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Bug reports for Ralph 5.11 and 5.12

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Message boards : RALPH@home bug list : Bug reports for Ralph 5.11 and 5.12

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Rhiju
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Message 1534 - Posted 8 May 2006 6:32:43 UTC

    Last modified: 10 May 2006 22:48:43 UTC

    In this version:

    (1) We tried to shrink the text in the workunit description so that the other text doesn\'t get pushed off the screen. Let us know how this looks.

    (2) We fixed a computational bug that accidentally slipped into 5.10.


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    Message 1536 - Posted 8 May 2006 9:57:01 UTC

      HM, could it be, that there is now no text to see ?

      Take a look:

      http://yeti.kor.b-s-m.de/rosetta_5_11.gif
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      Message 1537 - Posted 8 May 2006 17:41:03 UTC

        I have a bigger problem; at the moment it looks like RALPH-Wus are causing the problem.

        One of my maschines is a Win2K3-Server, running Exchange, Fax-Server, Virtual-Server and several more things. This box war crunching BOINC since nearly one year and I never had problems. The box has 2x XENON-CPU (HT), 3 GHz and 4 GHz of memory.

        The box was allowed to run BOINC-Tasks on 3 of the 4 virtuel CPUs.

        Yesterday I could see, that a lot of mails where not in my personal mailbox, but I could see them arriving on the server. When I suspended BOINC, all outstanding mails arrived in less than 1 minute in my personal mailbox.

        Well, first I thought, QMC was the problem, because in the past, sometimes QMC didn\'t like to give crunching power back to other tasks.

        Meanwhile I had only RALPH-5.11-er-Units on the server, one was taking a big amount of memory. The same behaviour as yesterday happened, Mails didn\'t arrive in my personal mailbox, that should have been there. When I suspended BOINC, nothing changed, but as I stopped the service, all mails came again in 1 minute into my personal mailbox.

        So, it can be the core client or RALPH that is causing the problem.

        I will let this box crunch other projects and see, if the problem comes back or not.

        Would be interesting, if someone else is watching some problems, maybe a possible memory leak in RALPH ?

        I canceled following WUs now:

        http://ralph.bakerlab.org/result.php?resultid=107134

        http://ralph.bakerlab.org/result.php?resultid=107115

        http://ralph.bakerlab.org/result.php?resultid=107025


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        Message 1538 - Posted 8 May 2006 20:28:38 UTC

          Last modified: 8 May 2006 20:30:00 UTC

          It\'s a bit frustrating to sign back onto this project, to find there is no work available. Although I am continuing to crunch Rosetta@home, this lack of Ralph work perhaps gives the impression that Ralph already has enough testers. However, perhaps I am a bit too impatient, and your intent is to send out sufficient work to test your new applications, without creating unnecessary additional \"make work\" just to keep people busy. I certainly would not want to do \"make work\" when my resources could be spent elsewhere such as Rosetta@home doing necessary work.

          Thanks!
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          Message 1539 - Posted 8 May 2006 21:00:44 UTC - in response to Message 1538.

            ...perhaps... your intent is to send out sufficient work to test your new applications, without creating unnecessary additional \"make work\" just to keep people busy.


            The project has stated that WUs will only be available as testing of a new release or of WUs is needed. Also they\'ve said that the results on Ralph and NOT used for the Rosetta science. I\'ve already expressed the idea that more WUs and taking steps to deliver WUs to more hosts will be beneficial. They\'ve changed some of the parameters in how much work they will send to a given host, but the WUs still seem to be gone virtually as soon as I realize that any exist. And when you have a \"connect to host every 2.5 days\" setting, it seems unlikely you\'ll ever get any unless you take manual steps to do so when you see some available.

            I\'ve suggested that if a given application version proves valid, then go ahead and USE the results for the science, and then they could keep a small but steady stream of WUs on Ralph and allow debts to be worked down and make things run more normally. See this thread. But, until then, WUs on Ralph basically consume time that could be better used on Rosetta. And so they keep the number of WUs to a minimum.
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            rbpeake

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            Message 1540 - Posted 8 May 2006 21:06:17 UTC - in response to Message 1539.

              I\'ve suggested that if a given application version proves valid, then go ahead and USE the results for the science, and then they could keep a small but steady stream of WUs on Ralph and allow debts to be worked down and make things run more normally...

              Make sense to me! Thanks for your reply, I will reign in my expectations (and my enthusiasm to some degree) and keep plugging away on Rosetta at the same time.

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              Message 1541 - Posted 8 May 2006 21:17:43 UTC - in response to Message 1537.

                Last modified: 8 May 2006 21:19:43 UTC

                I have a bigger problem; at the moment it looks like RALPH-Wus are causing the problem.

                One of my machines is a Win2K3-Server, running Exchange, Fax-Server, Virtual-Server and several more things. This box was crunching BOINC since nearly one year and I never had problems. The box has 2x XENON-CPU (HT), 3 GHz and 4 GHz of memory.

                The box was allowed to run BOINC-Tasks on 3 of the 4 virtual CPUs.

                etc....



                I have a similar problem first noticed with version 5.10 where internet access is blocked as well as local printing. Then the screen saver came up and the only way to stop it was end the ralph process! After about 15 seconds, the printer started and internet access returned. This is on a Dell Optiplex single processor three year old machine.

                Neal.

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                Message 1542 - Posted 8 May 2006 23:19:09 UTC - in response to Message 1540.

                  I\'ve suggested that if a given application version proves valid, then go ahead and USE the results for the science, and then they could keep a small but steady stream of WUs on Ralph and allow debts to be worked down and make things run more normally...

                  Make sense to me! Thanks for your reply, I will reign in my expectations (and my enthusiasm to some degree) and keep plugging away on Rosetta at the same time.

                  You can set the share for RALPH to a lower value. This works especially well if you are connect all the time (Not through a modem). The system will seek work according to your connection frequency settings, but it will not run up a high debt when there is no work because of the lower share value. When there is work it will have a high enough debt to always get at least a few work units.
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                  Rhiju
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                  Message 1543 - Posted 9 May 2006 3:08:21 UTC - in response to Message 1541.

                    I\'m sending out a bunch of jobs with ralph 5.12 with the WU description ... can anyone post if their graphics still gets pushed off the screen?

                    Neal and Yeti, we haven\'t changed anything in 5.10 that should eat up more memory, and certainly nothing should affect your internet access! If it is a memory issue, help is on the way -- our group has been making a concerted effort to trim the fat off rosetta, so that the memory footprint of many jobs will be reduced significantly, in some cases by a half! If you happen to get more information on how ralph or BOINC in general might be messing up your machines, please post.


                    I have a bigger problem; at the moment it looks like RALPH-Wus are causing the problem.

                    One of my machines is a Win2K3-Server, running Exchange, Fax-Server, Virtual-Server and several more things. This box was crunching BOINC since nearly one year and I never had problems. The box has 2x XENON-CPU (HT), 3 GHz and 4 GHz of memory.

                    The box was allowed to run BOINC-Tasks on 3 of the 4 virtual CPUs.

                    etc....



                    I have a similar problem first noticed with version 5.10 where internet access is blocked as well as local printing. Then the screen saver came up and the only way to stop it was end the ralph process! After about 15 seconds, the printer started and internet access returned. This is on a Dell Optiplex single processor three year old machine.

                    Neal.


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                    Message 1544 - Posted 9 May 2006 3:46:53 UTC

                      Version 5.12 Display.

                      On the Mac version you almost have it. Although the WU has not run long enough to get to the second model (where the problems usually start), all but the lowest lines are now showing. The lowest line displayed is the RMSD. All information below that is cut off (no project name or energy).
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                      Message 1545 - Posted 9 May 2006 7:19:31 UTC

                        Last modified: 9 May 2006 7:58:37 UTC

                        I noticed the goofy graphics. I also noticed that it\'s not universally 5.12. the 5.12 AB_CASP6 WU don\'t seem to have the problem. I don\'t have a list of the ones that do show problems, but I\'ll start a log. I might even capture a pic. If I have any 5.12 left, that is.

                        tony

                        Notice, my screen is set to full,not minimized.



                        then see this WU where everything seems normal at the bottom, but look at \"accepted energy\" analog display is out of the box. Also, note the single line of text beneath it. If more lines occur later, I\'ll repost a new pic of this wu.

                        And this one seems OK as well.



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                        Message 1546 - Posted 9 May 2006 8:04:28 UTC

                          Last modified: 9 May 2006 8:29:07 UTC

                          The first two pics of my last post were taken from the same puter. I managed to get the first one as it was finishing. I took the second one after it started
                          the new wu. Both were captured using \"show graphics\" and set to full display.

                          P.S sorry for breaking the forum, you may delete the pics after they\'ve been helpful. As you can see from the last pic, I figured out how to make them smaller

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                          Message 1547 - Posted 9 May 2006 9:09:16 UTC - in response to Message 1543.

                            Neal and Yeti, we haven\'t changed anything in 5.10 that should eat up more memory, and certainly nothing should affect your internet access! If it is a memory issue, help is on the way -- our group has been making a concerted effort to trim the fat off rosetta, so that the memory footprint of many jobs will be reduced significantly, in some cases by a half! If you happen to get more information on how ralph or BOINC in general might be messing up your machines, please post.


                            I just gave 5.12 a try, not good:

                            My mails have been delayed for exact the time, Rosetta was running. I let it run for 45 minutes, and my mails of these last 45 minutes didn\'t come through :-(

                            I suspended only the task of rosetta, so that BOINC kept running BBC and XtremLab and downloaded a WU from another project, SIMAP this time. It took less than 1 minute and all my outstanding mails came through.

                            As most of my boxes are live-machines, I have to stop crunching RALPH, until this get\'s worked out.

                            Hopefully, you will post a big message, when the version, you proposed, comes out; I will give it a try then. Or, you send a mail to my registered mail-adress, when it is time.

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                            Message 1549 - Posted 9 May 2006 9:19:35 UTC

                              Last modified: 9 May 2006 9:28:25 UTC

                              Here\'s a follow up on the WU from the middle pic below/above. Now the bottom is missing info. I stopped staring at it, and after the screensaver kicked in, I moved
                              the mouse. The \"full sized\" display that was showing was now, magically shown as a \"minimized\" box, I opened the box back to \"full\" and.....
                              Do\'h I forgot to resize it.
                              Note: this did not occur with the WU from the third pic when it went to screensaver and then back to a minimized display. It\'s got to be something about that particular
                              version, version types?.


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                              Message 1550 - Posted 9 May 2006 10:12:44 UTC

                                Last modified: 9 May 2006 10:15:35 UTC

                                this wu just went to screensaver, and I captured the following progression.

                                Notice how the middle pic looks right? If I change it from full to min, it also looks right.

                                In screensaver mode:


                                After moving mouse:


                                after restoring to full display:

                                Neal

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                                Message 1553 - Posted 9 May 2006 18:10:18 UTC

                                  I\'m running both Rosetta 5.07 and Ralph_Beta 5.11 and so far only the Ralph version is causing me problems. Anything unusual done since 5.07? When Ralph is running, my local printing is down and I can\'t access the machine with PCAnywhere from home via the internet. Within 15 seconds from when Ralph ends, both the printing and internet access start to work again. It doesn\'t seem to be a memory problem, but twice when the screen saver activated with Ralph running, I could not stop it. I have the task bar in \'auto hide\' mode, and it would not display. After Ralph stopped and another Boinc project started (ClimatePrediction) the computer resumed normal operation. Any other things I could do to isolate the possible problem? Neal.

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                                  Message 1554 - Posted 9 May 2006 18:37:53 UTC

                                    Last modified: 9 May 2006 18:40:48 UTC

                                    Not sure if this is totally related, though hmm... With 5.11 and now 5.12, when the rossetabeta process is running, I\'m noticing more sluggish performance when starting my media player to listen to an MP3 file, watch a torrent, whatever... It\'s gone from the media file being ready right away, to a wait for \"loading audio system...\" Never seemed to run into this before version 5.11, or with other projects only being loaded in memory.

                                    I updated the media player last night, and all seemed fine for awhile. Today, it\'s got a 10+ sec delay, whereas last night it didn\'t when I was crunching other stuff/no RALPH units for the app to be in memory. As the priority should be just as low with BOINC, I\'m surprised/mystified about this noticing as well, or what to believe of it Humph... I\'ll need to do further testing myself to even begin to try to make heads/tails of this.
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                                    Message 1555 - Posted 9 May 2006 19:29:28 UTC

                                      Last modified: 9 May 2006 19:33:54 UTC

                                      OK, I did some further checks. I went to uninstall the media player, at which point there was a long delay for even the control panel to open up while RALPH was running. It then wanted a reboot, so I let it. Making sure the prog directory is deleted so it would get a clean fresh install of the newer version (not that the older had given me this problem in like 6 months of useage), I then installed, it rebooted, and BOINC scheduled an Einstein unit to run, using (well I\'m using) akosf\'s u41.04 science app.

                                      It loaded up normally, no wait times, performance delays, or anything. So, I suspended Einstein, and forced it over to a RALPH WU after shutting down. I then tried to open the same exact media file again, and the performance delay/wait time was reintroduced.

                                      As these were the only 2 projects loaded thus far, there was less in memory this time then before. (Before I had QMC, CPDN, seasonal attribution, as well as crunch3r\'s SETI app loaded.) With all of that loaded, that only represented 711 MB of memory allocation according to Task Manager, and this computer has 1 GB of RAM. Right now, with this memory allocation is only 402 MB.

                                      In the past (though it could be worth a check again), without RALPH, but having both CPDN and seasonal attribution loaded (which are real taxing on the memory useage), I hadn\'t seen this. The RALPH app 5.11 and up does appear to be the difference between the performance delay on doing other stuff invoked vs. not invoked. Not sure if anyone else has noticed this or not...

                                      Further note: Resuming Einstein didn\'t fix this performance drag, though shutting down BOINC and restarting it, so Ralph 5.12 wasn\'t loaded in RAM did fix it however...

                                      Comp:

                                      - Athlon 64 3500+ Venice core (socket 939)
                                      - 1 GB Corsair 400 Pro DDR (2x 512 MB DIMMs)
                                      - MSI Neo 2 (nForce 3 chipset)
                                      - LVD SCSI HDs (Seagate Cheetahs), connected through an Adaptec SCSI card 29160
                                      - Windows XP Professional Service Pack 2

                                      Not sure if the other components would matter for a performance standpoint, though temp wise, things are kept nice and cool due to a fair number of fans and a Swifttech HSF, and Arctic Silver 5 thermal paste...
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                                      Message 1556 - Posted 9 May 2006 19:47:45 UTC

                                        Hm, the performance-problem related to screensaver or not:

                                        I\'m running BOINC as a service, with a specialized user-account; so no screensaver is available on my system, that had problems.


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                                        Message 1557 - Posted 9 May 2006 21:04:55 UTC

                                          I\'m definitely not running screensaver, though am running as a single user install...
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                                          Message 1558 - Posted 9 May 2006 23:51:37 UTC

                                            Something different to slow performance, has anyone else had the problem of very short completion times for Ralph 5.12 workunits?
                                            I just received 19 WU\'s (I have a 2 day cache) and the system has given me only 4 days (till 13th May) to complete them. I am using a dual AMD 848 machine and have suspended work for Einstein and Rosetta on this machine so that Ralph will have enough time to complete all the workunits. They were stamped with completion times of 4 hours 58 minutes each though this has now reduced to 4 hours 34 minutes each. this means I will get through about 4 to 5 per day per cpu.
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                                            Message 1559 - Posted 10 May 2006 0:56:38 UTC

                                              Here\'s one I see tonite. I have no background on this one:


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                                              Message 1560 - Posted 10 May 2006 1:27:10 UTC

                                                I experienced problem with resizing in windowed screensaver mode, still running 5.10... Is it fixed in 5.12? And a suggestion: would be nice to see what the lowest found RMSD/Energy was over each model!
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                                                Message 1561 - Posted 10 May 2006 1:31:20 UTC

                                                  Last modified: 10 May 2006 1:38:39 UTC

                                                  The following 4 pics are of the same wu. I\'m only moving the right hand side of the Ralph box and clicking another picture. At some point the bottom scrolls off the screen.





                                                  Rhiju
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                                                  Message 1562 - Posted 10 May 2006 1:37:53 UTC - in response to Message 1559.

                                                    Great, these posts on graphics have been useful. We\'ll probably have to limit our WU descriptions to one line so that the rest of the text doesn\'t get pushed off the screen for some clients.

                                                    Here\'s one I see tonite. I have no background on this one:



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                                                    Message 1563 - Posted 10 May 2006 3:03:34 UTC

                                                      Last modified: 10 May 2006 3:28:28 UTC

                                                      This is anecdotal only, but having seen Son Goku\'s post I will chip in that I too have seen my system get noticeably sluggish when Ralph is loaded,
                                                      only since about 5.11 or 5.12. I\'ve been running BOINC over a year with the same hardware (P4, HT restricted to one pseudo-cpu, 1GB memory)
                                                      and this hasn\'t happened before, and there are other projects I run like WCGrid\'s FightAids@Home which use more memory (virtual and not)
                                                      which don\'t cause this. I don\'t understand the reason, unless Task Mgr lies about memory and VM sizes (quite possible)...
                                                      but I\'ve had things happen like my specific applications consistently failing or small applications taking huge amounts of time to start up,
                                                      only once I have let Ralph run. Even if Ralph is not currently running, as long as it has run and is still in memory.

                                                      I know this sounds a bit nuts but I\'ve watched it several times by going through the sequence from boot up with all boinc projects suspended,
                                                      enabling different combinations of projects -- including combinations which add up to more memory usage -- and watching things flake out
                                                      as soon as Ralph has loaded and only when Ralph is loaded, with no other evidence of problems with the box.

                                                      Out of time to pursue it more, and I\'ll probably NNW Ralph for a while as I need this machine to function properly, and this problem seems like
                                                      a Twilight Zone ep. If more than one or two of us are affected I\'m happy to pursue it further when I get some time.

                                                      p.s. I do use the screen saver, going to blank screen after 5 minutes. Occasionally I\'ll run the graphics manually but not often. Single-user install.
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                                                      Message 1564 - Posted 10 May 2006 5:10:20 UTC

                                                        Last modified: 10 May 2006 5:11:23 UTC

                                                        Well, I do think a 1 liner is cutting things a little too tight for WU description, however there does come a point where large gfx can mount up...

                                                        BTW, just having the window not maximized, and then doing an (alt + print screen), will just copy the current app window to the clipboard, rather then the whole desktop. This would cut the start menu, and other such Windows items outa the screen capture...
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                                                        Message 1567 - Posted 10 May 2006 19:54:02 UTC

                                                          Last modified: 10 May 2006 20:08:45 UTC

                                                          Hello, in this screen i can\'t see the text in its entirety.

                                                          TEST_HOMOLOG_ABRELAX_hom008_1fna__503_3_0 using rosetta_beta version 512
                                                          And i see problems with Accepted Energy and RMSD.
                                                          Sorry for my bad english



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