Posts by kotenok2000

1) Message boards : Number crunching : Vote for BOINC (Message 2228)
Posted 23 days ago by kotenok2000
Post:
Voted
2) Message boards : Number crunching : Gpu app? (Message 2225)
Posted 18 Mar 2024 by kotenok2000
Post:
Opencl.
https://gitlab.com/Jukic/cmdock/-/tree/dev-opencl?ref_type=heads
3) Message boards : Number crunching : [Guide][Linux] Running SiDock@home tasks for CmDock on anonymous platform (Message 2167)
Posted 4 Jan 2024 by kotenok2000
Post:
I used 
meson setup  --prefix /opt/cmdock-0.2.0 build --buildtype release --optimization=3 -Dcpp_args=' -pipe -march=native  -mtune=native -flto '  -Dc_args=' -pipe -march=native  -mtune=native -flto '

 meson compile -C build -j 8

sudo meson install -C build


app_info.xml
<app_info>
<app>
        <name>cmdock-s</name>
        <user_friendly_name>CurieMarieDock 0.2.0 short tasks</user_friendly_name>
</app>
<app>
        <name>cmdock-l</name>
        <user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name>
</app>
<file_info>
        <name>cmdock-s_wrapper_0.2.0</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock-l_wrapper_0.2.0</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock-l_job_0.2.0.xml</name>
        <sticky/>
</file_info>
<file_info>
        <name>cmdock-s_job_0.2.0.xml</name>
        <sticky/>
</file_info>
<file_info>
        <name>docking_out</name>
        <sticky/>
</file_info>

<app_version>
        <app_name>cmdock-s</app_name>
        <version_num>100</version_num>
        <file_ref>
                <file_name>cmdock-s_wrapper_0.2.0</file_name>
                <main_program/>
        </file_ref>
        <file_ref>
                <file_name>cmdock</file_name>
                <open_name>cmdock</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>cmdock-s_job_0.2.0.xml</file_name>
                <open_name>job.xml</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>docking_out</file_name>
                <open_name>docking_out</open_name>
                <copy_file/>
        </file_ref>
</app_version>
<app_version>
        <app_name>cmdock-l</app_name>
        <version_num>100</version_num>
        <file_ref>
                <file_name>cmdock-l_wrapper_0.2.0</file_name>
                <main_program/>
        </file_ref>
        <file_ref>
                <file_name>cmdock</file_name>
                <open_name>cmdock</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>cmdock-l_job_0.2.0.xml</file_name>
                <open_name>job.xml</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>docking_out</file_name>
                <open_name>docking_out</open_name>
                <copy_file/>
        </file_ref>
</app_version>
</app_info>

cmdock-s_job_0.2.0.xml
<job_desc>
        <task>
                <application>cmdock</application>
                <stdout_filename>docking_log</stdout_filename>
                <command_line>-c -j 1 -b 1  -r target.prm -p "/opt/cmdock-0.2.0/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
                <checkpoint_filename>docking_out.chk</checkpoint_filename>
                <fraction_done_filename>docking_out.progress</fraction_done_filename>
                <setenv>CMDOCK_ROOT=/opt/cmdock-0.2.0/</setenv>
                <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.2.0/lib:$LD_LIBRARY_PATH</setenv>
                <setenv>PERL5LIB=/opt/cmdock-0.2.0/lib:$PERL5LIB</setenv>
        </task>
        <unzip_input>
                <zipfilename>ligands.zip</zipfilename>
        </unzip_input>
</job_desc>

cmdock-l_job_0.2.0.xml

<job_desc>
    <task>
        <application>cmdock</application>
        <stdout_filename>docking_log</stdout_filename>
        <command_line>-c -j 1 -b 1  -r target.prm -p "/opt/cmdock-0.2.0/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
        <checkpoint_filename>docking_out.chk</checkpoint_filename>
        <fraction_done_filename>docking_out.progress</fraction_done_filename>
        <setenv>CMDOCK_ROOT=/opt/cmdock-0.2.0/</setenv>
        <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.2.0/lib:$LD_LIBRARY_PATH</setenv>
        <setenv>PERL5LIB=/opt/cmdock-0.2.0/lib:$PERL5LIB</setenv>
    </task>
    <unzip_input>
        <zipfilename>ligands.zip</zipfilename>
    </unzip_input>
</job_desc>

Then i created symlink with 
ln -s /opt/cmdock-0.2.0/bin/cmdock cmdock

and created empty file with 
touch docking_out


Also downloaded boinc wrapper from https://boinc.berkeley.edu/dl/wrapper_26014_x86_64-pc-linux-gnu.zip
extracted, copied and renamed to cmdock-s_wrapper_0.2.0 and cmdock-l_wrapper_0.2.0
4) Message boards : News : CmDock source code (Message 2166)
Posted 4 Jan 2024 by kotenok2000
Post:
I used 
meson setup  --prefix /opt/cmdock-0.2.0 build --buildtype release --optimization=3 -Dcpp_args=' -pipe -march=native  -mtune=native -flto '  -Dc_args=' -pipe -march=native  -mtune=native -flto '

 meson compile -C build -j 8

sudo meson install -C build


app_info.xml
<app_info>
<app>
        <name>cmdock-s</name>
        <user_friendly_name>CurieMarieDock 0.2.0 short tasks</user_friendly_name>
</app>
<app>
        <name>cmdock-l</name>
        <user_friendly_name>CurieMarieDock 0.2.0 long tasks</user_friendly_name>
</app>
<file_info>
        <name>cmdock-s_wrapper_0.2.0</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock-l_wrapper_0.2.0</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock</name>
        <sticky/>
        <executable/>
</file_info>
<file_info>
        <name>cmdock-l_job_0.2.0.xml</name>
        <sticky/>
</file_info>
<file_info>
        <name>cmdock-s_job_0.2.0.xml</name>
        <sticky/>
</file_info>
<file_info>
        <name>docking_out</name>
        <sticky/>
</file_info>

<app_version>
        <app_name>cmdock-s</app_name>
        <version_num>100</version_num>
        <file_ref>
                <file_name>cmdock-s_wrapper_0.2.0</file_name>
                <main_program/>
        </file_ref>
        <file_ref>
                <file_name>cmdock</file_name>
                <open_name>cmdock</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>cmdock-s_job_0.2.0.xml</file_name>
                <open_name>job.xml</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>docking_out</file_name>
                <open_name>docking_out</open_name>
                <copy_file/>
        </file_ref>
</app_version>
<app_version>
        <app_name>cmdock-l</app_name>
        <version_num>100</version_num>
        <file_ref>
                <file_name>cmdock-l_wrapper_0.2.0</file_name>
                <main_program/>
        </file_ref>
        <file_ref>
                <file_name>cmdock</file_name>
                <open_name>cmdock</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>cmdock-l_job_0.2.0.xml</file_name>
                <open_name>job.xml</open_name>
                <copy_file/>
        </file_ref>
        <file_ref>
                <file_name>docking_out</file_name>
                <open_name>docking_out</open_name>
                <copy_file/>
        </file_ref>
</app_version>
</app_info>

cmdock-s_job_0.2.0.xml
<job_desc>
        <task>
                <application>cmdock</application>
                <stdout_filename>docking_log</stdout_filename>
                <command_line>-c -j 1 -b 1  -r target.prm -p "/opt/cmdock-0.2.0/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
                <checkpoint_filename>docking_out.chk</checkpoint_filename>
                <fraction_done_filename>docking_out.progress</fraction_done_filename>
                <setenv>CMDOCK_ROOT=/opt/cmdock-0.2.0/</setenv>
                <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.2.0/lib:$LD_LIBRARY_PATH</setenv>
                <setenv>PERL5LIB=/opt/cmdock-0.2.0/lib:$PERL5LIB</setenv>
        </task>
        <unzip_input>
                <zipfilename>ligands.zip</zipfilename>
        </unzip_input>
</job_desc>

cmdock-l_job_0.2.0.xml

<job_desc>
    <task>
        <application>cmdock</application>
        <stdout_filename>docking_log</stdout_filename>
        <command_line>-c -j 1 -b 1  -r target.prm -p "/opt/cmdock-0.2.0/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
        <checkpoint_filename>docking_out.chk</checkpoint_filename>
        <fraction_done_filename>docking_out.progress</fraction_done_filename>
        <setenv>CMDOCK_ROOT=/opt/cmdock-0.2.0/</setenv>
        <setenv>LD_LIBRARY_PATH=/opt/cmdock-0.2.0/lib:$LD_LIBRARY_PATH</setenv>
        <setenv>PERL5LIB=/opt/cmdock-0.2.0/lib:$PERL5LIB</setenv>
    </task>
    <unzip_input>
        <zipfilename>ligands.zip</zipfilename>
    </unzip_input>
</job_desc>

Then i created symlink with 
ln -s /opt/cmdock-0.2.0/bin/cmdock cmdock

and created empty file with 
touch docking_out


Also downloaded boinc wrapper from https://boinc.berkeley.edu/dl/wrapper_26014_x86_64-pc-linux-gnu.zip
extracted, copied and renamed to cmdock-s_wrapper_0.2.0 and cmdock-l_wrapper_0.2.0
5) Message boards : Number crunching : [Guide][Linux] Running SiDock@home tasks for CmDock on anonymous platform (Message 2164)
Posted 2 Jan 2024 by kotenok2000
Post:
Replace "meson setup --prefix /opt/cmdock-0.1.2 build" with "meson setup --prefix /opt/cmdock-0.2.0 build"
"meson compile" with "meson compile -C build"
and "meson install" with " sudo meson install -C build"

Then add following in /etc/profile
export CMDOCK_ROOT=/opt/cmdock-0.2.0
export PATH=$CMDOCK_ROOT/bin:$PATH
export LD_LIBRARY_PATH=$CMDOCK_ROOT/lib:$LD_LIBRARY_PATH
export PERL5LIB=$CMDOCK_ROOT/lib:$PERL5LIB
6) Message boards : Number crunching : WU become longer and longer (Message 2114)
Posted 4 Oct 2023 by kotenok2000
Post:
C:\programdata\BOINC\slots\#\docking_log should display more correct estimated time for completion.
7) Message boards : Number crunching : Howe can i run CurieMarieDock 0.2.0 short tasks on x86-64 cpu using anonymous platform on windows? (Message 1798)
Posted 15 Jan 2023 by kotenok2000
Post:
Howe can i run CurieMarieDock 0.2.0 short tasks on x86-64 cpu using anonymous platform on windows?
8) Questions and Answers : Windows : Why is rxdock only for linux? (Message 300)
Posted 19 Dec 2020 by kotenok2000
Post:
thank you.
9) Questions and Answers : Windows : Why is rxdock only for linux? (Message 270)
Posted 17 Dec 2020 by kotenok2000
Post:
Why is rxdock only for linux?
https://www.sidock.si/sidock/apps.php
10) Message boards : News : New application: CurieMarieDock (Message 188)
Posted 3 Dec 2020 by kotenok2000
Post:
I noticed in docking_log link to "https://www.curiedock.org/" but it does not work




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