[AMBER] centos 7 install Ambertools20 error, final link failed: Bad value

From: He DC <virolog.outlook.com>
Date: Mon, 29 Jun 2020 14:50:32 +0000

Hi, Dear Amber Users,

I hold an user account and try using cmake to compile and install the AmberTools20 on the cluster.
The info about the cluster
CentOS Linux release 7.7.1908 (Core)
Linux version 3.10.0-1062.el7.x86_64
gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) )

With module list
  1) gcc/9.2.0 3) anaconda/2019.3
  2) mpich/3.3.2 4) cmake/3.15.7

However, I meet some errors when I did make install

[ 28%] Building Fortran object AmberTools/src/lapack/CMakeFiles/lapack.dir/dtrsyl.f.o
[ 28%] Linking Fortran shared library liblapack.so
/usr/bin/ld: /usr/local/lib/libblas.a(dgemm.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile
…………………….
/usr/bin/ld: /usr/local/lib/libblas.a(dcopy.o): relocation R_X86_64_PC32 against symbol `memcpy..GLIBC_2.14' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [AmberTools/src/lapack/CMakeFiles/lapack.dir/build.make:3671: AmberTools/src/lapack/liblapack.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2936: AmberTools/src/lapack/CMakeFiles/lapack.dir/all] Error 2
make: *** [Makefile:152: all] Error 2

I was firstly trying to google this error and failed to find out any useful information.
So, I send this mass email to ask for help.
Did anybody meet the similar problem?
Any suggestions?

Best regards,
DH



P.S compile info
**************************************************************************
If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES
-- **************************************************************************
-- 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: -----------------------------------------------------
-- 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: ------------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- readline - used for the console functionality of cpptraj
-- 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
-- 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
--                                Features:
-- MPI:                     OFF
-- OpenMP:                  OFF
-- CUDA:                    OFF
-- Build Shared Libraries:  ON
-- Build GUI Interfaces:    ON
-- Build Python Programs:   ON
--  -Python Interpreter:    Internal Miniconda (version 3.7)
-- Build Perl Programs:     ON
-- Build configuration:     RELEASE
-- Target Processor:        x86_64
-- Build Documentation:     OFF
-- Sander Variants:         normal LES API LES-API
-- Install location:        /data/home/hedongchang/apps/amber20/
-- Installation of Tests:   ON
--                               Compilers:
--         C: GNU 9.2.0 (/data/apps/gcc-9.2.0/bin/gcc)
--       CXX: GNU 9.2.0 (/data/apps/gcc-9.2.0/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 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 - Not included in AmberTools
-- pmemd - Not included in AmberTools
-- **************************************************************************
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Received on Mon Jun 29 2020 - 08:00:03 PDT