 1. the configure script failed to find patches; this may be because you
>> have made local changes to the code that don't work with the patches, or
>> because of some other problem. (We need to work on getting better error
>> messages when update_amber fails, or have manual instructions that could
>> better pinpoint which patch is failing and why).
>> Suggestion is to upgrade to a fresh AmberTools14 and try that.
>> 2. You ran configure with gnu compilers specified (at least as far as one can
>> tell in the configure log file), but the make.out indicates that you are using
>> mpicc, etc. from the Intel compiler suite. You must configure MPI to use the
>> same compilers that were used at configure time. Typing "mpicc -show" will
>> indicate exactly what mpicc is doing "under the hood", and may help in getting
>> a consistent implementation.
> Ah, good catch. I didn't notice this. This would definitely cause
> problems and needs to be fixed.
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Oct 07 2014 - 11:30:03 PDT
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