Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7)

From: Jason Swails <>
Date: Sat, 21 Nov 2015 07:25:26 -0500

On Fri, Nov 20, 2015 at 11:51 PM, Elvis Martis <>

> Hello Jason,
> Many thanks for your reply, I tried to compile AMBER14 with CUDA-7.5, but
> as you had already guessed, it failed with similar errors.
> I am using AmberTools15, and I have not touched the source code for sure.
> As far as patching updates is concerned, I could not apply all the patches
> as the patching failed at update.5 with following error message (red text),
> and the other patches from update.6 to update.13 were neither downloaded
> nor applied.
> -----------------------------------------------
> Applying Amber 14/update.5
> PatchingError: .patches/Amber14_Unapplied_Patches/update.5 failed to apply.
> No changes made from this patch
> ------------------------------------------------
> Is there any other way, using which I can manually apply these patches??

​No. The only reason that these patches would *fail* to update is if the
source code was in some way changed or the update tracking was broken. The
only way to really "accidentally" break the update tracking is to untar a
fresh copy of AmberTools or Amber on top of an existing amber14 directory
that has already been updated. This would trick update_amber into thinking
that the updates have already been applied when in fact you replaced the
source code with an unpatched copy. There are other things that can go
wrong with this approach, too, so you should never do that.

> By typing ./update_amber --version, I get following output
> -----------------------------------------------------
> AmberTools version 15.06 <this looks fine to me>
> Amber version 14.04 <this is different from what you suggested, and
> I guess because no patches were applied after update.4>

​What this tells me is that your Amber 14 source code is corrupt. I'm not
sure how it happened, but the source code has clearly been changed somehow
compared to the "official" release with bug fixes. Since there's no way
for us to know *how* it's been changed (especially if you do not know
yourself), or what those changes are, the only thing that we can suggest is
to delete your Amber installation and start over. Make sure you start from
Amber14.tar.bz2 (the original tarball release) -- do not just copy it from
some other place since that is an easy way for this kind of thing to happen
in the first place.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Nov 21 2015 - 04:30:03 PST
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