Posts by Harrison Neal

1) Message boards : Number crunching : NOD32 3 says Virus in file! (Message 52533) Posted 16 Apr 2008 by Harrison Neal Post: And never ever there was false positive or false negative! I'll join in for the heck of it. One day I woke up to my computers and half of my customers' computers having AVG reporting files within QuickBooks as a virus. More specifically, they were Help Files made in Macromedia/Adobe Flash, to which I can only assume other products were affected as well. As far as false negatives, I've seen a decent chunk of spyware that has just flown right over AVG at the time of infection. No one is perfect; you're bound to have some problem with just about anything. AVG works relatively well; now if only it scanned a little faster, had more malware cleaning tools built-in rather than sometimes directing the user to an external tool, and that incident mentioned above didn't happen... I chose NOD32 because, when I used the trial (simply for comparative purposes), it scanned a heck of a lot faster than any other virus scanner I've seen, and because I've seen it catch a few things, some of which were quite nasty, that others let by. However, I've also seen it let a few things slip by as well, so it's not perfect either. If only this incident with Minirosetta didn't happen... Although the problem is gone, for future reference, you can set exclusions in many Anti-Virus programs to temporarilly ignore false positives. When NOD32 on my computer started griping about minirosetta, I just told it to exclude minirosetta, and problem solved. Of course, for those a bit more paranoid, you could be more specific, only whitelisting it from the bakerlab.org site and in the RALPH/Rosetta Folders in BOINC. Also, cleaning a computer is usually a different story than preventing the problem. Heck, most of the computers I've had to clean involved me finding a third-party freeware tool designed specifically to cure a common virus/malware/et cetera. Otherwise, AVG Anti-Malware with all it's bells and whistles can scan not only files but also the registry, making it more ideal for cleaning a computer, while NOD32 has it's own set of bells and whistles (remembering these are two different products), most of which focused on preventing anything from getting in in the first place. Don't get me wrong... I'll usually reccomend AVG, among one or two other free ones, simply because most people I know don't want to pay for an Anti-Virus (although some, after trying the free AVG, will in fact pay for one of the full-blown versions), and most of the computers that I put AVG on usually die of old age before they get another virus... most. Just my five cents.
2) Message boards : Number crunching : Problems with (X)ubuntu 7.10? (Message 48172) Posted 31 Oct 2007 by Harrison Neal Post: As it turns out, *buntu's default runlevel is 2, and just relies on a recovery mode entry in Grub to avoid launching unnecessary "services", among other things. Nonetheless, I'm now experimenting with the BOINC version on that computer, to see if it'll behave like it used to. And, just to clarify - the tasks that this computer has choked up on had exit code 139, while that thread mentioned exit code 193 (unless any of the dead result links in fact had exit code 139...). -HN
3) Message boards : Number crunching : Problems with (X)ubuntu 7.10? (Message 48089) Posted 29 Oct 2007 by Harrison Neal Post: After two updates and two restarts, the task stuck at 100% finally coughed up a segmentation violation with exit status 139 (along with mentioning that the Rosetta core seemed "stuck"). I'll try putting it in runlevel 2 tonight and watch it for a few days, to see if it'll hang again. If that doesn't work, I'll take your advice and try putting BOINC 5.8 on it. And, also - unfortunately, this computer has a hard-wired limit of 192MB RAM... I couldn't put more in it if I tried (and I have). Thanks, -HN
4) Message boards : Number crunching : Preemption Failures on Linux (Message 48063) Posted 27 Oct 2007 by Harrison Neal Post: I apologize for the previous overkill post, but here's something else - The AMD K6 350MHz computer with 192MB RAM has stalled on a Rosetta@Home task both with and without the "Leave Applications in Memory" setting enabled. It gets stuck at 100%, says it is waiting to run, but will refuse to run nor send the results. Both tasks start with "mcr1__BOINC_RG_FULLWEIGHT_SYMM_FOLD_AND_DOCK_RELAX-mcr1_-mfr__2128_", if that helps. Once again, I believe this has never happened with Xubuntu 7.04 and BOINC 5.4 on this computer; it has only happened with Xubuntu 7.10 and BOINC 5.10. Computer: http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=617847 Task with Leave Applications in Memory disabled: http://boinc.bakerlab.org/rosetta/result.php?resultid=114100598 Task with Leave Applications in Memory enabled: http://boinc.bakerlab.org/rosetta/result.php?resultid=115401178
5) Message boards : Number crunching : Problems with (X)ubuntu 7.10? (Message 48062) Posted 27 Oct 2007 by Harrison Neal Post: I personally have never tried to throttle the CPU, but, of the computers I have that support speed throttling through /sys/devices/system/cpu/cpu#/cpufreq, the governor is currently at "performance", and the current frequency is equal to the maximum frequency, so my interpretation is that they are all running as fast as they can. (First off, is that a correct interpretation [given the fact that some don't have a cpufreq folder]?) Also, in the "Preemption Failures on Linux" thread ( http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3649 ), I confirmed that troggling that setting solved all my problems, or so it seemed. It seems like the only problem I've seen after changing the leave applications in memory setting (as in I saw the problem this morning) is isolated to a single computer, and this same problem has happened before changing that setting: A Rosetta@Home task simply stalls at 100%, BOINC reports it as "Waiting to run", but BOINC will refuse to run it nor send the results. It should be noted that Rosetta@Home is still in memory on this computer. I also never saw this happen with Xubuntu 7.04, and it was crunching Rosetta@Home on Xubuntu 7.04 for about 3 weeks. It's been attempting to crunch Rosetta@Home on Xubuntu 7.10 for about a week, and this particular problem has occured twice. The only difference between this computer and the rest of the computers is that this particular computer only meets the minimum disk space requirement; it's running an AMD K6 at 350MHz and is maxed out with 192MB RAM. Obviously, since this is below the minimum requirements, I understand there is a chance I simply would have to say the computer is too old to crunch Rosetta@Home properly, but, in the off chance that this computer shouldn't be encountering this problem (or, put another way, since I haven't seen this problem in a previous version of the BOINC Software), I'm posting this. The Computer: http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=617847 Task that failed before turning on leave applications in memory setting; aborted: http://boinc.bakerlab.org/rosetta/result.php?resultid=114100598 Task that is still stuck "waiting to run": http://boinc.bakerlab.org/rosetta/result.php?resultid=115401178 It might be worth mentioning that both tasks begin with "mcr1__BOINC_RG_FULLWEIGHT_SYMM_FOLD_AND_DOCK_RELAX-mcr1_-mfr__2128_". If there is anything I would need to do to help determine why it is that Rosetta@Home is simply stalling, please post it. Thanks, -HN
6) Message boards : Number crunching : Preemption Failures on Linux (Message 48044) Posted 26 Oct 2007 by Harrison Neal Post: Since I goofed and was apparently supposed to post here instead of starting another thread ( http://boinc.bakerlab.org/rosetta/forum_thread.php?id=3684 ), here's some information. Since following the advice in this thread and turning on the option to leave applications in memory, I haven't seen any problems. However, what is strange is that, in contrast to DJStarfox's post, Xubuntu 7.04 with BOINC 5.4 (<5.8.16) worked without any problems, but Xubuntu 7.10 with BOINC 5.10 (>5.8.16) seemed to cause the problems. I've updated these computers on a daily basis thus far (on the days when updates were available), so I'd probably expect that they were fully updated or updated as of the previous day at any one time. In the thread I started, I showed which computers seemed to run fine before upgrading to Xubuntu 7.10 along with BOINC 5.10, and I showed which tasks had errors besides exit code 193. Tasks that began with "mcr1__BOINC_RG_FULLWEIGHT_SYMM_FOLD_AND_DOCK_RELAX-mcr1_-mfr__2128" suffered from exit code 139 on two different computers, and both produced a stack trace. The first task mentioned the errors "ERROR:: Exit from: fragments.cc line: 465 FILE_LOCK::unlock(): close failed.: Bad file descriptor" and "* glibc detected * corrupted double-linked list: 0x09821b78 *". These tasks are: http://boinc.bakerlab.org/rosetta/result.php?resultid=114287567 http://boinc.bakerlab.org/rosetta/result.php?resultid=113947212 Tasks that contained "LARS_ABRELAX_40_GOODRMS_FITTED_SAVE_ALL_OUT" suffered from exit code 1 on two different computers. Both mentioned the error "ERROR:: Exit from: fragments.cc line: 465 FILE_LOCK::unlock(): close failed.: Bad file descriptor". These tasks are: http://boinc.bakerlab.org/rosetta/result.php?resultid=115098768 http://boinc.bakerlab.org/rosetta/result.php?resultid=115032344 Tasks that contained "LARS_ABRELAX_40_NATIVE_FITTED_SAVE_ALL_OUT" suffered from exit code 1 on three different computers, and both produced a stack trace. All of which mentioned the error "ERROR:: Exit from: fragments.cc line: 465 FILE_LOCK::unlock(): close failed.: Bad file descriptor", and the second task mentioned the error "* glibc detected * corrupted double-linked list: 0x092845c0 ". These tasks are: http://boinc.bakerlab.org/rosetta/result.php?resultid=115061214 http://boinc.bakerlab.org/rosetta/result.php?resultid=114999850 http://boinc.bakerlab.org/rosetta/result.php?resultid=115068071 The following task was stuck at 100% for several days. It's status was "Waiting to run", but BOINC seemed to refuse to run it. After aborting the task, BOINC briefly reported the task as having worked over 50 CPU Hours (before clicking Abort, it reported ~3 hours). http://boinc.bakerlab.org/rosetta/result.php?resultid=114100598 And, finally, the following tasks encountered exit code 193, which contained either "LARS_ABRELAX_40_GOODRMS_FITTED_SAVE_ALL_OUT", "LARS_ABRELAX_40_NATIVE_FITTED_SAVE_ALL_OUT", "CNTRL_01ABRELAX_SAVE_ALL_OUT" or "BOINC_SYMM_FOLD_AND_DOCK_RELAX" in the task name, and they all contained a stack trace. The fifth, sixth and ninth task mentioned the error "ERROR:: Exit from: fragments.cc line: 465 FILE_LOCK::unlock(): close failed.: Bad file descriptor", and the eighth task mentioned the error " glibc detected * corrupted double-linked list: 0x097a1070 ***". These tasks are: http://boinc.bakerlab.org/rosetta/result.php?resultid=115146613 http://boinc.bakerlab.org/rosetta/result.php?resultid=115144619 http://boinc.bakerlab.org/rosetta/result.php?resultid=115140556 http://boinc.bakerlab.org/rosetta/result.php?resultid=115136485 http://boinc.bakerlab.org/rosetta/result.php?resultid=115123778 http://boinc.bakerlab.org/rosetta/result.php?resultid=115121065 http://boinc.bakerlab.org/rosetta/result.php?resultid=115110213 http://boinc.bakerlab.org/rosetta/result.php?resultid=115099640 http://boinc.bakerlab.org/rosetta/result.php?resultid=115075271 http://boinc.bakerlab.org/rosetta/result.php?resultid=115023948 http://boinc.bakerlab.org/rosetta/result.php?resultid=114208827 http://boinc.bakerlab.org/rosetta/result.php?resultid=114080616 http://boinc.bakerlab.org/rosetta/result.php?resultid=114065860 http://boinc.bakerlab.org/rosetta/result.php?resultid=113973418 http://boinc.bakerlab.org/rosetta/result.php?resultid=113958341 http://boinc.bakerlab.org/rosetta/result.php?resultid=113910476 http://boinc.bakerlab.org/rosetta/result.php?resultid=113901480 In case you're wondering what pathetic excuses for hardware these tasks are running on, here they are: http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=625082 Pentium III 450MHz, 512MB RAM http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=625047 Pentium II 350MHz, 512MB RAM http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=617847 AMD K6 350MHz, 192MB RAM http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=622444 Transmeta Crusoe TM5800 1GHz, 768MB RAM They've all had badblocks run in write mode without any problems, and MemTest86+ comes up clean as well. They are allowed to use all of the physical memory and swap space (1GB), most services that I don't use and would consume excess memory have been disabled (GDM, WPA, etc.), and they were all using less than 150MB RAM and no swap space without BOINC running. They have NOT been overclocked (quite frankly, it's amazing half of these things will even turn on...). Once again, they worked under BOINC 5.4 with applications not left in memory, and BOINC 5.10 with applications left in memory. All the above failed tasks occured under BOINC 5.10 with applications not left in memory. -Harrison N.
7) Message boards : Number crunching : Problems with (X)ubuntu 7.10? (Message 48009) Posted 25 Oct 2007 by Harrison Neal Post: Sure enough, I find something that might explain the situation after I open my big mouth. Oops. However, there are still these results, which may or may not be related to another post which describes Rosetta@home having problems when Rosetta@home is not suspended in memory (I'm including these because they don't have exit code 193): http://boinc.bakerlab.org/rosetta/result.php?resultid=115098768 http://boinc.bakerlab.org/rosetta/result.php?resultid=115061214 http://boinc.bakerlab.org/rosetta/result.php?resultid=114287567 http://boinc.bakerlab.org/rosetta/result.php?resultid=113947212 http://boinc.bakerlab.org/rosetta/result.php?resultid=114999850 http://boinc.bakerlab.org/rosetta/result.php?resultid=115032344 http://boinc.bakerlab.org/rosetta/result.php?resultid=115068071
8) Message boards : Number crunching : Problems with (X)ubuntu 7.10? (Message 48008) Posted 25 Oct 2007 by Harrison Neal Post: Hello All- It seems like some older computers I have that were running Xubuntu 7.04 and Rosetta@home tasks peacefully are choking on Xubuntu 7.10 and Rosetta@home. Granted, this is OLD hardware, which is why I'm running sanity checks on this hardware as I type (badblocks, MemTest86, etc.), but the time stamps on the tasks that have failed or otherwise acted quirky all seem to be after the installation of Xubuntu 7.10 (otherwise I'd finish the sanity checks). It also seems suspicious that only the Rosetta@home project is giving these computers grief - other projects, such as World Community Grid, aren't having the same problems as Rosetta@home (or at least I haven't seen them yet). It should be noted that all the computers have 4 partitions - the first for swap, the second for the root directory, the third for the home directory, and the fourth for BOINC files (/var/lib/boinc-client). The reason being that I prefer to freshly install new versions of OSes as opposed to doing an in-place upgrade, and the above partition layout makes that easier (for me, anyway). I don't see how this would definitely be a problem (perhaps files from the older BOINC conflicting...?), but, heck, I've seen stranger things before. I've also reset the Rosetta@home project on all these computers as well. I don't believe a task has finished/failed after the reset, but, assuming the hardware checks come back clean, I'll let them run and see what happens. The computers that seem to be griping over Rosetta@home on Xubuntu 7.10 (which has BOINC 5.10.8; Xubuntu 7.04 had BOINC 5.4.11) are as follows: http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=625082 http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=625047 http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=617847 http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=622444 I also just got another computer and put Xubuntu 7.10 on it without any previous installation on the Hard Drive. It seems to be working perfectly fine, thus far. It can be found here: http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=642904 If there is a known issue or something I've done that goes against a "proper" method, please mention it. Thanks for your help in advance, -Harrison N.