Posts by kotenok2000

1) Message boards : News : Temporarily work unavailabilities (Message 2438)
Posted 31 Mar 2025 by kotenok2000
Post:
What is the next target?
2) Message boards : News : Temporarily work unavailabilities (Message 2433)
Posted 23 Mar 2025 by kotenok2000
Post:
Maybe Swine acute diarrhea syndrome coronavirus (SADS-CoV PLpro) next?
3) Message boards : News : Target # 23: Ebola GP1 (Message 2360)
Posted 9 Dec 2024 by kotenok2000
Post:
Fortunately there are precompiled binaries.
https://gitlab.com/Jukic/cmdock/-/releases
4) Message boards : News : Target # 23: Ebola GP1 (Message 2357)
Posted 9 Dec 2024 by kotenok2000
Post:
Will you have another vote for the next target?
5) Message boards : News : Target # 23: Ebola GP1 (Message 2349)
Posted 7 Dec 2024 by kotenok2000
Post:
I have noticed that cmdock has a job file for x86-64 pc cmdock-l at https://www.sidock.si/sidock/download/cmdock-l_job_2.02_x86_64-pc-linux-gnu.xml and https://www.sidock.si/sidock/download/cmdock-l_job_2.02_windows_x86_64.xml
When i have compared them with https://www.sidock.si/sidock/download/cmdock-s_job_2.02_arm-unknown-linux-gnueabihf.xml cmdock they were almost identical.
They even use same command line parameters. <command_line>-c -j 1 -b 1 -r target.prm -p "$PWD\data\scripts\dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out</command_line>
6) Message boards : News : Target # 23: Ebola GP1 (Message 2347)
Posted 7 Dec 2024 by kotenok2000
Post:
No. I use WSL1
https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux
7) Message boards : News : Target # 23: Ebola GP1 (Message 2343)
Posted 7 Dec 2024 by kotenok2000
Post:
I was able to use Anonymous Platform to run short tasks on x86_64 cpu with linux.
https://www.sidock.si/sidock/forum_thread.php?id=125
8) Message boards : Number crunching : Gpu app? (Message 2324)
Posted 16 Oct 2024 by kotenok2000
Post:
There was an update to opencl branch a week ago(October 8, 2024 at 18:26:25 AM GMT)
https://gitlab.com/Jukic/cmdock/-/commits/dev-opencl/?ref_type=heads
9) Message boards : Number crunching : No short tasks (Message 2323)
Posted 15 Oct 2024 by kotenok2000
Post:
You will have to either run them on arm cpu with 32 bit armv7 libs installed or use this anonymous platdform guide

https://www.sidock.si/sidock/forum_thread.php?id=125&postid=2167#2167
10) Message boards : News : Target # 23: Ebola GP1 (Message 2310)
Posted 1 Sep 2024 by kotenok2000
Post:
cmdock.exe for #23
same for #24
11) Message boards : News : Target # 23: Ebola GP1 (Message 2296)
Posted 14 Jul 2024 by kotenok2000
Post:
TN-Grid was able to do it.
https://web.archive.org/web/20230101144605/https://gene.disi.unitn.it/test/gene_science.php
12) Message boards : News : Target # 23: Ebola GP1 (Message 2294)
Posted 13 Jul 2024 by kotenok2000
Post:
What is the estimation of the end date of corona_RdRp_v2 ?
13) Message boards : Number crunching : No short tasks (Message 2291)
Posted 11 Jul 2024 by kotenok2000
Post:
I have 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 '
14) Message boards : Number crunching : No short tasks (Message 2288)
Posted 11 Jul 2024 by kotenok2000
Post:
Is it ok if i run short tasks using app_info.xml and compiled cmdock?
15) Message boards : Number crunching : Can you add estimated completion dates to protein targets? (Message 2257)
Posted 23 Apr 2024 by kotenok2000
Post:
Can you add estimated completion dates to research progress in server status?
Like http://gene.disi.unitn.it/test/gene_science.php
?
16) Message boards : Number crunching : Vote for BOINC (Message 2228)
Posted 27 Mar 2024 by kotenok2000
Post:
Voted
17) 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
18) 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
19) 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
20) 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


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