I just recently compiled Amber18 and AmberTools19 on Centos7. Trying to build using the most recent versions of gcc and openmpi (10.1.0 and 4.0.3) produced error in some way relating to “lapack” for me as well (did not save the output).
Rather than trying to figure out how to solve this problem I reverted to using the same set of compilers I use on Ubuntu 18.04 LTS (gcc7 and OpenMPI 2.1.1) and the compile and tests ran and finished without errors.
I have no idea what is causing this issue. I have not put any energy into finding out why right now as I needed a working installation right away. However, checking the configure file I realise that the tested versions of gnu compilers are listed as 4.8.4 +, I am not completely sure what the + indicates regarding upper limit of tested versions though I suspect this might have something to do with the observed issues.
At some point in time I will try to dig into this and probably try to recompile using intel compilers (icc/ifort) as these have been tested for 12-17 and as far as I can see, 17 is the latest available version.
Hope this helps
// Gustaf
> On 29 Jun 2020, at 16:50, He DC <virolog.outlook.com> wrote:
>
>
> 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 - 23:30:03 PDT
