Dear Raman,
Thanks for quick response.
No the GPU is off as shown below.
Will just setting it on fix it?
If yes, which command should I use for the same?
Thank you.
(base) [exx.c107739 build]$ nvidia-smi
Thu Dec 10 16:18:53 2020
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 430.40 Driver Version: 430.40 CUDA Version: 10.1
|
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr.
ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
M. |
|===============================+======================+======================|
| 0 GeForce RTX 208... Off | 00000000:02:00.0 On |
N/A |
| 26% 32C P8 14W / 250W | 421MiB / 7981MiB | 1%
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name Usage
|
|=============================================================================|
| 0 1720 G /usr/bin/X
152MiB |
| 0 2557 G /usr/bin/gnome-shell
87MiB |
| 0 3509 G ...6, --gpu-preferences=KAAAAAAAAAAgAAAgAA
179MiB |
+-----------------------------------------------------------------------------+
On Thu, Dec 10, 2020 at 7:58 PM Raman Preet Singh <
ramanpreetsingh.hotmail.com> wrote:
> Does nvidia-smi show the GPU is running?
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> 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,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> 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
>
> P Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
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
P Please consider the environment before printing this e-mail
_______________________________________________
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Received on Thu Dec 10 2020 - 03:30:02 PST
