Re: [AMBER] numpy error with pdb4amber on cluster

From: Vaibhav Dixit <>
Date: Thu, 16 Dec 2021 18:34:07 +0530

Dear David,
I have the cmake already installed on the system as shown by the version
option below.
I tared the AmberTools20 and Amber20 files, then moved to amber20_src/build
directory and did ./run_cmake as suggested in the manual.
With this, I get the following errors telling the configuration is
incomplete because some operations are not permitted!
AS you suggested earlier Amber doesn't require root access, thus why some
operations are not permitted is not clear to me.
Please suggest to me how to fix this.
FYI the AmberTools and Amber20 tar files are 461M and 99M in size, I hope
these are ok.
Looking forward to your valuable and insightful suggestions.
Thank you and best regards.

[vaibhavdixit.bitspilani.login4 build]$ ./run_cmake
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.14.3
-- For how to use this build system, please read this wiki:
-- For a list of important CMake variables, check here:
-- Amber source found, building AmberTools and Amber
-- Downloading Python 3 Miniconda
-- Detected Linux OS. Downloading the Linux installer
-- Using 64 bit miniconda
-- Using cached Miniconda installer at
Installing Miniconda Python.
Unpacking payload ...
error while loading shared libraries: failed to map segment from
shared object: Operation not permitted
error while loading shared libraries: failed to map segment from
shared object: Operation not permitted
CMake Error at cmake/UseMiniconda.cmake:146 (message):
  Miniconda installer failed! Please fix what's wrong, or disable Miniconda.
Call Stack (most recent call first):
  cmake/PythonInterpreterConfig.cmake:64 (download_and_use_miniconda)
  CMakeLists.txt:121 (include)
-- Configuring incomplete, errors occurred!
See also
See also
If the cmake build report looks OK, you should now do the following:
    make install
    source /scratch/vaibhavdixit.bitspilani/amber20/
Consider adding the last line to your login startup script, e.g. ~/.bashrc
[vaibhavdixit.bitspilani.login4 build]$
[vaibhavdixit.bitspilani.login4 vaibhavdixit.bitspilani]$ cmake --version
cmake version 3.14.3
CMake suite maintained and supported by Kitware (
[vaibhavdixit.bitspilani.login4 vaibhavdixit.bitspilani]$
[vaibhavdixit.bitspilani.login4 vaibhavdixit.bitspilani]$ ls -arlth
total 598M
drwxrwxr-x   4 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 4.0K Apr  1
 2021 AmberMdPrep-master
-rw-rw-r--   1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani  99M Aug 10
17:49 Amber20.tar.bz2
-rw-rw-r--   1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 461M Aug 10
17:50 AmberTools20.tar.bz2
-rw-rw-r--   1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani  39M Nov  8
-rw-rw-r--   1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 172K Nov  8
-rw-rw-r--   1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani  13K Dec  4
drwxr-xr-x 597 root                    root                     36K Dec 14
19:15 ..
drwx------   6 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 4.0K Dec 14
20:26 .
drwxrwxr-x  16 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 4.0K Dec 14
20:38 cpptraj-master
drwxrwxr-x  13 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 4.0K Dec 14
20:45 amber20_src
drwxrwxr-x  18 vaibhavdixit.bitspilani vaibhavdixit.bitspilani  16K Dec 16
17:08 1BVY
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
NCBI bibliography:
Please consider the environment before printing this e-mail
On Mon, Dec 13, 2021 at 8:14 PM David A Case <> wrote:
> On Sun, Dec 12, 2021, Vaibhav Dixit wrote:
> >I just tried to install ambertools via the run_cmake option using "module
> >load cmake" option but I'm getting the following error message.
> Sorry: I don't know what exactly you mean by "using 'module load cmake'
> option".  Can you state exactly what you did?
> I have a vague recollection that other people have seen problems trying to
> get cmake via conda.  But my memory on this is pretty shaky.  I always just
> grab a cmake executable from  Note that a working executable
> has to be in your PATH; it is not enough to just point to some folder in
> the
> run_cmake script.
> ....dac
> _______________________________________________
> AMBER mailing list
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Received on Thu Dec 16 2021 - 05:30:03 PST
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