Work units for Mac

Questions and Answers : Macintosh : Work units for Mac
Message board moderation

To post messages, you must log in.

Previous · 1 · 2 · 3 · Next

AuthorMessage
bozz4science

Send message
Joined: 31 Oct 20
Posts: 32
Credit: 841,194
RAC: 1
Message 107 - Posted: 9 Nov 2020, 14:52:38 UTC - in response to Message 105.  
Last modified: 9 Nov 2020, 14:52:59 UTC

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!
ID: 107 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Volunteer moderator
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 323
Credit: 22,883,627
RAC: 11,970
Message 108 - Posted: 9 Nov 2020, 15:40:50 UTC

Try, please without "-b": top -n 1 -p .
ID: 108 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
bozz4science

Send message
Joined: 31 Oct 20
Posts: 32
Credit: 841,194
RAC: 1
Message 109 - Posted: 9 Nov 2020, 15:56:32 UTC - in response to Message 108.  
Last modified: 9 Nov 2020, 15:59:47 UTC

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.
ID: 109 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
[AF>Le_Pommier] Jerome_C2005

Send message
Joined: 24 Oct 20
Posts: 23
Credit: 1,084,026
RAC: 0
Message 197 - Posted: 3 Dec 2020, 20:32:57 UTC
Last modified: 3 Dec 2020, 20:34:02 UTC

Hello

I just realize you have a Mac app : great !!

I was only crunching on linux so i just attached sidock to my brand new iMac :
<core_client_version>7.16.12</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
20:49:19 (64601): wrapper (7.5.26013): starting
application $PWD/build/cmdock missing
</stderr_txt>
]]>

See here.

They all fail for the same reason.

The Mac app is not a "stand-alone" boinc application ?

I need to install more stuff locally ?

Thanks.
ID: 197 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Dotsch

Send message
Joined: 28 Oct 20
Posts: 14
Credit: 4,698
RAC: 0
Message 205 - Posted: 4 Dec 2020, 8:57:16 UTC - in response to Message 197.  

The cmdock and sidock applications have several application contents, which are complete bundled by the project and downloaded by the BOINC client.
The cmdock application has an error, which must be fixed by the project. - But, the sidock application work without any problem. You can also select the application you would like to crunch with the application preferences.
ID: 205 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Profile Natalia
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 9 Oct 20
Posts: 181
Credit: 2,689,264
RAC: 449
Message 208 - Posted: 4 Dec 2020, 14:22:03 UTC

Errors fixed, version cmdock-boinc 1.2 for Mac should work!
ID: 208 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Dotsch

Send message
Joined: 28 Oct 20
Posts: 14
Credit: 4,698
RAC: 0
Message 211 - Posted: 4 Dec 2020, 15:55:01 UTC

Thank you! The new app is working.
ID: 211 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
[AF>Le_Pommier] Jerome_C2005

Send message
Joined: 24 Oct 20
Posts: 23
Credit: 1,084,026
RAC: 0
Message 222 - Posted: 5 Dec 2020, 21:09:29 UTC

Yep they didn't crash from the start, they are running now, thanks !
ID: 222 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
[AF>Le_Pommier] Jerome_C2005

Send message
Joined: 24 Oct 20
Posts: 23
Credit: 1,084,026
RAC: 0
Message 231 - Posted: 7 Dec 2020, 21:44:47 UTC
Last modified: 7 Dec 2020, 21:45:43 UTC

I found a new issue on macOS : the tasks do not suspend.

If I tell boinc to suspend processing globally, boinc "thinks" all is suspended but the tasks actually continue to run !

ID: 231 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
gemini8

Send message
Joined: 23 Oct 20
Posts: 12
Credit: 2,636,512
RAC: 2,402
Message 296 - Posted: 19 Dec 2020, 8:29:04 UTC - in response to Message 231.  

Hello.
Thanks for your work!

I'm successfully running SiDock@home on a MacBook Pro running El Capitan.
I also tried SiDock@home on a MacBook running Lion.
Unfortunately the tasks error out on the latter.
<core_client_version>7.6.34</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
09:16:53 (289): wrapper (7.5.26013): starting
09:16:53 (289): wrapper: running worker ()
worker: line 14:   292 Segmentation fault: 11  DYLD_FALLBACK_LIBRARY_PATH="$CMDOCK_ROOT/build" "$CMDOCK_ROOT/build/cmdock" -r target.prm -p "$CMDOCK_ROOT/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out > docking_log
09:16:54 (289): worker exited; CPU time 0.010226
09:16:54 (289): app exit status: 0x8b00
09:16:54 (289): called boinc_finish(195)

</stderr_txt>
]]>

Might this be an issue with using Lion?
- - - - - - - - - -
Greetings, Jens
ID: 296 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Profile Natalia
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 9 Oct 20
Posts: 181
Credit: 2,689,264
RAC: 449
Message 298 - Posted: 19 Dec 2020, 9:36:58 UTC - in response to Message 231.  

I found a new issue on macOS : the tasks do not suspend.

If I tell boinc to suspend processing globally, boinc "thinks" all is suspended but the tasks actually continue to run !



I will try to fix that, it is an old bug :)
ID: 298 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Profile Natalia
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 9 Oct 20
Posts: 181
Credit: 2,689,264
RAC: 449
Message 299 - Posted: 19 Dec 2020, 9:37:19 UTC - in response to Message 296.  

Hello.
Thanks for your work!

I'm successfully running SiDock@home on a MacBook Pro running El Capitan.
I also tried SiDock@home on a MacBook running Lion.
Unfortunately the tasks error out on the latter.
<core_client_version>7.6.34</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
09:16:53 (289): wrapper (7.5.26013): starting
09:16:53 (289): wrapper: running worker ()
worker: line 14:   292 Segmentation fault: 11  DYLD_FALLBACK_LIBRARY_PATH="$CMDOCK_ROOT/build" "$CMDOCK_ROOT/build/cmdock" -r target.prm -p "$CMDOCK_ROOT/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out > docking_log
09:16:54 (289): worker exited; CPU time 0.010226
09:16:54 (289): app exit status: 0x8b00
09:16:54 (289): called boinc_finish(195)

</stderr_txt>
]]>

Might this be an issue with using Lion?


We should look at it.
ID: 299 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Profile Natalia
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 9 Oct 20
Posts: 181
Credit: 2,689,264
RAC: 449
Message 302 - Posted: 19 Dec 2020, 17:55:40 UTC
Last modified: 19 Dec 2020, 17:56:20 UTC

Please check a new version of RxDock 1.0. At least on my computer it handles CPU throttling and suspending tasks via BOINCManager. It is interesting if it works on MacOS Lion. I plan to do the same job with CMDock (without success so far).
ID: 302 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
gemini8

Send message
Joined: 23 Oct 20
Posts: 12
Credit: 2,636,512
RAC: 2,402
Message 311 - Posted: 20 Dec 2020, 12:13:12 UTC - in response to Message 302.  

Thanks again for your work!
Unfortunately I'll not be able to test on Lion during the next days while staying away from home.
My MacBook is only used for testing (and important challenges), so I can't control it via BAM! for now.

Will try RxDock with my MacBook Pro as soon as it finishes old work.
- - - - - - - - - -
Greetings, Jens
ID: 311 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
gemini8

Send message
Joined: 23 Oct 20
Posts: 12
Credit: 2,636,512
RAC: 2,402
Message 312 - Posted: 20 Dec 2020, 13:16:12 UTC - in response to Message 311.  
Last modified: 20 Dec 2020, 13:16:48 UTC

Will try RxDock with my MacBook Pro as soon as it finishes old work.

RxDock is running on El Capitan.
Thanks again!
- - - - - - - - - -
Greetings, Jens
ID: 312 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
[AF>Le_Pommier] Jerome_C2005

Send message
Joined: 24 Oct 20
Posts: 23
Credit: 1,084,026
RAC: 0
Message 325 - Posted: 21 Dec 2020, 9:43:58 UTC - in response to Message 298.  

I found a new issue on macOS : the tasks do not suspend.

If I tell boinc to suspend processing globally, boinc "thinks" all is suspended but the tasks actually continue to run !

I will try to fix that, it is an old bug :)

Thanks !

Note that this only happens with Curie tasks, the RxDock do suspend properly.
ID: 325 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
gemini8

Send message
Joined: 23 Oct 20
Posts: 12
Credit: 2,636,512
RAC: 2,402
Message 334 - Posted: 23 Dec 2020, 17:25:45 UTC

No luck with Lion:
https://www.sidock.si/sidock/results.php?hostid=1095
- - - - - - - - - -
Greetings, Jens
ID: 334 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Magiceye04

Send message
Joined: 31 Jan 21
Posts: 4
Credit: 4,560,392
RAC: 0
Message 546 - Posted: 5 Feb 2021, 21:44:24 UTC

OK. Now the only available app for RXDoc is for Mac.
The only WUs that are available ware RXDOCK.
Is there a chance that anything else than a mac contribut on RXdock?
ID: 546 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Crtomir
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 11 Nov 20
Posts: 47
Credit: 83,493
RAC: 0
Message 549 - Posted: 6 Feb 2021, 0:31:10 UTC - in response to Message 546.  

Dear MAC users, currently we have not official apple developer account, thus we can not issue mac version. If some one has idea to help us to solve this issue please contact jukic dot marko at gmail dot com ;-)
ID: 549 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
shift
Avatar

Send message
Joined: 6 Feb 21
Posts: 8
Credit: 330,759
RAC: 0
Message 569 - Posted: 7 Feb 2021, 8:32:49 UTC - in response to Message 334.  

@Gemini8/Jens is there a chance your Lion is 32 bit instead of 64 bit? The SiDock app appears to need 64 bit.
ID: 569 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Previous · 1 · 2 · 3 · Next

Questions and Answers : Macintosh : Work units for Mac

©2024 SiDock@home Team