Smina for mol2

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Steve Hawker*

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Message 4710 - Posted: 6 Feb 2017, 14:12:18 UTC

According to my task list I have 22 tasks. But on my machine I have none.

Can someone explain this?
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4712 - Posted: 6 Feb 2017, 17:32:12 UTC - in response to Message 4710.  

I don't see any one.
Do you say that you see it in BM or on web site?
Krzysztof 'krzyszp' Piszczek

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Steve Hawker*

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Message 4719 - Posted: 6 Feb 2017, 23:03:47 UTC

On the website:

https://boinc.drugdiscoveryathome.com/results.php?hostid=518&offset=0&show_names=0&state=0&appid=7

I've now "got" 67. I tried a reset but they didn't arrive.
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Conan

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Message 4721 - Posted: 7 Feb 2017, 0:22:40 UTC

The fact that over 5,300 work units have been sent out but none have been returned in the last 24 hours, seems a bit odd, unless they are really huge work units.

Unfortunately I did not receive any so can't see what has happened, but some work should of come back by now.

So did anybody actually get these new work units?

Conan
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Sergey Kovalchuk

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Message 4735 - Posted: 8 Feb 2017, 15:26:16 UTC
Last modified: 8 Feb 2017, 15:28:49 UTC

Host #56 received message "No tasks are available for Smina for mol2"
Server status page - 54k unsent tasks
Maybe these tasks are not for Linux x86_64
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Gunde

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Message 4736 - Posted: 8 Feb 2017, 18:56:39 UTC - in response to Message 4735.  

Got plenty of mol2 to Linux x64 after i added it today.

Try again and suspend other project.
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Gunde

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Message 4737 - Posted: 8 Feb 2017, 18:56:39 UTC - in response to Message 4735.  
Last modified: 8 Feb 2017, 18:57:58 UTC

**Post fail**
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Trotador

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Message 4785 - Posted: 20 Feb 2017, 19:24:05 UTC

Hi

Server Status page shows thousands of available units but my host with Linux does not pick any. Are they real?, only 12 active users in last 24h seems odd.
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Gunde

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Message 4787 - Posted: 21 Feb 2017, 23:04:37 UTC - in response to Message 4785.  

They are real.
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Chris Skull

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Message 4790 - Posted: 27 Feb 2017, 19:18:07 UTC

Hello,
is that correct ? All my valid units have this output:

core_client_version>7.6.31</core_client_version>
<![CDATA[
<stderr_txt>
20:04:44 (24786): wrapper (7.5.26014): starting
20:04:44 (24786): wrapper: running smina_mol2 (--cpu 1 --config conf.txt --ligand smina_mol2_data.sdf --out smina_mol2_out.mol2 --log smina_mol2_log.txt)
==============================
*** Open Babel Warning in Init
Cannot open element.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open types.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open resdata.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open bondtyp.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open aromatic.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open atomtyp.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open phmodel.txt defaulting to compiled data.
20:11:16 (24786): smina_mol2 exited; CPU time 384.728000
20:11:16 (24786): called boinc_finish(0)

</stderr_txt>
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4791 - Posted: 28 Feb 2017, 11:54:53 UTC

It's normal, as application doesn't get some files (not required) and set some variables to default values.
Krzysztof 'krzyszp' Piszczek

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Conan

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Message 4875 - Posted: 31 Jul 2017, 21:59:52 UTC

These work units are all failing again, received 12 all failed. See this example

<core_client_version>7.4.25</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
23:28:34 (9288): wrapper (7.5.26014): starting
23:28:34 (9288): wrapper: running smina_mol2 (--cpu 1 --autobox_ligand ligand.pdb -r receptor.pdb --scoring vinardo --exhaustiveness 30 -l smina_mol2_data.sdf --out smina_mol2_out.mol2 --log smina_mol2_log.txt --num_modes 1)
==============================
*** Open Babel Warning in Init
Unable to open data file 'space-groups.txt'
==============================
*** Open Babel Warning in Init
Cannot initialize database 'space-groups.txt' which may cause further errors.
==============================
*** Open Babel Warning in Init
Cannot open element.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open types.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open resdata.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open bondtyp.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open aromatic.txt defaulting to compiled data.
==============================
*** Open Babel Warning in Init
Cannot open atomtyp.txt defaulting to compiled data.


Error: could not open "receptor.pdb" for reading.
23:28:35 (9288): smina_mol2 exited; CPU time 0.015997
23:28:35 (9288): app exit status: 0x100
23:28:35 (9288): called boinc_finish(195)

</stderr_txt>
]]>
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mmonnin

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Message 4876 - Posted: 31 Jul 2017, 22:09:32 UTC - in response to Message 4875.  

I got some earlier today as well but they are all fine now.

This one just a few WUs after yours:
https://boinc.drugdiscoveryathome.com/result.php?resultid=79986
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[BOINC@Poland]goofyx
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Message 4877 - Posted: 31 Jul 2017, 22:44:37 UTC - in response to Message 4876.  

smina_mol2 is start again and right now should be ok
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Profile Steve Dodd

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Message 4878 - Posted: 31 Jul 2017, 23:23:03 UTC

Will this application be coming to Windows? (Sorry if this is answered somewhere else)
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scole of TSBT

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Message 4879 - Posted: 1 Aug 2017, 1:01:52 UTC - in response to Message 4878.  
Last modified: 1 Aug 2017, 1:03:31 UTC

Will this application be coming to Windows? (Sorry if this is answered somewhere else)

You can run the vina app under Windows

btw...WOOHOO! Glad to see the project back online!
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mmonnin

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Message 4882 - Posted: 1 Aug 2017, 2:11:32 UTC - in response to Message 4879.  

Will this application be coming to Windows? (Sorry if this is answered somewhere else)

You can run the vina app under Windows

btw...WOOHOO! Glad to see the project back online!


If it is like other VINA apps it will run much better in a Linux OS though.

I'm excited as well. I was just a day or two short of the 100k badge prior to the shutdown. I'm going for that 1mil badge. They look awesome.
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[BOINC@Poland]goofyx
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Message 4883 - Posted: 1 Aug 2017, 5:29:46 UTC - in response to Message 4878.  

Will this application be coming to Windows? (Sorry if this is answered somewhere else)


At this moment we have no plan to make smina on windows
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4885 - Posted: 1 Aug 2017, 15:03:47 UTC - in response to Message 4883.  

Unfortunately smina can not be compiled as portable application for Windows (at least I can't do this after loads of experiments).
Krzysztof 'krzyszp' Piszczek

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mmonnin

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Message 4887 - Posted: 1 Aug 2017, 22:05:46 UTC

mol2 out of work already. :(
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