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)
Description:
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)
Description:
Fixes cuda MPI support for electric fields
update.3 (modifies pmemd)
Description:
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)
Description:
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 <david.case.rutgers.edu>
Subject: Re: [AMBER] update_amber URL time out problem
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180523121309.5bshxce2ylamdaif.vpn-client-172-16-8-12.rutgers.edu>
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
