Hi all,
I removed cmake. And create a symbolic link as cmake, directing to cmake3 under /usr/bin.
In this way I kinda force system to use cmake3.
I re-ran ¡°./run_cmake¡± and then ¡°make install¡± but similar error was reported:
[ 31%] Built target sff
[ 32%] Built target gbnsr6
[ 32%] Linking C shared library libcifparse.so
CMakeFiles/cifparse.dir/lex.cif.c.o:(.bss+0x8): multiple definition of `cifpin'
CMakeFiles/cifparse.dir/cifparse.c.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [AmberTools/src/cifparse/libcifparse.so] Error 1
make[1]: *** [AmberTools/src/cifparse/CMakeFiles/cifparse.dir/all] Error 2
make: *** [all] Error 2
========================================================================
Below is the build report:
**************************************************************************
-- Build Report
-- Compiler Flags:
-- C No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O0
-- C Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
--
-- CXX No-Opt: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0
-- CXX Optimized: -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native
--
-- Fortran No-Opt: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0
-- Fortran Optimized: -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3 -mtune=native
--
-- 3rd Party Libraries
-- ---building bundled: -----------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- lapack - for fundamental linear algebra calculations
-- arpack - for fundamental linear algebra calculations
-- ucpp - used as a preprocessor for the NAB compiler
-- netcdf - for creating trajectory data files
-- netcdf-fortran - for creating trajectory data files from Fortran
-- fftw - used to do Fourier transforms very quickly
-- xblas - used for high-precision linear algebra calculations
-- boost - C++ support library
-- perlmol - chemistry library used by FEW
-- ---using installed: ------------------------------------------------------
-- zlib - for various compression and decompression tasks
-- libbz2 - for bzip2 compression in cpptraj
-- libm - for fundamental math routines if they are not contained in the C library
-- ---disabled: ------------------------------------------------
-- c9x-complex - used as a support library on systems that do not have C99 complex.h support
-- readline - used for the console functionality of cpptraj
-- lio - used by Sander to run certain QM routines on the GPU
-- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver
-- pupil - used by Sander as an alternate user interface
-- plumed - used as an alternate MD backend for Sander
-- mkl - alternate implementation of lapack and blas that is tuned for speed
-- mbx - computes energies and forces for pmemd with the MB-pol model
-- Features:
-- MPI: OFF
-- OpenMP: OFF
-- CUDA: OFF
-- Build Shared Libraries: ON
-- Build GUI Interfaces: ON
-- Build Python Programs: ON
-- -Python Interpreter: Internal Miniconda (version 3.8)
-- Build Perl Programs: ON
-- Build configuration: RELEASE
-- Target Processor: x86_64
-- Build Documentation: OFF
-- Sander Variants: normal LES API LES-API
-- Install location: /home/gqshi/amber20/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 10.2.0 (/usr/local/bin/gcc)
-- CXX: GNU 10.2.0 (/usr/local/bin/g++)
-- Fortran: GNU 4.8.5 (/usr/bin/gfortran)
-- Building Tools:
-- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil
-- NOT Building Tools:
-- quick - In-development programs are disabled.
-- pymdgx - In-development programs are disabled.
-- gpu_utils - Requires CUDA
-- **************************************************************************
-- Environment resource files are provided to set the proper environment
-- variables to use AMBER and AmberTools. This is required to run any Python
-- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
--
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /home/gqshi/amber20//amber.sh file in your shell. Consider adding the line
-- test -f /home/gqshi/amber20//amber.sh && source /home/gqshi/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/gqshi/amber20//amber.csh file in your shell. Consider adding the line
-- test -f /home/gqshi/amber20//amber.csh && source /home/gqshi/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /home/gqshi/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gqshi/amber20_src/build
·¢¼þÈË: ʯ¹ÈÇß
·¢ËÍʱ¼ä: 2021Äê4ÔÂ13ÈÕ 11:48
ÊÕ¼þÈË: 'amber.ambermd.org' <amber.ambermd.org>
Ö÷Ìâ: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin'
Dear AMBER community.
I ran into a set of problems when installing AMBER20 on CentOS 7.
Below are the steps I followed and the error messages I ran into during ¡°make install¡±.
My questions are:
1. Should I keep using cmake3 for CentOS 7? But apparently during ¡°make install¡± step, still cmake is called.
2. Should I re-build AMBER20 with cmake?
How should I proceed¡.? Please let me know if more information are needed.
Thank you!
Guqin
=============================================================================================================
1. ## go to: https://ambermd.org/InstCentOS.php
## and install all packages needed for CentOS 7
2. ## according to: https://ambermd.org/pmwiki/index.php/Main/CMake-Quick-Start
## on CentOS 7, cmake3 should be used in all commands in place of cmake
yum install cmake3
3. ## go to amber20_src/build
## edit run_cmake file: all cmake has been changed to cmake3
./run_cmake
## the build report looks complicated but seemingly no errors.
4. ## under amber20_src/build
make install
## 4a. at around 29%, error said "cmake is not found"
apparently I don't have a way to change cmake to cmake3 in this step...so I installed cmake with yum.
yum install cmake
make install
## 4b. at 32% got below error messages:
## Scanning dependencies of target cifparse
## [ 32%] Building C object AmberTools/src/cifparse/CMakeFiles/cifparse.dir/cifparse.c.o
## [ 32%] Building C object AmberTools/src/cifparse/CMakeFiles/cifparse.dir/lex.cif.c.o
## [ 32%] Building C object AmberTools/src/cifparse/CMakeFiles/cifparse.dir/cifp.tab.c.o
## [ 32%] Linking C shared library libcifparse.so
## CMakeFiles/cifparse.dir/lex.cif.c.o:(.bss+0x8): multiple definition of `cifpin'
## CMakeFiles/cifparse.dir/cifparse.c.o:(.bss+0x0): first defined here
## collect2: error: ld returned 1 exit status
## make[2]: *** [AmberTools/src/cifparse/libcifparse.so] Error 1
## make[1]: *** [AmberTools/src/cifparse/CMakeFiles/cifparse.dir/all] Error 2
## make: *** [all] Error 2
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Received on Mon Apr 12 2021 - 23:30:02 PDT
