Did the GPU worked earlier?
I have run into such issues mostly when the OS updates (Ubuntu, in my case). There are several ways to address this which you could find under CUDA installation directions on NVIDIA website, Quora or other places. You may need to try more than one of the methods depending on your system configuration (OS, hardware, etc.). However, I often find it to be a recurrent issue when fixed by any of these methods and the best option that I find in such case is to just remove CUDA Toolkit and the driver. A fresh install of CUDA Toolkit with drivers is often the remedy. Nouveau drivers will need to be shutdown.
You may need to recompile Amber once CUDA Toolkit is re-installed.
One thing to note is that if you are using CUDA 10.x or before, you will need to compile with gcc 7 or so.
Let me know if you need any further info.
Regards,
Raman
Get Outlook for Android<
https://aka.ms/ghei36>
________________________________
From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Sent: Thursday, December 10, 2020 1:01:22 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20
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
_______________________________________________
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
Received on Thu Dec 10 2020 - 04:30:02 PST
