Re: [AMBER] AmberTools installation issue

From: Rybenkov, Valentin V. via AMBER <>
Date: Tue, 19 Jul 2022 15:51:00 +0000

Hello David,

Many thanks for the reply.

No, it did not work. I renamed the CMakeCahe.txt in the amber22_src/build directory, ran ./run_cmake -DBUILD_PERL=FALSE (no problems here),
then make install (the same error).

Somehow, the Perl module is still being built. Is there another place that instructs make to build Perl?

One thing that comes to mind, I did not uninstall CMake 23, which I initially downloaded from My machine is calling the local version of CMake regardless. Is there a config file (or similar) from the first installation of cmake that interferes with the build process?

I found a line in CMakeCache.txt that defines the “var” directory. "var” is the write-protected directory writing into which generates the error.

//Modifiable single-machine data (var)

Can this variable be redefined somewhere so as to use a user-accessible directory instead of var?

Valentin V. Rybenkov
University of Oklahoma
101 Stephenson Parkway
Norman, OK 73019

From: David A Case <>
Sent: Tuesday, July 19, 2022 7:48:27 AM
To: Rybenkov, Valentin V. <>; AMBER Mailing List <>
Subject: Re: [AMBER] AmberTools installation issue

On Sun, Jul 17, 2022, Rybenkov, Valentin V. via AMBER wrote:

>This is an update to the installation error of AmberTools22. I traced the
>error to a specific line in makefiles. The error involves an attempt to
>write into a privileged area. It occurs on line
>$(MAKE) $(MAKESILENT) -f CMakeFiles/Makefile2 PerlMol
>of the “# Target rules for targets named PerlMol’ of the main Makefile.
>Then into the block “# Target rules for target
>AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir” of
>Then into the file
>AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir/build.make, line “cd
>&& /usr/bin/make”,
>Specifically, the instruction “/usr/bin/make”
>generates an error, using presumably the Makefile in
>I do not understand why this script tries to write into a write-protected
>directory. This seems to be a bug in the installation package. Is there a
>way to bypass it?

Thanks for the detailed report, but I don't know why you are seeing this
problem, but no one else has reported it. There is no specific mention of
"/var" in this Makefile, and you may be correct that the C compiler is
choosing it. This is code from the Perl community, and we didn't write it.

We test Amber on CentOS 7 in a pretty vanilla virutal machine, and don't see
the problem.

Try adding the following define to your run_cmake script:


Remove the CMakeCache.txt file, and re-run the script, followed by make
install. That should skip the problem.

....hope this helps...dac

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Received on Thu Aug 04 2022 - 13:34:52 PDT
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