I got two units running so far for a day plus 10 hours and still less than 70% finished, with the estimated time to go 19 hours. Keep running or abort?

Miklos, are the tasks actually consuming CPU time? Or is the BOINC Manager just showing they are active, but they are not actually getting CPU? Which machine are you seeing this on? What do your CPU preferences look like for the venue of that machine?

---

Rosetta Moderator: Mod.Sense

Give BOINC Manager some time to get used to the new project resource share. It will balance out when the work cache is refreshed.

I meant the other way round!
When RAM issues started appearing, I put in a “no new tasks” order in hopes of avoiding an overload.
Only after moving over RAM and adjusting resource share to a third did I let Rosetta sync for new tasks. It got three or so.
I go to bed, and when I awake every single slot is full of Rosetta tasks, with WCG in cashe waiting to run.

Oh, and now we have a task that was validated after running for 24 hours, but the output says the task ran into errors comparing the reference and working pose.

Task 1136464489
Name 5kn1wr9d_jhr_design1_COVID-19_SAVE_ALL_OUT_903675_1_0
Workunit 1023518897
Created 29 Mar 2020, 11:56:42 UTC
Sent 29 Mar 2020, 12:11:53 UTC
Report deadline 6 Apr 2020, 12:11:53 UTC
Received 29 Mar 2020, 23:55:06 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 3925665
Run time 11 hours 24 min 31 sec
CPU time 11 hours 13 min 43 sec
Validate state Valid
Credit 120.37
Device peak FLOPS 4.49 GFLOPS
Application version Rosetta v4.07
windows_intelx86
Peak working set size 1,212.31 MB
Peak swap size 1,215.32 MB
Peak disk usage 486.06 MB
Stderr output
<core_client_version>7.14.2</core_client_version>
<![CDATA[
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.07_windows_intelx86.exe -run:protocol jd2_scripting -parser:protocol jhr_boinc.xml @flags -in:file:silent 5kn1wr9d_jhr_design1_COVID-19.silent -in:file:silent_struct_type binary -silent_gz -mute all -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 5kn1wr9d_jhr_design1_COVID-19.zip -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 2854141
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.

ERROR: Assertion `copy_pose.size() == native.size()` failed. MSG:the reference pose must be the same size as the working pose
ERROR:: Exit from: ......srcprotocolsprotein_interface_designfiltersRmsdFilter.cc line: 323
16:41:46 (5404): called boinc_finish(0)

</stderr_txt>
]]>

Is there any possibility this could be from the fact that Rosetta is a 32-bit application, but some COVID-19 WUs (the 2GB ones) could be trying to request even more memory than normal (over 4GB), resulting in the Out Of Memory error?

I ask this because I have a 32 core Threadripper that has 64 GB of ram, and I share these resources between World Community Grid, LHC@Home, and Rosetta@home, meaning it's rare that all 32 cores are crunching Rosetta@home at the same time. However, even in the worse case scenario of running 32 Rosetta tasks at once, with the 2GB per WU rule I would still meet the RAM requirement, not to mention that worse case there's around 10GB of Swap space.

This thought comes up as all the errored COVID-19 work units on my machines all errored out on other machines as well.

Just a hunch.

Is there any possibility this could be from the fact that Rosetta is a 32-bit application, but some COVID-19 WUs (the 2GB ones) could be trying to request even more memory than normal (over 4GB), resulting in the Out Of Memory error?

The memory usage of a given task is reported in the details page for the task. I haven't seen any using more than 1.5GB. Please point me to any that are larger if you run across some.

---

Rosetta Moderator: Mod.Sense

I have some problems too. Ryzen 9 3950X, 32 threads and 64 GB of RAM but 18 WUs ended with an error while only 4 are ok.
I set Rosetta@Home to work for only an hour, let's see what happens now.

---

ASUS X570 E-Gaming
AMD Ryzen 9 3950X, 16 core / 32 thread 4.4 GHz
AMD Radeon Sapphire RX 480 4GB Nitro+
Nvidia GTX 1080 Ti Gaming X Trio
4x16 GB Corsair Vengeance RGB 3466 MHz

Ok 5 tasks completed, but... ONLY 2 POINTS PER TASK?!

---

ASUS X570 E-Gaming
AMD Ryzen 9 3950X, 16 core / 32 thread 4.4 GHz
AMD Radeon Sapphire RX 480 4GB Nitro+
Nvidia GTX 1080 Ti Gaming X Trio
4x16 GB Corsair Vengeance RGB 3466 MHz

Please see, Admin bcov's post about new application and creation of work units

---

Rosetta Moderator: Mod.Sense

I have some problems too. Ryzen 9 3950X, 32 threads and 64 GB of RAM but 18 WUs ended with an error while only 4 are ok.
I set Rosetta@Home to work for only an hour, let's see what happens now.

As I've just written to someone else, please don't change your runtime to 1hr when we have so few tasks available - every one you get running 1hr stops someone else running them for 8hrs and your very high spec machine will be wasted, while your machine will hit the servers for more tasks 7hrs earlier and 8 times as often.

Even if you complete 1hr tasks, for 1/8th the benefit, it means they won't be reissued.
It's actually better if you run for 8hrs, 78ths of your tasks fail, and those failed tasks get reissued to others who can run them successfully for 8hrs
Crazy as it might seem, that's true, while others will get more tasks and the server is less overused.

People need to stop doing crazy self-defeating things to get around a problem caused by something else entirely. I sit here amazed.

PS: I'm not the police

---

So you think I have to set the tasks to work for 8 hours? But I've had 18 errors and only 4 ok in the last day with tasks set to work for 8 hours...

---

ASUS X570 E-Gaming
AMD Ryzen 9 3950X, 16 core / 32 thread 4.4 GHz
AMD Radeon Sapphire RX 480 4GB Nitro+
Nvidia GTX 1080 Ti Gaming X Trio
4x16 GB Corsair Vengeance RGB 3466 MHz

Any models that do complete normally prior to the error are still reported in and granted credit.

By running for a longer runtime preference, you are attempting more models. The more models you attempt, the higher the chance that you run in to one that sees a problem. Let's see how many of these problems they were able to fix in the new release.

Please see, Admin bcov's post about new application and creation of work units

---

Rosetta Moderator: Mod.Sense

So you think I have to set the tasks to work for 8 hours? But I've had 18 errors and only 4 ok in the last day with tasks set to work for 8 hours...

I don't mean to be rude, but the vast majority of your Computation errors were access violations within the first hour of running, so having 1hr tasks isn't going to solve the problem.
Others are far better able to point at the real cause than me - it's definitely something that's come up before. Shorter runtimes are never the solution and do cause problems elsewhere.

I overclock my PC and see these kinds of things when running right at the limit - and Rosetta is a massively demanding project, like running Prime95 24/7. If there's any weakness, Rosetta will find it

---

To all who have problems with too high memory consumption. To allow "waiting for memory" functions works properly please disable (if enabled) "leave non-GPU WU in memory while suspended" . On web preferences or local client:

BOINC flaws does not allow it to manage memory properly with this option active - due some errors it does not count memory consumption by such suspended tasks and can hoard all system RAM which lead to crashes/reboots/or very intensive disk swapping.
Because if BOINC see what RAM consumption is too high (above limit set in the preferences) it try to suspend some of WUs to reduce RAM usage ("waiting for memory"), and try to start other WUs (as it can use less RAM compared to suspended and CPU cores will not go idle). But if "leave non-GPU WU in memory while suspended" option is active such measures do not decrease RAM usage, but only increase it even more worsen situation.

Or as alternative use direct manual restriction to BOINC which limit how many R@H tasks can be run simultaneously and fill the remain CPU cores with tasks from other BOINC projects with low RAM usage. My advice would be join WCG if you look for other good disease fighting/medicine projects. It usually use small amounts of RAM (< 100 MB per WU) and almost do not compete for RAM with R@H WUs.

To do so you can create file with name "app_config.xml"
And place it in the R@H home folder in BOINC data folder ( /projects/boinc.bakerlab.org_rosetta/app_config.xml)
There is a template for such file

<app_config>
   <app>
      <name>minirosetta</name>
      <max_concurrent>6</max_concurrent>
   </app>
   <app>
      <name>rosetta</name>
      <max_concurrent>3</max_concurrent>
   </app>
</app_config>

In this example BOINC is allowed to run up to 6 "minirosetta" WUs at max (which usually use relative modest amounts of RAM like 150-400 MB) and up to 3 full rosetta WUs including new which can use huge amounts of RAM (up to 3000 MB per biggest WUs). And up to 9 WUs per R@H project total (6+3).
You can play with number for your system. My advice will be 2 GB per rosetta WU and 1 GB per minirosetta WU.
For example if your system has 16 GB RAM with 8core/16 threads CPU: limit it to something like 6 Rosetta + 4 minirosetta WUs to avoid out of RAM issues. Or 4 + 8.
And let WCG (or other project of your choice) to use all remaining CPU slots.

Also of you low on RAM but want ROSETTA ONLY setup - consider turning off HT/SMT features on you CPU. It decrease total CPU throughput (by 20-30% on average) but also decrease RAM usage by two fold because number of concurrent running WUs will be halved but speed of running each WU will increase substantially.

P.S.
2 Mod.Sense
Please copy or link this message as guidance to other new users having issues with too high RAM usage in other threads. I think this issues and questions will be quite common in the coming days/weeks with that flow on new users boarding in.

Thanks for posting your experience. At the same time, many have found problems running <without> that option checked at times when memory is less of an issue. It's hard to know what to do for the best. I would certainly say, when memory isn't the issue, that option should always be checked for the same reason you mention - Boinc doesn't seem to handle memory well after coming out of sleep or after a shutdown.

The suggestion I do like is limiting the full number of Rosetta tasks that can run concurrently. MiniRosetta always seem to use less RAM and slipping in a few WCG tasks as well is always very low on memory use and can help solve the issue.

Also, running tasks to completion rather than switching to another project partway through will lower the occasions that a task is held in memory.
And maximising the amount of RAM dedicated to Boinc helps prevent the issue arising. And restricting the number of background tasks running too.
I'm on my 8Gb RAM laptop atm and I've managed to allow 65% in use and 85% not in use without too much difficulty.

Anyway, interesting comment

---

Getting a few of these, signal 4, Illegal Instruction.
Corupt stack? Corupt execuable? Optimezer fault?

https://boinc.bakerlab.org/rosetta/result.php?resultid=1138758573
and the crash report

Process:               rosetta_4.12_x86_64-apple-darwin [22468]
Path:                  /Library/Application Support/BOINC Data/*/rosetta_4.12_x86_64-apple-darwin
Identifier:            rosetta_4.12_x86_64-apple-darwin
Version:               0
Code Type:             X86-64 (Native)
Parent Process:        ??? [630]
Responsible:           rosetta_4.12_x86_64-apple-darwin [22468]
User ID:               503

Date/Time:             2020-04-03 07:08:43.780 -0700
OS Version:            Mac OS X 10.12.6 (16G2136)
Report Version:        12


Time Awake Since Boot: 1800000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes:       0x0000000000000001, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Illegal instruction: 4
Termination Reason:    Namespace SIGNAL, Code 0x4
Terminating Process:   exc handler [0]

Application Specific Information:
/Library/Application Support/BOINC Data/slots/3/../../projects/boinc.bakerlab.org_rosetta/rosetta_4.12_x86_64-apple-darwin

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   rosetta_4.12_x86_64-apple-darwin	0x00000001053e0692 0x1025ac000 + 48449170
1   rosetta_4.12_x86_64-apple-darwin	0x0000000102645b94 0x1025ac000 + 629652
2   dyld                          	0x000000010f3cea1b ImageLoaderMachO::doModInitFunctions(ImageLoader::LinkContext const&) + 385
3   dyld                          	0x000000010f3cec1e ImageLoaderMachO::doInitialization(ImageLoader::LinkContext const&) + 40
4   dyld                          	0x000000010f3ca4aa ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int, char const*, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 338
5   dyld                          	0x000000010f3c9524 ImageLoader::processInitializers(ImageLoader::LinkContext const&, unsigned int, ImageLoader::InitializerTimingList&, ImageLoader::UninitedUpwards&) + 138
6   dyld                          	0x000000010f3c95b9 ImageLoader::runInitializers(ImageLoader::LinkContext const&, ImageLoader::InitializerTimingList&) + 75
7   dyld                          	0x000000010f3bb47a dyld::initializeMainExecutable() + 195
8   dyld                          	0x000000010f3bf8c6 dyld::_main(macho_header const*, unsigned long, int, char const**, char const**, char const**, unsigned long*) + 3966
9   dyld                          	0x000000010f3ba249 dyldbootstrap::start(macho_header const*, int, char const**, long, macho_header const*, unsigned long*) + 470
10  dyld                          	0x000000010f3ba036 _dyld_start + 54

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00007fb773807260  rbx: 0x00007fb773807e90  rcx: 0x00007fb773807264  rdx: 0x0000000000000000
  rdi: 0x0000000000000000  rsi: 0xfffffffffffffffc  rbp: 0x00007fff5d650570  rsp: 0x00007fff5d6504b0
   r8: 0x0000000000000004   r9: 0x00007fb773807260  r10: 0x00000000fffff800  r11: 0xffffffff00000000
  r12: 0x0000000000000004  r13: 0x0000000000000002  r14: 0x0000000000001b50  r15: 0x00007fb774003a00
  rip: 0x00000001053e0692  rfl: 0x0000000000010246  cr2: 0x0000000102760480
  
Logical CPU:     3
Error Code:      0x00000000
Trap Number:     6


Binary Images:
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External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 105687878
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=333.5M resident=0K(0%) swapped_out_or_unallocated=333.5M(100%)
Writable regions: Total=57.1M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=57.1M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        2 
MALLOC                            47.3M       14 
MALLOC guard page                   32K        7 
STACK GUARD                       56.0M        2 
Stack                             8192K        2 
__DATA                            22.9M      196 
__IMAGE                            528K        2 
__LINKEDIT                       128.8M        5 
__TEXT                           204.7M      196 
__UNICODE                          556K        2 
shared memory                       12K        4 
===========                     =======  ======= 
TOTAL                            468.9M      421 

Thanks for posting your experience. At the same time, many have found problems running <without> that option checked at times when memory is less of an issue. It's hard to know what to do for the best. I would certainly say, when memory isn't the issue, that option should always be checked for the same reason you mention - Boinc doesn't seem to handle memory well after coming out of sleep or after a shutdown.

Yes, I agree with you. If RAM usage is not issue then better to keep this option on. As it help to avoid few other known BOINC issues (for example with sleep mode and with lost of some progress of running WUs during projects switches by BOINC scheduler on multiprojects setups especially if checkpoints are not working properly ).

There is a good update.

Looks like in latest BOINC versions (v 7.16.x and later) BOINC developers finally fixed "waiting for memory" behavior.
It no longer conflicts with "leave non-GPU WU in memory while suspended" option.

Before fix:
If BOINC suspend task due to exceeding allowed RAM usage and option "leave non-GPU WU in memory while suspended" was enabled tasks stays in RAM while "waiting for memory" . And so this way any attempts of BOINC client to free some RAM via suspending some of running WU led to the exact opposite effect: RAM usage only increased(because it consumed by more and more tasks in "waiting for memory" state) until some of tasks or systems as a whole crash due to out of RAM errors.

After the fix:
BOINC client now ignores "leave non-GPU WU in memory while suspended" options for task in "waiting for memory" state and unload them from RAM anyway regardless of this option.
Option now apply to task suspended due to other reasons (like manual user request or CPU switch to another project).

So I retract my recommendation made in this post to avoid use of this option on machines with limited memory - provided BOINC client updated to one of the last versions (>= 7.16.x) .

Also there is no longer useful to limit number of R@H task running in parallel via <max_concurrent> </max_concurrent> settings in the app_config.xml
Its more efficient and easy to tune "use at most" memory settings. And BOINC should do the rest automatically to not exceed these values.

This should be this way from beginning, but unfortunately due to some errors in the BOINC code did not work as expected.
But it work now!