Posts by dekim

41) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6172) Posted 11 Apr 2017 by dekim Post: You can ignore those warnings. They are harmless. I will hopefully have those warnings removed in the next release soon.
42) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6171) Posted 11 Apr 2017 by dekim Post: please keep those going.
43) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6166) Posted 6 Apr 2017 by dekim Post: Since the android app is a separate application, the credit per decoy running average will only use results from android jobs. But there is the issue of possibly adding a correction factor to try to normalize the credits coming from the standard app vs the arm app given the same protocol. I'll have to look into this and it would require running some benchmarks and updating the standard app. The arm app is running the latest Rosetta version.
44) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6162) Posted 5 Apr 2017 by dekim Post: I agree. I'll talk to the researcher. The long run time is due to filtering logic. Even on one of our local machines it takes about an hour to generate a model (after quite a few filtered attempts).
45) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6157) Posted 4 Apr 2017 by dekim Post: These work units should eventually finish. I suggest not killing them. We'll see if we can reduce the run times for future batches.
46) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6155) Posted 1 Apr 2017 by dekim Post: Yes, I've noticed these warnings on some devices but can't reproduce them on mine. I'll have to figure out what libraries aren't being used but linked against. Thanks!
47) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6152) Posted 29 Mar 2017 by dekim Post: I updated the android app to 3.82. I think I managed to work out the major issues.
48) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6150) Posted 28 Mar 2017 by dekim Post: I'm seeing a lot of early errors from the 3.80 android app so I'll probably revert to the previous version after letting it run through the night. edit: I reverted back to 3.79 as 3.81.
49) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6147) Posted 17 Mar 2017 by dekim Post: Eventually when it's necessary, but I'm focusing on android for the moment. The XML changes are not backwards compatible so the next update will likely be under a new app name. However, there hasn't been a significant research related need to update the pc platforms yet. There are a lot of android users joining our project and there's potential for significantly more in the near future.
50) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6145) Posted 17 Mar 2017 by dekim Post: 3.78 uses the latest Rosetta code which has gone through some refactoring, mainly for scripting XML compliance. There are also changes in the cyclic peptide folding protocol. I also finally fixed a bug in the BOINC API which was causing random seg faults on my test device but it looks like there are still some bugs on other android platforms/versions (judging from the few jobs that have already been processed).
51) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6143) Posted 17 Mar 2017 by dekim Post: I just updated the android app to 3.78. 3.78 is only being tested for android.
52) Message boards : RALPH@home bug list : minirosetta_beta_3.76 and minirosetta_android_3.76 (Message 6096) Posted 1 Dec 2016 by dekim Post: This application update uses a relatively recent version of the Rosetta source and includes various new features and updates, including new design filters and protocols. Since it's been a while since the last update, we expect that there may be issues that will be revealed during this test process. We'll send out test jobs shortly. Thanks!
53) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6056) Posted 17 Mar 2016 by dekim Post: I just updated the minirosetta_beta application to 3.72. The 32 bit linux version has not been updated yet due to some memory issues while compiling. I hope to have it available soon.
54) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6043) Posted 5 Feb 2016 by dekim Post: I'm getting quick client/computer errors for the backrub_design tasks. From the stderr out: minirosetta_3.71_x86_64-apple-darwin(50310,0x7fff732a2300) malloc: * error for object 0x4b4fc3ef02e87d9a: pointer being freed was not allocated * set a breakpoint in malloc_error_break to debug Also gaurav_rsmn_0161_65_daa2_2_SAVE_ALL_OUT_20296_50_0 is claiming a file transfer error: # cpu_run_time_pref: 14400 reached end of minirosetta::main() ====================================================== DONE :: 2 starting structures 13443.3 cpu seconds This process generated 13 decoys from 13 attempts ====================================================== BOINC :: WS_max 2.65622e+08 BOINC :: Watchdog shutting down... BOINC :: BOINC support services shutting down cleanly ... called boinc_finish </stderr_txt> <message> upload failure: <file_xfer_error> <file_name>gaurav_rsmn_0161_65_daa2_2_SAVE_ALL_OUT_20296_50_0_0</file_name> <error_code>-161 (not found)</error_code> </file_xfer_error> Are those results truly lost? I'm not sure what is causing the backrub error but the gaurav jobs have a filter that may sometimes remove all models so the result is as expected for that test. I think the filter has been updated so that at least 1 model is generated in the next test batch but I'm not sure. Vikram, the one submitting those jobs is testing this.
55) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6039) Posted 5 Feb 2016 by dekim Post: The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation? thanks for the info Yes, I'm running a test of a new type of job that runs small perturbations of the protein backbone and then does a round of design. The design protocol can use a lot of memory. I realize that this will be problematic and will see if we can distribute these jobs to high memory machines. We may just not be able to run these on R@h. R@H means Rosseta, doesn`t it? It is good for the investigation you could look for ways of distributing these units. The only effective way I could think of is limiting the quantity of units downloaded, by the user as in CEP project in WCG or by the project. Distributing them only to hosts with lot of memory could just not be enough if the hosts have also a lot of available threads (like mine). A good thing I'm seeing with these units is that Boinc/Ralph seems to take into account the amount of available system memory and limits the menory used, even limiting the quantity of units in execution below the quantity of available threads, and the systems does not stall and hang as used to happen in these cases. Is it correct ? I'm not sure. There haven't been that many reports of stalling/hanging etc... I think I was able to debug our scheduler so that it should not send out these high memory jobs to low memory clients. Hopefully it can now be a matter of setting the limits.
56) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6037) Posted 4 Feb 2016 by dekim Post: The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation? thanks for the info Yes, I'm running a test of a new type of job that runs small perturbations of the protein backbone and then does a round of design. The design protocol can use a lot of memory. I realize that this will be problematic and will see if we can distribute these jobs to high memory machines. We may just not be able to run these on R@h.
57) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6036) Posted 4 Feb 2016 by dekim Post: "Is this the new graph??" Yes.
58) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6023) Posted 28 Jan 2016 by dekim Post: thanks, there is an error in the job submission and will get fixed. I alerted the researcher that submitted these tests about the issue and fix.
59) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6020) Posted 21 Jan 2016 by dekim Post: The android app requires Android version 4.1+. I'm not sure what is going on with your Motorola. Seems to run ok. Are there any network issues?
60) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6017) Posted 20 Jan 2016 by dekim Post: This error is due to the large memory requirement of the test job. I resubmitted the job with a memory bound which hopefully should avoid such errors.

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