Re: [AMBER] update_amber URL time out problem

From: Meng Wu <>
Date: Thu, 24 May 2018 03:07:55 +0000

Hi Prof. David,

    Thanks for your answer. I have tried "$AMBERHOME/update_amber --check-updates", it could check the updates, but then I typed "./update_amber --upgrade", it stopped in the update.5: PatchingError: .patches/Amber16_Unapplied_Patches/update.5 failed to apply. No changes made from this patch. Then I downloaded the update files to local and applied them as the third-party patches using '--apply-patch=', I typed "./update_amber --show-applied-patches" and now it shows:

Amber 16 Applied Patches:
update.1 (modifies pmemd, pmemd.cuda, pmemd.cuda.MPI)
        Adds support for GPU Eternal Electric Fields:
        1) Adds support for external electric fields on GPU (serial + MPI)
        2) Cleans up some extraneous code in serial electric fields
        3) Adds test cases for GPU electric fields

update.2 (modifies pmemd.cuda.MPI)
        Fixes cuda MPI support for electric fields

update.3 (modifies pmemd)
        Adds support for KNL and Xeon optimizations
        1) Adds MPI/OpenMP support for Intel Compilers
        2) Adds performance enhancements for Xeon processors
        3) Adds Intel Xeon Phi KNL specific performance optimizations

update.4 (modifies pmemd)
        This patch adds the NFE module(with ABMD and SMD methods) to PMEMD and updates related test files.

Third-party Patches:
update.11, update.1, update.8, update.7, update.5, update.13, update.10, update.3, update.6, update.12, update.4, update.2

    Does this mean I have applied all the updates for Amber16 successfully? If yes, then how could I make these updates effective at one time? Just use './configure gnu' and then 'make install'?

Best regards
Meng Wu

Message: 23
Date: Wed, 23 May 2018 08:13:09 -0400
From: David A Case <>
Subject: Re: [AMBER] update_amber URL time out problem
To: AMBER Mailing List <>
Content-Type: text/plain; charset=us-ascii

On Wed, May 23, 2018, Meng Wu wrote:
> I am going to apply the update patches to Amber16 in our HPC, but
> when run the command "$AMBERHOME/update_amber --update" there an
> error appeared: urllib2.URLError: <urlopen error timed out> , does
> it mean something wrong with our internet?

It's hard to tell, but worth trying again to see if the problem goes
away, or trying on a different computer. What is the result of typing
"$AMBERHOME/update_amber --check-updates"?

Have you ever used the update_amber option before? It is possible that
your browser is using a proxy, and you need to tell update_amber about
that. Type "$AMBERHOME/update_amber --help" for information about that.

...good luck....dac


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Received on Wed May 23 2018 - 20:30:02 PDT
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