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-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.14.3 -- For how to use this build system, please read this wiki: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake -- For a list of important CMake variables, check here: -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options -- ************************************************************************** -- 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 /scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh Installing Miniconda Python. PREFIX=/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/install Unpacking payload ... /scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/install/conda.exe: error while loading shared libraries: libz.so.1: failed to map segment from shared object: Operation not permitted /scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/install/conda.exe: error while loading shared libraries: libz.so.1: 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 "/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/CMakeOutput.log". See also "/scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/CMakeError.log". If the cmake build report looks OK, you should now do the following: make install source /scratch/vaibhavdixit.bitspilani/amber20/amber.sh 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 (kitware.com/cmake). [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 11:20 cpptraj-master.zip -rw-rw-r-- 1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 172K Nov 8 20:25 AmberMdPrep-master.zip -rw-rw-r-- 1 vaibhavdixit.bitspilani vaibhavdixit.bitspilani 13K Dec 4 20:00 st-master.zip 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 Regards, 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, Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com https://niperguwahati.ac.in/DOC/profile/dixit.pdf https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/ ORCID ID: https://orcid.org/0000-0003-4015-2941 NCBI bibliography: https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/ http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra Please consider the environment before printing this e-mail On Mon, Dec 13, 2021 at 8:14 PM David A Case <david.case.rutgers.edu> 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 kitware.com. 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 > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 16 2021 - 05:30:03 PST