I am trying to install OpenCL for BEAGLE. First, I have downloaded intel_sdk_for_opencl_applications_2020.3.494.tar.gz from here. Then I unzipped it & run install.sh. Installation was successful. I have BEAGLE installed so I have decided to go to build folder in beagle-lib & run cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME .. in order to go on to run make install but I get the next message:
-- JAVA_HOME=
-- JNI_INCLUDE_DIRS=/usr/lib/jvm/java/include;/usr/lib/jvm/java/include/linux;/usr/lib/jvm/java/include
-- JNI_LIBRARIES=/usr/lib/jvm/java/lib/libjawt.so;/usr/lib/jvm/java/lib/server/libjvm.so
-- Not using libtools for plugins
-- Could NOT find OpenCL (missing: OpenCL_LIBRARY OpenCL_INCLUDE_DIR)
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)
-- Configuring done
-- Generating done
-- Build files have been written to: /export/home/rinkman/beagle-lib/build
I have tried to set variables both environmental & shell to
OpenCL_LIBRARY=~/intel/system_studio_2020/opencl/SDK/include/CL/cl.h
OpenCL_INCLUDE_DIR=True
But the result of running cmake is the same. I have verified that variables were set up right. So I cannot understand what is wrong. I want to use OpenCL framework in BEAGLE when I am running BEAST 2 software. Please, could anyone help with this?
P.S. I am a noviciate in Linux.
My result of running beast -beagle-info:
BEAST v2.6.6, 2002-2021
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
Centre for Computational Evolution
University of Auckland
[email protected]
[email protected]
Institute of Evolutionary Biology
University of Edinburgh
[email protected]
David Geffen School of Medicine
University of California, Los Angeles
[email protected]
Downloads, Help & Resources:
http://beast2.org/
Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2
BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer
--- BEAGLE RESOURCES ---
0 : CPU
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
One on my computer with Windows for comparison:
BEAST v2.6.6, 2002-2021
Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard
Centre for Computational Evolution
University of Auckland
[email protected]
[email protected]
Institute of Evolutionary Biology
University of Edinburgh
[email protected]
David Geffen School of Medicine
University of California, Los Angeles
[email protected]
Downloads, Help & Resources:
http://beast2.org/
Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2
BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Tim Vaughan, Chieh-Hsi Wu, Walter Xie
Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer
--- BEAGLE RESOURCES ---
0 : CPU
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU
1 : NVIDIA GeForce 940MX
Global memory (MB): 2048
Clock speed (Ghz): 1.19
Number of cores: 384
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH COMPUTATION_ASYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_NONE THREADING_NONE PROCESSOR_GPU FRAMEWORK_CUDA
2 : Intel(R) HD Graphics 620 (OpenCL 2.1 )
Global memory (MB): 3219
Clock speed (Ghz): 1.00
Number of compute units: 24
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH COMPUTATION_ASYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_NONE THREADING_NONE PROCESSOR_GPU FRAMEWORK_OPENCL
3 : Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz (OpenCL 2.1 (Build 10))
Global memory (MB): 8067
Clock speed (Ghz): 2.50
Number of compute units: 4
Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH COMPUTATION_ASYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_OPENCL
2
Answers
The solution was to set variables through
-Dincmakeascmake -DOpenCL_INCLUDE_DIR=~/intel/system_studio_2020/opencl/SDK/include/ -DOpenCL_LIBRARY=~/intel/system_studio_2020/opencl/SDK/lib64/libOpenCL.so.1.2 -DCMAKE_INSTALL_PREFIX:PATH=$HOME ... The compiling was successful after that.make testwas executed without any problems. I detected the file libhmsbeagle-opencl.so.40.0.0 in ~/lib folder.This means that the CMake variables
OpenCL_LIBRARYandOpenCL_INCLUDE_DIRare missing, because OpenCL could not be found.Setting those two as environment variables changes nothing.
You need to tell CMake where things are, if they are not installed in standard directories (as seems to be the case with your OpenCL installation).
Try adding
-DOCL_ROOT=path/to/base/of/your/OpenCLto your call to CMake for a package-specific hint, or-DCMAKE_LIBRARY_PATH=path/to/...to make CMake search in that path (in addition to standard paths) for any package it might be looking for. Make sure you cleaned away all cached files beforehand, so that CMake runs clean and does not use cached values.