Re: [AMBER] updates for amber12 bugfix18 & 19 fail

From: Jason Swails <>
Date: Tue, 3 Sep 2013 08:18:57 -0400

On Tue, Sep 3, 2013 at 4:08 AM, Vijay Manickam Achari

> I can not compile amber12 since I get update failure during installation..
> Could anyone help?
> The message I get as below:
> [root.glycogpu amber12]# ./configure -mpi gnu
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
> Available AmberTools 13 patches:
> No patches available
> Available Amber 12 patches:
> bugfix.18.bz2 (modifies No information available)
> Released on No information available (written by No information available)
> Description:
> No information available
> bugfix.19 (modifies pmemd.cuda)
> Released on Aug. 15, 2013 (written by Ross Walker, Scott Le Grand, and Ben
> Madej)
> Description:
> Minor fixes and updates to the GPU code:
> 1. Adds support for CUDA 5.5. - via accompanying AMBERTools 13 bugfix.16.
> 2. Disables NMROPT on multiple GPUs due to unfixed bugs in the MPI version
> at present.
> 3. Enables support for GTX-Titan and GTX780 GPUs and checks that the
> minimum
> required driver version of v325.15 is installed.
> 4. Fix spurious crash with kNLBuildNeighborListOrthogonal16_kernel
> for systems containing large vacuum bubbles or very low density.
> 5. Updates GPU code citation.
> 6. Adds missing test case output for GPU Jarinski Tests.
> 7. Updates GPU code to v12.3.1
> There are patches available. Do you want to apply them now? [y/n]
> (Recommended Y)
> y
> Preparing to apply updates... please wait.
> No new updates available for AmberTools 13
> Applying Amber 12/bugfix.18
> PatchingError: .patches/Amber_Unapplied_Patches/bugfix.18 failed to apply.
> No changes made from this patch
> Automatic patching failed! Check the errors before re-configuring

Run these commands and tell me what the output is:

patch -p0 -N --dry-run < .patches/Amber_Unapplied_Patches/bugfix.18

[root.glycogpu amber12]# ll

Unrelated, but I would strongly suggest _against_ installing Amber as root.
 You would be better off changing the ownership of your Amber12 directory
to your standard user and install from there instead. This is good advice
for any package -- if you can avoid installing something as root, you
should do so. Package managers can be trusted (e.g., apt-get, yum, zypper,
etc.), but I even change the ownership of /usr/local to a standard account
so I rarely even have to run "make install" from any package using root
privileges. [You are of course free to disregard this advice, I just
thought I'd give my unrequested opinion.]

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 03 2013 - 05:30:05 PDT
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