BEAGLE do not see and/or not use OpenCL

Question

[Mordovian Guy]

Hello, everyone!

It is said that BEAST 2 can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS.

I installed both BEAST 2 & BEAGLE onto them. This gives me a boost by 3.6 times. It was said too that using OpenCL with BEAGLE gives me more speed-up. Nonetheless, my calculations takes from twelve hours to 3 days so I got really interested in this. Installing it on Windows were very simple. When I ran beast -beagle_info​, I saw:

                    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
                   [e-mail]
                    [e-mail]

               Institute of Evolutionary Biology
                    University of Edinburgh
                       [e-mail]

                David Geffen School of Medicine
             University of California, Los Angeles
                       [e-mail]

                  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

However, it still uses only resourse #0, even through forced beast -beagle_order 3 -threads 1 filename.xml. Although, in comparison to Linux case, it was more successful. ​

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. After that, 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

It was solved through manual specification of directories cmake -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 test was executed without any problems. I detected the file libhmsbeagle-opencl.so.40.0.0 in ~/lib folder. But beast -beagle_info did not show OpenCL. As there are older versions of BEAST & BEAGLE on the root, I tried to change very roughly startup script to run only my local BEAGLE but nothing changed:

#!/bin/sh

if [ -z "$BEAST" ]; then
        ## resolve links - $0 may be a link to application
        PRG="$0"

        # need this for relative symlinks
        while [ -h "$PRG" ] ; do
            ls=`ls -ld "$PRG"`
            link=`expr "$ls" : '.*-> \(.*\)$'`
            if expr "$link" : '/.*' > /dev/null; then
                PRG="$link"
            else
                PRG="`dirname "$PRG"`/$link"
            fi
        done

        # make it fully qualified
        saveddir=`pwd`
        BEAST0=`dirname "$PRG"`/..
        BEAST=`cd "$BEAST0" && pwd`
        cd "$saveddir"
fi

BEAST_LIB="$BEAST/lib"

if [ -z "$JAVA_HOME" ]; then
  JAVA=java
else
  JAVA="$JAVA_HOME"/bin/java
fi

# use BEAGLE_LIB if the BEAGLE library is not in a standard location
if [ -n "$BEAGLE_LIB" ]; then
        if [ -n "$BEAST_EXTRA_LIBS" ]; then
                BEAST_EXTRA_LIBS="$BEAST_EXTRA_LIBS:$BEAGLE_LIB"
        else
                BEAST_EXTRA_LIBS="$BEAGLE_LIB"
        fi
fi

# Explicitly add /usr/local/lib to library search path to ensure 
# beast continues to find beagle when installed here.  (This is
# necessary due to known problems with certain JREs.)
if [ -z "$LD_LIBRARY_PATH" ]; then
    export LD_LIBRARY_PATH=/usr/local/lib
else
    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":/usr/local/lib
fi

BEAST_EXTRA_LIBS="$HOME/lib/"

# use BEAST_EXTRA_LIBS variable to load BEAGLE and other libraries from non-default locations 
# this assumes that the library path contains all these libraries (or are set through LD_LIBRARY_PATH)
#if [ -n "$BEAST_EXTRA_LIBS" ]; then 
#  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx1g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
#else        
#  "$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx1g -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*
#fi
"$JAVA" -Dlauncher.wait.for.exit=true -Xms256m -Xmx1g -Djava.library.path="$BEAST_EXTRA_LIBS" -Duser.language=en -cp "$BEAST_LIB/launcher.jar" beast.app.beastapp.BeastLauncher $*

Please, could anyone help with this?

P.S. I am a noviciate in unix-systems.

Best regards,