Posts by bozz4science

1) Message boards : Number crunching : 100% (Message 1113)
Posted 18 Aug 2021 by bozz4science
Post:
Great! Thanks for the update :)
2) Message boards : Number crunching : 100% (Message 1110)
Posted 16 Aug 2021 by bozz4science
Post:
Is this solution you are talking about already implemented in the latest app version or do I need to act on the client side? I do still have this issue on my Win10 host regularly.
3) Message boards : Science : Other uses of docking than viruses? (Message 1109)
Posted 16 Aug 2021 by bozz4science
Post:
Thanks for the update! Will you open a test channel to allow beta testing as a separate app here on Sidock@H or will you run tests exclusively internally?
4) Message boards : Number crunching : 100% (Message 1104)
Posted 8 Aug 2021 by bozz4science
Post:
When will this issue be addressed? The pb is pointless if it is stuck at 100% for the majority of its runtime. If the bug pointed out below will already solve this issue, could you please implement it? Thanks
5) Message boards : Science : Other uses of docking than viruses? (Message 1103)
Posted 8 Aug 2021 by bozz4science
Post:
Just wanted to check on the development progress of the GPU client. As Scripps which is the institute that developed the GPU client of AutoDock also took several months, I was wondering if you are making good progress with the development effort of your docking software. Looking forward to your feedback
6) Message boards : News : SiDock@home becomes a general drug discovery project (Message 1017)
Posted 6 Jun 2021 by bozz4science
Post:
That is great news! Glad you made that decision. Looking forward to contribute long-term to new research goals and diseases.
7) Message boards : News : Release CmDock v 0.1.3 (Message 1016)
Posted 6 Jun 2021 by bozz4science
Post:
I agree that small changes to the code of an application (progress bar, checkpoint) although implementation was not trivial shouldn't call for new applications. I'd much rather see you introduce new versions of the same app as long as you don't change much of the internal code logic. Additionally, very long application names are very confusing and hard to retrace.

Why not simply have CurieMarieDock 1.01 / CurieMarieDock 1.02 etc and CurieMarieDock 2.0 for major updates.

CurieMarieDock on BOINC --> CurieMarieDock on BOINC + zipped input --> CurieMarieDock on BOINC + zipped input, checkpoints and progress bar vs.
CurieMarieDock 1.0 --> CurieMarieDock 1.1 --> CurieMarieDock 2.0

You can always convey the changes within each application version within the application release notes in the news section.

Especially confusing otherwise as you as a project won't roll out WUs from older applications as you mean to fully transition to the latest app. Old/Retired apps will only clutter the applications page.
Furthermore, runtime tracking via WUProp will be distrorted highly if you keep introducing new apps for each "minor" update instead of just iterating the internal development version number of the apps.

And regarding the rollout of new apps. Why not set up a "Beta" app which can then be used as a main test channel before introducing a new app. (Beta CurieMarieDock). Might have caught various glitches beforehand, such as the non-working progress bar in the new app "CurieMarieDock on BOINC + zipped input, checkpoints and progress bar".

Just a few ideas.
8) Message boards : Number crunching : No checkpoints? (Message 882)
Posted 4 May 2021 by bozz4science
Post:
I second that thought. Might be wise to hold back on this plan for the while being. But just a litlle longer or else I fear that you might lose volunteers with powerful systems who understandibly get angry with you about loads of kWh being potentially lost.
9) Message boards : Number crunching : Cities as .png files in project directory (Message 881)
Posted 4 May 2021 by bozz4science
Post:
Ah, I see. Thanks for the quick reply!
10) Message boards : Number crunching : No checkpoints? (Message 877)
Posted 4 May 2021 by bozz4science
Post:
Approaching the BOINC Pentalon, I am curious as to where you stand on checkpointing. What is the issue holding you up atm to implement this feature?
11) Message boards : Number crunching : Cities as .png files in project directory (Message 876)
Posted 4 May 2021 by bozz4science
Post:
Why are there several photo .png files of cities downloaded via the client in SiDock's project directory?

Names of these files are f.ex. Dubai, Hong-Kong, Abu-Dhabi.... What purpose do they serve if at all?
12) Message boards : News : Transition to production project (Message 271)
Posted 17 Dec 2020 by bozz4science
Post:
Very smooth transition. Congrats!
Looking forward to continue computing for this project in the future.
13) Message boards : News : Transition to production project (Message 244)
Posted 10 Dec 2020 by bozz4science
Post:
Awesome! Great progress so far.

By the way, do you plan to keep the project after the finish of the ongoing covid-related research and extend the scope of this project beyond the current research focus?
14) Questions and Answers : Macintosh : Work units for Mac (Message 109)
Posted 9 Nov 2020 by bozz4science
Post:
Unfortunately the MacOS terminal (zsh shell) still outputs yet another invalid error --> invalid option or syntax: -p
Seeing the pid-option from the prior output, I tried top -n 1 -pid <PID of a rbdock process> and it gave back the following.

Output
Processes: 473 total, 7 running, 466 sleeping, 1694 threads
Load Avg: 17.89, 14.48, 11.54 CPU usage: 84.95% user, 9.49% sys, 5.55% idle SharedLibs: 220M resident, 60M data, 17M linkedit.
MemRegions: 149916 total, 2284M resident, 103M private, 792M shared. PhysMem: 8099M used (1887M wired), 92M unused.
VM: 7533G vsize, 1993M framework vsize, 1271228(0) swapins, 1820351(0) swapouts. Networks: packets: 8996911/7031M in, 8644059/6201M out.
Disks: 55222355/249G read, 5023410/56G written.

PID 94001
COMMAND rbdock
%CPU TIME 75.00%
#TH 1/1
#WQ 0
#POR 14
MEM 72M
PURG 0B
CMPRS 4148K
PGRP 1173
PPID 93987
STATE running
BOOSTS *0[1]
%CPU_ME 0.00000
%CPU_OTHRS 0.00000
UID 503
FAULTS 43774
COW 91
MSGS 54
MSGR 14
SYSBSD 35418
SYSM 138
CSW 943651+
PAGE 0
IDLE 0
POWE 62.0

Edit
On Mac it seems that the top command does not support/have batch mode as the -b option does not exist.
15) Questions and Answers : Macintosh : Work units for Mac (Message 107)
Posted 9 Nov 2020 by bozz4science
Post:
Hey hoarfrost! Thanks for getting back to me. I looked up the corresponding process ID via activity manager of one of the rbdock processes currently running. I typed in ~ user$ top -b -n 1 -p 94626 (user is just anonymised here)
and the output was the following.
_____________
invalid option or syntax: -b
top usage: top
[-a | -d | -e | -c <mode>]
[-F | -f]
[-h]
[-i <interval>]
[-l <samples>]
[-ncols <columns>]
[-o <key>] [-O <secondaryKey>]
keys: pid (default), command, cpu, cpu_me, cpu_others, csw,
time, threads, ports, mregion, mem, rprvt, purg, vsize, vprvt,
kprvt, kshrd, pgrp, ppid, state, uid, wq, faults, cow, user,
msgsent, msgrecv, sysbsd, sysmach, pageins, boosts, instrs, cycles
[-R | -r]
[-S]
[-s <delay>]
[-n <nprocs>]
[-stats <key(s)>]
[-pid <processid>]
[-user <username>]
[-U <username>]
[-u]


Am I typing in the command correctly by just inserting the process ID number into the placeholder as shown above? It seems that the command is not accepting the options that are chosen here. Any ideas of what I might be doing wrong or could try instead? Thanks!
16) Questions and Answers : Macintosh : Work units for Mac (Message 104)
Posted 9 Nov 2020 by bozz4science
Post:
Just wanted to check back to you shortly as I the majority of my tasks reporting ~70 MB (±5 MB) physical memory but ~4.15 GB (±150 MB) virtual memory. It seems to me that my Mac system is currently overwhelmed by the RAM requirements of the tasks. Should I scale them back to address this, i.e. running 2 instead of 4 tasks simultaneously? I am crunching on a system with 8 GB RAM.
17) Questions and Answers : Macintosh : Work units for Mac (Message 103)
Posted 8 Nov 2020 by bozz4science
Post:
Just wanted to update you shortly. First MacOS WU (11.06 app version) recently finished and validated. Runtime seems to be in line what can be expected from the results returned so far from my other machines. No hiccups whatsoever. Seems to be working just fine
https://fightcovid.boinc.ru/sidocktest/result.php?resultid=177970

Looking forward to contribute with my Mac as well. Thanks again for helping the development of the MacOS version of the app Dotsch!
18) Questions and Answers : Macintosh : Work units for Mac (Message 100)
Posted 8 Nov 2020 by bozz4science
Post:
I’ll give it another shot and report back to you whether it works or not. Thanks for the quick bug fix!

Edit: I am now ~15 min into the new MacOS supported WUs with version 11.06 and they seem to be crunching away just fine. Will get back to you once I know if they finish and validate successfully. Seems you all did a good job of porting this application.
19) Questions and Answers : Macintosh : Work units for Mac (Message 98)
Posted 8 Nov 2020 by bozz4science
Post:
No. Unfortunately all 8 WU errored out almost immediately (5-30 sec runtime each). All "stderr" files state an error 195 (0x000000C3) EXIT_CHILD_FAILED.

Pls see for reference the following WU f.ex. https://fightcovid.boinc.ru/sidocktest/result.php?resultid=174785

I paste the stderr file here for convenience.

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
18:08:47 (4592): wrapper (7.5.26013): starting
18:08:47 (4592): wrapper: running get_fraction_done (ligands.sdf docking_log fraction_done 500 TARGET_PRO_1.mol2)
18:08:47 (4592): wrapper: running worker ($PWD 500 TARGET_PRO_1.mol2)
/bin/bash:
: No such file or directory
18:08:48 (4592): worker exited; CPU time 0.015192
18:08:48 (4592): app exit status: 0x7f00
18:08:48 (4592): called boinc_finish(195)

</stderr_txt>
]]>
20) Message boards : Cafe : welcome (Message 94)
Posted 8 Nov 2020 by bozz4science
Post:
Have you seen this page?

Thanks for this hint. Will take a look later tonight!


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