Hello,
My name is Alain, I am a Computer Engineer and I work in a research group at the University of Alcalá (Madrid, Spain) focused on scientific calculation, we need to install AmberTools20 (only the CPU version at the moment) in parallel in our calculation Cluster. After installing the serial version of AmberTools20 we have tried to install the parallel version but due to a bug or a libraries error the installation of AmberTools20 in parallel stops at 21% and several error messages appear, we don't know how to fix these problems. We are currently using: CentOS 6.9 (Final) with Sun Grid Engine and TORQUE (with OpenMPI) as queuing system.
This is the output of the command "./run cmake" when trying to install AmberTools20 in the parallel version and the output of the subsequent command "make install" which is where the errors / bugs appear :
[root.nodo100 build]# ./run_cmake
-- **************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.19.0
-- 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 not found, only building AmberTools
-- MPI C Compiler: /opt/openmpi/bin/mpicc
-- MPI CXX Compiler: /opt/openmpi/bin/mpicxx
-- MPI Fortran Compiler: /opt/openmpi/bin/mpif90
-- If these are not the correct MPI wrappers, then set MPI_<language>_COMPILER to the correct wrapper and reconfigure.
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
-- Found and removed RPATH control flags from MPI flags
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Miniconda is installed in the build directory!
-- Found perl make: /usr/bin/make
-- Perl modules well be installed to AMBERHOME/lib/perl
-- Running updater...
-- >>> Preparing to apply updates... please wait.
-- >>> No new updates available for AmberTools 20
-- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true.
-- Checking whether to use built-in libraries...
CMake Warning (dev) at /opt/cmake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (OpenMP_C)
does not match the name of the calling package (OpenMPFixed). This can
lead to problems in calling code that expects `find_package` result
variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
cmake/hanjianwei/FindMKL.cmake:194 (find_package)
cmake/3rdPartyTools.cmake:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /opt/cmake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
does not match the name of the calling package (OpenMPFixed). This can
lead to problems in calling code that expects `find_package` result
variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
cmake/hanjianwei/FindMKL.cmake:194 (find_package)
cmake/3rdPartyTools.cmake:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /opt/cmake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args`
(OpenMP_Fortran) does not match the name of the calling package
(OpenMPFixed). This can lead to problems in calling code that expects
`find_package` result variables (e.g., `_FOUND`) to follow a certain
pattern.
Call Stack (most recent call first):
cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args)
cmake/hanjianwei/FindMKL.cmake:194 (find_package)
cmake/3rdPartyTools.cmake:221 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Cannot search for FFTW Fortran headers because the serial headers were not found
-- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS FFTW_LIBRARY_MPI FFTW_INCLUDES_MPI FFTW_MPI_WORKS)
-- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND)
-- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND)
-- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES)
-- Could NOT find xblas. Please set XBLAS_LIBRARY to point to libxblas.a.
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- The ARPACK library was not found. Please set ARPACK_LIBRARY to point to it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
CMake Warning (dev) at /opt/cmake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (PnetCDF_C)
does not match the name of the calling package (PnetCDF). This can lead to
problems in calling code that expects `find_package` result variables
(e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/FindPnetCDF.cmake:273 (find_package_handle_standard_args)
cmake/FindPnetCDF.cmake:396 (find_package_component)
cmake/3rdPartyTools.cmake:339 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR)
-- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB,
APBS_PMGC_LIB, APBS_MG_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES)
CMake Warning (dev) at /opt/cmake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:424 (message):
The package name passed to `find_package_handle_standard_args` (JNI) does
not match the name of the calling package (JNIFixed). This can lead to
problems in calling code that expects `find_package` result variables
(e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
cmake/patched-cmake-modules/FindJNIFixed.cmake:323 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/FindPUPIL.cmake:19 (find_package)
cmake/3rdPartyTools.cmake:368 (find_package)
CMakeLists.txt:194 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
-- Could not find the Java development libraries, so PUPIL can't be used. (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB)
-- Could not find lio. If you want to use it, set LIO_HOME to point to a built lio source directory.
-- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5")
-- Checking for Python package mpi4py -- not found
-- Checking for perl module Chemistry::Mol
-- Checking for perl module Chemistry::Mol - found at /home/apps/Chem/amber20/lib/perl/Chemistry/Mol.pm
-- Found PerlModules: TRUE
-- Could NOT find Boost (missing: timer chrono) (found version "1.41.0")
-- The following libraries were found on your system, but are not being used: mkl
-- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble.
-- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=<names>.
-- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE.
-- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it.
-- Generating amber source scripts
-- Configuring subdirs...
-- FFTW: compiler supports stack alignment: TRUE
-- Found bash: /bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
-- Reticulating splines...
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: -----------------------------------------------------
-- 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
-- mpi4py - MPI support library for MMPBSA.py
-- pnetcdf - used by cpptraj for parallel trajectory output
-- ---using installed: ------------------------------------------------------
-- blas - for fundamental linear algebra calculations
-- lapack - 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
-- perlmol - chemistry library used by FEW
-- ---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: ON
-- 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 MPI LES-MPI
-- Install location: /home/apps/Chem/amber20/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 4.8.5 (/opt/gcc/bin/gcc)
-- CXX: GNU 4.8.5 (/opt/gcc/bin/g++)
-- Fortran: GNU 4.8.5 (/opt/gcc/bin/gfortran)
[root.nodo100 build]# make install
[ 0%] Built target ucpp
[ 0%] Built target fftw3_threads_obj
[ 2%] Built target fftw_api
[ 2%] Built target dft
[ 2%] Built target dft_scalar
[ 3%] Built target dft_scalar_codelets
[ 7%] Built target dft_sse2_codelets
[ 8%] Built target rdft
[ 8%] Built target rdft_scalar
[ 9%] Built target rdft_scalar_r2cb
[ 11%] Built target rdft_scalar_r2cf
[ 11%] Built target rdft_scalar_r2r
[ 11%] Built target rdft_sse2_codelets
[ 12%] Built target fftw_kernel
[ 12%] Built target reodft
[ 12%] Built target simd_support
[ 12%] Built target fftw
[ 13%] Built target libfftw_bench
[ 13%] Built target fftw_benchmark_common_obj
[ 13%] Built target fftw_benchmark
[ 13%] Built target fftw_wisdom
[ 13%] Built target fftw_mpi
[ 13%] Built target fftw_mpi_benchmark
[ 13%] Built target dispatch
[ 14%] Built target netcdf3
[ 14%] Built target netcdf
[ 15%] Built target ncgen
[ 15%] Built target ncgen3
[ 15%] Built target nccopy
[ 15%] Built target ncdump
[ 15%] Built target netcdff
[ 15%] Built target xblas_build
[ 16%] Built target arpack
[ 20%] Built target pnetcdf_fortran_obj
[ 20%] Built target pnetcdf_c_obj
[ 20%] Built target pnetcdf
[ 20%] Built target ncvalid
[ 20%] Built target mpi4py
[ 20%] Built target boost_build
[ 20%] Built target amber_common
[ 21%] Built target rism
[ 21%] Linking Fortran shared library libpbsa.so
/usr/bin/ld: BFD version 2.20.51.0.2-5.47.el6_9.1 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size
/usr/bin/ld: Please report this bug.
collect2: error: ld returned 1 exit status
make[2]: *** [AmberTools/src/pbsa/libpbsa.so] Error 1
make[2]: *** Deleting file `AmberTools/src/pbsa/libpbsa.so'
make[1]: *** [AmberTools/src/pbsa/CMakeFiles/libpbsa.dir/all] Error 2
make: *** [all] Error 2
Thanks for your help.
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Received on Thu Dec 10 2020 - 05:00:03 PST
