Re: [AMBER] compile parallel mpi

From: Jason Swails <>
Date: Fri, 6 Dec 2013 11:50:40 -0500

On Fri, Dec 6, 2013 at 9:55 AM, Zahra Khatti <> wrote:

> Dear amberists
> I installed amber12 and ambertools13 , but I couldn't compile parallel mpi
> of amber.
> when I run the configure script after installing some compilers and
> libraries:
> sudo apt-get install csh flex gfortran g++ xorg-dev \ zlib1g-dev libbz2-dev
> ./configure gnu
> I got an error for fftw3 lib. then I entered:
> ./configure -nofftw3 gnu
> I got this error:
> IOError: [Errno 13] Permission denied:
> '.patches/AmberTools13_Unapplied_Patches/update.21'
> Automatic patching failed! Check the errors before re-configuring
> How can I configure?!

This error indicates to me a permission issue. The updating script
attempted to download update.21 to the file
.patches/AmberTools13_Unapplied_Patches/update.21 but was told that it did
not have permission to write that file.

Make sure that your user has ownership of $AMBERHOME (and all directories
therein) before trying to do any type of compiling. The following command
should give you ownership:

sudo chown -R `whoami` $AMBERHOME

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Dec 06 2013 - 09:00:07 PST
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