Posts by Ed Johnson

1) Message boards : Number crunching : Minirosetta 3.62-3.65 (Message 78733)
Posted 8 Sep 2015 by Profile Ed Johnson
Post:
Task ID 756094939 failed under Linux, too.



Hi all,
These seem to be mine but I am not sure what is going on. I submitted them a week ago and they seemed to have run fine until the update yesterday. Could you provide me with more information about the jobs that are failing?

Thanks,
Franziska

Hi Franziska,

Any news on the FFD work units?
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 78626)
Posted 30 Aug 2015 by Profile Ed Johnson
Post:
According to the server status board. Several boxes are down right now:

http://boinc.bakerlab.org/rosetta/rah_status.php

There was a big windstorm in the Pacific Northwest yesterday. Power was cut to the University of Washington: I believe it's been restored but would assume Rosetta@home is in recovery mode.


If that's the case, do you have any idea why I have still been able to download new tasks the entire time--just unable to upload?


I'm not affiliated with the project and was really just speculating. But there are multiple servers: perhaps the file system of one but not the rest became corrupt and needs to be restored.

Or something.


I just went through all my active tasks, and although most uploads from each of my computers aren't successful, occasionally some task uploads have been successful in the last two days. So it seems like however many servers are still working, the number must be significantly reduced, but not all servers are down.

3) Questions and Answers : Macintosh : Boinc processes running on high priority (Message 51545)
Posted 21 Feb 2008 by Profile Ed Johnson
Post:
I can confirm that this is an Apple bug with OS X 10.5.x
You can chime in here at Apple support:

http://discussions.apple.com/thread.jspa?messageID=6662466
4) Questions and Answers : Macintosh : Boinc processes running on high priority (Message 51544)
Posted 21 Feb 2008 by Profile Ed Johnson
Post:
Hi,

boinc processes are running in high priority on leopard, thus slowing down all other processes. Boinc used to run on a nice priority to only consume idle CPU time. Any suggestions ?

Thanks !
- Andreas


Hi,

Using OS X 10.5.2, and Firefox is absolutely crippled when rosetta is running. I checked out the ps -Afl to get this info below. (Hopefully, formatted well here, and I'm only showing part of my processes.)

The closer the number is to zero for PRI, aka Priority, the more cpu time a process gets.

You can see that Firefox and Thunderbird get a horrible PRI from OS X at 97, and rosetta processes have the top priority, 12, even over system processes!
And yes, rosetta processes did use the NI, Nice, option to request a low priority from the system.

I'm a little astounded that OS X 10.5.2 is this screwed up.
I suppose we should post this on a message board at Apple to get this addressed?

 
UID   PID  PPID   C     STIME TTY           TIME CMD                                                                    F PRI NI       SZ    RSS WCHAN     S   ADDR
  0     1     0   0   0:25.86 ??         0:31.46 /sbin/launchd                                                       4000  31  0   600816    540 -      Ss   593cc50
  0    10     1   0   0:00.77 ??         0:00.89 /usr/libexec/kextd                                                  4000  31  0    75968   1068 -      Ss   593c310
  0    11     1   0   0:15.07 ??         0:28.72 /usr/sbin/DirectoryService                                          4000  31  0    79236   2924 -      Ss   593c7b0
  0    12     1   0   0:02.28 ??         0:03.35 /usr/sbin/notifyd                                                   4000  31  0   600248    420 -      Ss   593c560
  0    13     1   0   0:06.45 ??         0:09.43 /usr/sbin/syslogd                                                   4000  31  0   601332    484 -      Ss   593c0c0
  0    14     1   0   1:42.83 ??         3:11.65 /usr/sbin/configd                                                   4008  31  0    76980   1564 -      Ss   593be70
 65    15     1   0   0:03.78 ??         0:06.91 /usr/sbin/mDNSResponder -launchd                                    4000  31  0    77376   1292 -      Ss   593bc20
  1    16     1   0   0:06.62 ??         0:16.50 /usr/sbin/distnoted                                                 4100  31  0    75356    740 -      Ss   593b9d0
 65    18     1   0   0:07.53 ??         0:09.67 /sbin/launchd                                                       4000  31  0   599792    384 -      Ss   593b530
501 44173   153   0   0:00.55 ??         0:01.40 /System/Library/CoreServices/Dock.app/Contents/Resources/Dashboa    4000  63  0   291804  15564 -      S    10246a00
501 44912   136   0  30:04.53 ??        96:26.15 /Applications/Firefox.app/Contents/MacOS/firefox-bin -psn_0_1909    4000  97  0   644052 238028 -      S    102467b0
501 45142   136   0   0:00.01 ??         0:00.01 /System/Library/PrivateFrameworks/KerberosHelper.framework/Resou    4000  31  0    76412    860 -      S    6ded250
 32 53210   179   0   1:45.84 ??        59:01.55 rosetta_beta_5.93_i686-apple-darwin aa t847 _ -relax -looprlx -l    4000  12 19   318008 146788 -      SN   5ef7090
 32 53372   179   0   1:29.99 ??        46:34.87 rosetta_beta_5.93_i686-apple-darwin aa t847 _ -relax -looprlx -l    4000  12 19   319280 148516 -      SN   593b2e0
501 53537   136   0   1:10.99 ??         3:29.72 /Applications/Thunderbird.app/Contents/MacOS/thunderbird-bin -ps    4000  97  0   391044  73056 -      S    5ef5970
501 53560   136   0   0:07.23 ??         0:17.42 /Applications/OpenOffice.org 2.3.app/Contents/MacOS/droplet -psn    4000  46  0   284484   6304 -      S    6df0090
501 53572     1   0   0:00.01 ??         0:00.02 sh /Applications/OpenOffice.org 2.3.app/Contents/MacOS/soffice /    4000  31  0   600172    676 -      S    6dedde0
501 53605 53572   0   0:03.60 ??         0:13.16 /Applications/OpenOffice.org 2.3.app/Contents/MacOS/soffice.bin     4000  31  0   228908  75544 -      S    593ca00
501 60495     1   0   0:00.48 ??         0:01.12 /System/Library/Frameworks/CoreServices.framework/Frameworks/Met   84000  14 17   134936   7156 -      SNs  6def750
5) Message boards : Number crunching : Leave applications in memory while suspended preference does not work (Message 31481)
Posted 20 Nov 2006 by Profile Ed Johnson
Post:
Hi again River,

I did some more testing, and now I see what you are talking about. If I open up a boatload of memory intensive applications, then my available physical memory dips into the teens. At this point, the rosetta process did indeed start to release physical memory. The Mem Usage dropped from 90MB, to 45MB, then to 22MB. After opening another slew of programs, it dropped to 14MB of Mem Usage.

This is an acceptable amount to me.

fyi, I administrate a couple small businesses and have boinc installed on lots of machines. I am trying to make sure that the lesser powered machines don't take too much of a hit running rosetta. I think setting rosetta to run after 15 minutes of inactivity will keep users from experiencing too much disk thrash during their work routine. 15 minutes usually means they have left for a meeting, lunch, or some other task that will keep them away from their computer for a bit. I will let rosetta stay in memory as well.

Thanks,

Ed
6) Message boards : Number crunching : Leave applications in memory while suspended preference does not work (Message 31480)
Posted 20 Nov 2006 by Profile Ed Johnson
Post:
...
All of my preference changes worked except for my leaving application in memory to no. Rosetta eats up over 100MB of memory and >100MB virtual memory per WU, and I cannot afford to leave it in memory when I am doing work.
...


Leave in memory, in the BOINC settings, means that the app is not removed from virtual memory (VM) when it suspends, like when you are doing work.

It does not stop it from being removed from physical memory (RAM).



Hi River,

Do you have a reference for your statement about how Windows handles the rosetta process' memory?

I have been experimenting with bringing Rosetta in and out of memory while viewing the Windows Task Manager Performance Tab. The Physical Memory Available and Commit Charge Total do not change by more than a couple MB when I suspend rosetta and leave in memory. However, if I remove rosetta from memory, then those two quantities do change by roughly the full amount of the Mem Usage used by rosetta.

Furthermore, the latest Rosetta process uses approximately 90MB in Mem Usage column, and VM Size of 130MB. These figures do not change when Rosetta is suspended and left in memory. This paragraph from wikipedia says that rosetta is using up the physical ram, and not permitting other processes from using it in this situation.

"The "Mem Usage" column in Task Manager's "Processes" display shows each process's current working set. This is a count of physical memory (RAM) rather than virtual address space. It represents the subset of the process's virtual address space that is valid, meaning that it can be referenced without incurring a page fault."

http://en.wikipedia.org/wiki/Commit_charge

If it was 0MB of Mem Usage and 130MB of VM Size when rosetta was suspended, then I believe your assertion would be correct. However, that does not appear to be how Windows handles rosetta's memory when it is suspended (and left in memory.)

Thoughts? References?

Thanks,

Ed
7) Message boards : Number crunching : Leave applications in memory while suspended preference does not work (Message 31401)
Posted 19 Nov 2006 by Profile Ed Johnson
Post:
I've never heard of such a bug. Could you be a little more specific about what you are expecting to see in your xml file and in how you are observing R@H consuming memory?


This part was cleared up by a reply from the main Boinc forums:

http://boinc.berkeley.edu/dev/forum_thread.php?id=1324#6524

"When the "leave applications in memory when suspended" is set to No, it doesn't show up in global_prefs.xml

That's the way to see it isn't used.
If it's set to Yes, there'd be a single entry like <leave_apps_in_memory/> in the file. "
8) Message boards : Number crunching : Leave applications in memory while suspended preference does not work (Message 31389)
Posted 18 Nov 2006 by Profile Ed Johnson
Post:
Hi,

I run only Rosetta@home.
I have set:
Leave applications in memory while suspended = 'no' on my web account with Rosetta. I have updated my clients. I use only the default preferences. I have not setup home, school or work preferences.

All of my preference changes worked except for my leaving application in memory to no. Rosetta eats up over 100MB of memory and >100MB virtual memory per WU, and I cannot afford to leave it in memory when I am doing work.

C:Program FilesBOINCglobal_prefs.xml does NOT have an entry for leaving application in memory. Even though it updated all my other changes correctly.

Is this a bug with Boinc? Can I correct the global_prefs.xml by hand until this bug is fixed?

Thanks,

Ed J.
Boinc 5.4.11

----------
global_prefs.xml file

- {global_preferences}
{source_project}http://boinc.bakerlab.org/rosetta/{/source_project}
{source_scheduler}http://boinc.bakerlab.org/rosetta_cgi/cgi{/source_scheduler}
{mod_time}1163882196{/mod_time}
{run_if_user_active /}
{idle_time_to_run}5{/idle_time_to_run}
{cpu_scheduling_period_minutes}60{/cpu_scheduling_period_minutes}
{work_buf_min_days}0.1{/work_buf_min_days}
{max_cpus}2{/max_cpus}
{cpu_usage_limit}100{/cpu_usage_limit}
{disk_interval}60{/disk_interval}
{disk_max_used_gb}1{/disk_max_used_gb}
{disk_max_used_pct}10{/disk_max_used_pct}
{disk_min_free_gb}1{/disk_min_free_gb}
{vm_max_used_pct}25{/vm_max_used_pct}
{max_bytes_sec_down}0{/max_bytes_sec_down}
{max_bytes_sec_up}0{/max_bytes_sec_up}
{/global_preferences}

------------
Settings from Rosetta@home web account

Processor usage
Do work while computer is running on batteries?
(matters only for portable computers) no
Do work while computer is in use? no
Do work only after computer is idle for 5 minutes
Do work only between the hours of (no restriction)
Leave applications in memory while suspended? no
(suspended applications will consume swap space if 'yes') no
Switch between applications every
(recommended: 60 minutes) 60 minutes
On multiprocessors, use at most 2 processors
Use at most 100 percent of CPU time
9) Questions and Answers : Preferences : Leave applications in memory while preempted? yes/no (Message 31388)
Posted 18 Nov 2006 by Profile Ed Johnson
Post:
Hi,

I have a similar problem, but I am adding more detail:

I run only Rosetta@home.
I have set:
Leave applications in memory while suspended = NO on my web account with Rosetta. I have updated my clients. I use only the default preferences. I have not setup home, school or work preferences.

All of my preference changes worked except for my leaving application in memory to no. Rosetta eats up over 100MB of memory, and I cannot afford to leave it in memory when I am doing work.

C:Program FilesBOINCglobal_prefs.xml does NOT have an entry for leaving application in memory. Even though it updated all my other changes correctly.

Is this a bug with Boinc? Can I correct the global_prefs.xml by hand until this bug is fixed?

Thanks,

Ed J.

Boinc 5.4.11

----------
global_prefs.xml file

- {global_preferences}
{source_project}http://boinc.bakerlab.org/rosetta/{/source_project}
{source_scheduler}http://boinc.bakerlab.org/rosetta_cgi/cgi{/source_scheduler}
{mod_time}1163882196{/mod_time}
{run_if_user_active /}
{idle_time_to_run}5{/idle_time_to_run}
{cpu_scheduling_period_minutes}60{/cpu_scheduling_period_minutes}
{work_buf_min_days}0.1{/work_buf_min_days}
{max_cpus}2{/max_cpus}
{cpu_usage_limit}100{/cpu_usage_limit}
{disk_interval}60{/disk_interval}
{disk_max_used_gb}1{/disk_max_used_gb}
{disk_max_used_pct}10{/disk_max_used_pct}
{disk_min_free_gb}1{/disk_min_free_gb}
{vm_max_used_pct}25{/vm_max_used_pct}
{max_bytes_sec_down}0{/max_bytes_sec_down}
{max_bytes_sec_up}0{/max_bytes_sec_up}
{/global_preferences}

------------
Settings from Rosetta@home web account

Processor usage
Do work while computer is running on batteries?
(matters only for portable computers) no
Do work while computer is in use? no
Do work only after computer is idle for 5 minutes
Do work only between the hours of (no restriction)
Leave applications in memory while suspended? no
(suspended applications will consume swap space if 'yes') no
Switch between applications every
(recommended: 60 minutes) 60 minutes
On multiprocessors, use at most 2 processors
Use at most 100 percent of CPU time






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