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________________________________
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Sent: Thursday, December 10, 2020 12:56:05 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20
Dear All,
I'm getting the following message while trying to install GPU version of
Amber20.
The serial and parallel versions installed as expected without errors
(tests passed).
The messages show that MPI, OpenMP and CUDA are OFF.
Additionally, there are many files that it can't find.
I'm using Amber18 on this machine with one RTX2080 installed and supplied
by Exxact. Thus I do have /usr/local/cuda/bin in my path but since I'm not
an expert in GPU installations I can't easily figure out why the default
cuda libraries and GPU settings are not working for Amber20.
Obviously, the next step "make install and make test.cuda.serial" failed
since these are dependent on correct configuration in the run_cmake step
(which failed).
Can someone please suggest to me, what I need to fix here for a smooth
installation?
Thank you very much and best regards.
(base) [exx.c107739 build]$ ./run_cmake
--
**************************************************************************
-- Starting configuration of Amber version 20.0.0...
-- CMake Version: 3.19.1
-- 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 found, building AmberTools and Amber
-- MPI C Compiler: /usr/local/mpich-3.2.1/bin/mpicc
-- MPI CXX Compiler: /usr/local/mpich-3.2.1/bin/mpicxx
-- MPI Fortran Compiler: /usr/local/mpich-3.2.1/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
-- 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
-- >>> No new updates available for Amber 20
-- Updater done. If you want to install updates, then set the
APPLY_UPDATES variable to true.
-- Checking whether to use built-in libraries...
-- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY
READLINE_IS_LINKABLE)
-- Could NOT find Termcap (missing: TERMCAP_LIBRARY TERMCAP_INCLUDE_DIR)
-- Cannot use internal readline because its dependency
(libtermcap/libtinfo/libncurses) was not found.
-- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to
point to your MKL installation location.
CMake Warning (dev) at
/usr/local/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
/usr/local/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
/usr/local/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.
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY
MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY)
-- 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 not found. Please specify library location.
-- LAPACK requires BLAS
-- A library with LAPACK API not found. Please specify library location.
-- The ARPACK library was not found. Please set ARPACK_LIBRARY to point to
it. (missing: ARPACK_LIBRARY ARPACK_WORKS)
CMake Warning (dev) at
/usr/local/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
/usr/local/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")
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system
program_options iostreams regex timer chrono filesystem graph)
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX. To locate it, add its install dir to the prefix
path.
-- 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: /usr/bin/bash
-- netcdf-fortran: Detected TS29113 support in Fortran compiler
-- Reticulating splines...
** (gedit:1471): WARNING **: 16:05:58.932: Error querying file info: Error
when getting information for file
¡§/home/exx/Downloads/amber20_src/build/config.h.tmp¡¨: No such file or
directory
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:
-----------------------------------------------------
-- 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
-- pnetcdf - used by cpptraj for parallel trajectory output
-- ---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
-- mpi4py - MPI support library for MMPBSA.py
-- perlmol - chemistry library used by FEW
-- ---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 MPI LES-MPI
-- Install location: /home/exx/Downloads/amber20/
-- Installation of Tests: ON
-- Compilers:
-- C: GNU 4.8.5 (/usr/bin/gcc)
-- CXX: GNU 4.8.5 (/usr/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/exx/Downloads/amber20//amber.sh file in your shell. Consider
adding the line
-- test -f /home/exx/Downloads/amber20//amber.sh && source
/home/exx/Downloads/amber20//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/exx/Downloads/amber20//amber.csh file in your shell. Consider
adding the line
-- test -f /home/exx/Downloads/amber20//amber.csh && source
/home/exx/Downloads/amber20//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /home/exx/Downloads/amber20/
-- Configuring done
-- Generating done
-- Build files have been written to: /home/exx/Downloads/amber20_src/build
If the cmake build report looks OK, you should now do the following:
make install
source /home/exx/Downloads/amber20/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
(base) [exx.c107739 build]$
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e¢e
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Dec 10 2020 - 03:00:03 PST
