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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 -- ************************************************************************** -- Setting C compiler to gcc -- Setting CXX compiler to g++ -- Setting Fortran compiler to gfortran -- Amber source found, building AmberTools and Amber -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- The Fortran compiler identification is GNU 7.5.0 -- Check for working C compiler: /home/apps/gcc-7.5.0/bin/gcc -- Check for working C compiler: /home/apps/gcc-7.5.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/apps/gcc-7.5.0/bin/g++ -- Check for working CXX compiler: /home/apps/gcc-7.5.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working Fortran compiler: /home/apps/gcc-7.5.0/bin/gfortran -- Check for working Fortran compiler: /home/apps/gcc-7.5.0/bin/gfortran -- works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /home/apps/gcc-7.5.0/bin/gfortran supports Fortran 90 -- Checking whether /home/apps/gcc-7.5.0/bin/gfortran supports Fortran 90 -- yes -- Testing if stdlib.h can be included... -- Testing if stdlib.h can be included... yes -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found CUDA: /home/apps/cuda-10.1 (found version "10.1") -- Downloading Python 3 Miniconda -- Detected Linux OS. Downloading the Linux installer -- Using 64 bit miniconda Downloading http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -> /scratch/vaibhavdixit.bitspilani/amber20_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh ############################################################################################################################################################################################ 100.0% 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]$ 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 Fri, Dec 3, 2021 at 6:32 PM David A Case <david.case.rutgers.edu> wrote: > On Fri, Dec 03, 2021, Vaibhav Dixit wrote: > > >Is it possible to have a user-specific installation of ambertools on > >super-computers that doesn't require admin access? > > Yes. Nothing in Amber requires admin access. Instead of un-tarring the > file in /home/apps/amber, un-tar in your home directory, and work from > there. Take the miniconda option (using the default python3). > > > File > > >"/home/apps/amber/tmp/install_gnu/lib/python2.7/site-packages/ParmEd-at20RC5_54.g5702a232fe.dirty-py2.7-linux-x86_64.egg/parmed/utils/pairlist.py", > >line 5, in <module> > > import numpy as np > >ImportError: No module named numpy > > What options did you request relating to python and miniconda? > > ...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 Sat Dec 11 2021 - 22:00:02 PST