Hi,
I am trying to install pmemd.cuda. I installed the serial and MPI version
successfully then I installed NVIDIA CUDA then I changed run_cmake to
install the GPU version. Here is what I get and I don't know what to do
(OS: wsl2 ubuntu 22):
-- CUDA version 11.5 detected
-- Configuring for SM3.5, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1, SM7.0, SM7.5
and SM8.0
-- Checking CUDA and GNU versions -- compatible
-- 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 22
-- >>> No new updates available for Amber 22
-- 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_WORKS)
-- 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-3.20/Modules/FindPackageHandleStandardArgs.cmake:438
(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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY)
CMake Warning (dev) at
/usr/local/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:438
(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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY)
CMake Warning (dev) at
/usr/local/share/cmake-3.20/Modules/FindPackageHandleStandardArgs.cmake:438
(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:223 (find_package)
CMakeLists.txt:205 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find OpenMP_Fortran (missing: OpenMP_pthread_LIBRARY)
-- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY
MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY
OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS)
-- hints given to look for KMMD in DIR:
-- found KMMD?: KMMD_LIB-NOTFOUND
-- found INCLUDES?:
-- Did not find an external KMMD library, should be able to use bundled. If
you have a custom version then set the path with -DKMMD_DIR (missing:
KMMD_LIB)
-- 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 Protobuf (missing: Protobuf_LIBRARIES
Protobuf_INCLUDE_DIR)
-- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS
XBLAS_FORTRAN_WORKS)
-- 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)
-- Could NOT find PnetCDF (missing: PnetCDF_LIBRARY PnetCDF_INCLUDE_DIR
PnetCDF_WORKS)
-- 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)
-- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2
JAVA_AWT_INCLUDE_PATH)
-- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB
PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS)
-- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS)
-- 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
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system
program_options iostreams regex timer chrono filesystem graph)
-- Could NOT find NCCL (missing: NCCL_INCLUDE_DIR NCCL_LIBRARY)
-- Could NOT find MBX (missing: MBX_DIR)
-- Could not find MBX. To locate it, add its install dir to the prefix
path.
-- Could NOT find tng_io (missing: tng_io_DIR)
-- Could not find tng_io. To locate it, add its install dir to the prefix
path.
-- KMMD not added to 3RDPARTY_SUBDIRS :
-- : cpptraj/src/readline;fftw-3.3
-- 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.
-- Building the GTI version of pmemd.cuda
CMake Error at cmake/PMEMDCompilerFlags.cmake:230 (message):
NCCL is selected for inter-GPU communications but was not found.
Call Stack (most recent call first):
CMakeLists.txt:211 (include)
-- Configuring incomplete, errors occurred!
See also "/mnt/d/amber22/amber22_src/build/CMakeFiles/CMakeOutput.log".
See also "/mnt/d/amber22/amber22_src/build/CMakeFiles/CMakeError.log".
If the cmake build report looks OK, you should now do the following:
make install
source /mnt/d/amber22/amber22/amber.sh
Consider adding the last line to your login startup script, e.g. ~/.bashrc
cat run_cmake:
------------------------
#!/bin/bash
# This file gives some sample cmake invocations. You may wish to
# edit some options that are chosen here.
# For information on how to get cmake, visit this page:
#
https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Quick-Start
# For information on common options for cmake, visit this page:
#
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
# (Note that you can change the value of CMAKE_INSTALL_PREFIX from what
# is suggested below, but it cannot coincide with the amber22_src
# folder.)
AMBER_PREFIX=$(dirname $(dirname `pwd`))
if [ `uname -s|awk '{print $1}'` = "Darwin" ]; then
# For macOS:
if [ -x /Applications/CMake.app/Contents/bin/cmake ]; then
cmake=/Applications/CMake.app/Contents/bin/cmake
else
cmake=cmake
fi
$cmake $AMBER_PREFIX/amber22_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
-DCOMPILER=CLANG -DBLA_VENDOR=Apple \
-DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=FALSE \
-DDOWNLOAD_MINICONDA=FALSE \
2>&1 | tee cmake.log
else
# Assume this is Linux:
cmake $AMBER_PREFIX/amber22_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=TRUE -DNCCL=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
fi
if [ ! -s cmake.log ]; then
echo ""
echo "Error: No cmake.log file created: you may need to edit run_cmake"
exit 1
fi
echo ""
echo "If the cmake build report looks OK, you should now do the following:"
echo ""
echo " make install"
echo " source $AMBER_PREFIX/amber22/amber.sh"
echo ""
echo "Consider adding the last line to your login startup script, e.g.
~/.bashrc"
echo ""
------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:37:47 PDT
