Rosetta 4.1+ and 4.2+

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Message 95360 - Posted: 25 Apr 2020, 19:24:40 UTC - in response to Message 95356.  

When you are pushing 70 models an hour, it doesn't leave much time to bring in numerous steps. The WU you cited shows no sign of any problems.
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Message 95363 - Posted: 25 Apr 2020, 19:59:08 UTC - in response to Message 95360.  

When you are pushing 70 models an hour, it doesn't leave much time to bring in numerous steps. The WU you cited shows no sign of any problems.


Ok I just wasn't sure because those units say Stage: unknown for most of the time that they crunch. Good to know it isn't an issue
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Message 95536 - Posted: 29 Apr 2020, 12:28:20 UTC
Last modified: 29 Apr 2020, 12:29:35 UTC

Have come back to Rosetta after a bit of a break.
Using the same computer that I have used before (Windows 32 bit XP OS with 4 cores) but all work units are failing to start.

Get the message couldn't start app: CreateProcess() failed - (unknown error)

Stopped the virus scanner from scanning the Boinc files but this has made no difference. Also upgraded to a much later Boinc version but to no avail.

Is it a memory issue? Being 32 bit I have less than 4 GB available.

Conan
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Message 95547 - Posted: 29 Apr 2020, 14:08:08 UTC

I don't want to know why Windows XP is used in 2020. At least put Linux on that computer and it will work.
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Message 95573 - Posted: 29 Apr 2020, 23:55:20 UTC

Thanks Millenium for the reply, However the comment does not solve my problem.

Why use XP in 2020, because it still works, does what I want it to (mostly) and is installed on a computer that is pushing 10 years old.
There is no need to change if something isn't broken then why fix it. Plus life and finances sometimes dictate what a person is able to do outside what they have to do.
It is mainly used for web browsing and Boinc.

I have been a member of Rosetta since 2005 and have not had issues like this before unless on Ralph where they are supposed to occur.
My linux machine is busy doing other things, so I will go back to TN-Grid, work units there work fine with no errors.

Not to worry plenty of other things to do.

Have a good day
Conan
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Message 95584 - Posted: 30 Apr 2020, 7:03:03 UTC - in response to Message 95573.  
Last modified: 30 Apr 2020, 7:03:59 UTC

Well, a 10 year old quad core machine with 4GB RAM isn't bad at all. Why aren't you running something nice on it like a recent version of Lubuntu (or Xubuntu)? It's free and pretty efficient on old hardware.

If your processor is from 10 years ago, it should definitely support 64-bit - this would enhance crunching speed as well. A quick test showed that on a 4GB machine, a 32-bit Puppy Linux could use 3.5GB RAM, while a 64-bit Puppy Linux could use all of it (running from RAM disk while at it). That's not a negligible difference at all.

I would definitely not connect an XP machine to a network (or to a power outlet for that matter). It's almost 20 years old now and has gone unmaintaned for years. You are begging to get hacked.

/OFF We're in the process of evaluating software to run on 15-20 year old hardware for charity donations and whether it would be usable and the outlook seems pretty good up until now.
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Message 95590 - Posted: 30 Apr 2020, 10:16:50 UTC - in response to Message 95573.  

Thanks Millenium for the reply, However the comment does not solve my problem.

Why use XP in 2020, because it still works, does what I want it to (mostly) and is installed on a computer that is pushing 10 years old.
There is no need to change if something isn't broken then why fix it. Plus life and finances sometimes dictate what a person is able to do outside what they have to do.
It is mainly used for web browsing and Boinc.

I have been a member of Rosetta since 2005 and have not had issues like this before unless on Ralph where they are supposed to occur.
My linux machine is busy doing other things, so I will go back to TN-Grid, work units there work fine with no errors.

Not to worry plenty of other things to do.

Have a good day
Conan


To be fair to Millennium the question was for your benefit (and the security of the Boinc servers).

XP is massively insecure, they stopped putting security patches out for it years ago. Not only is your network likely to be attacked through it but it would be a route into any PCs you connect to.
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Message 95597 - Posted: 30 Apr 2020, 11:23:58 UTC

Security is the main problem indeed, having a Windows XP connected to internet is madness. It if was offline then, uh, no problem. That's why I suggested Linux, as you already know it's free, fast and, being updated, secure. I too indeed have an old quadcore which I still use, slapped Linux on it and it's perfect for what it does.
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Message 95608 - Posted: 30 Apr 2020, 14:46:31 UTC - in response to Message 95597.  

Security is the main problem indeed, having a Windows XP connected to internet is madness.

Some years ago, a guy did a test of a machine (probably XP) with absolutely no patches, but behind a router.
That was back in the days of Red Alert and the port vulnerabilities, when most machines did not last 10 seconds.

It had absolutely no infections after several days. But it was not used for web browsing.
A dedicated machine is safe with anything if you know what you are doing. Most people don't.
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Message 95640 - Posted: 30 Apr 2020, 23:58:17 UTC

It's OK everyone.
I am not going to cause a security issue here at Rosetta or anywhere else.
Yes I am using XP, yes it on the net, yes I connect to BOINC projects and yes I do some web searches now and then.

It is not really an issue, that computer is behind a router + Firewall and also my Anti-Virus programme that is always up to date.
I have not had problems with this.

it mainly does BOINC and it still works.

When and if the upgrade comes that I dream about then I might consider retiring it or as suggested put Linux on it, time will tell.

Thanks for your concerns, valid reasons all noted.
Can't do much about it at the moment.

Hopefully a cure for this Covid 19 virus comes along and the world becomes a happier place.

Thanks again
Conan
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Message 95652 - Posted: 1 May 2020, 9:22:56 UTC
Last modified: 1 May 2020, 9:23:26 UTC

@Conan
i am using winxp too and all ok no problem. if i need run some modern soft (not sup winxp) always can use win7-win8.1

to all those who write above about winxp-don't impose your own wishes on a person,if he wants to use winxp let him use it so far, as long as it suits him
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Message 95661 - Posted: 1 May 2020, 10:53:05 UTC - in response to Message 95652.  

@Conan
i am using winxp too and all ok no problem. if i need run some modern soft (not sup winxp) always can use win7-win8.1

to all those who write above about winxp-don't impose your own wishes on a person,if he wants to use winxp let him use it so far, as long as it suits him


Rather than imposing our own wishes on Conan it was more a case of pointing out the dangers both to his own system and to the systems he connects to.

I have no way of imposing my wishes on anyone, nor would I want to.
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Message 95666 - Posted: 1 May 2020, 13:57:38 UTC
Last modified: 1 May 2020, 13:59:02 UTC

WoW, this one seems more algorithm-depended than all others...

<core_client_version>7.6.33</core_client_version>
<![CDATA[
<message>
- exit code 1 (0x1)
</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.15_windows_x86_64.exe -abinitio::fastrelax 1 -ex2aro 1 -frag3 00001.200.3mers.index -in:file:native 00001.pdb -silent_gz 1 -frag9 00001.200.9mers.index -out:file:silent default.out -ex1 1 -abinitio::rsd_wt_loop 0.5 -relax::default_repeats 5 -abinitio::use_filters false -abinitio::increase_cycles 10 -abinitio::rsd_wt_helix 0.5 -beta 1 -abinitio::rg_reweight 0.5 -in:file:boinc_wu_zip ZN5I2D63_RiAFP_fiber_solenoid_Peralta_published_data.zip -out:file:silent default.out -silent_gz -mute all -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 2934427

ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta).
ERROR:: Exit from: ......srccoreenergy_methodsRamaPreProEnergy.cc line: 148
BOINC:: Error reading and gzipping output datafile: default.out
06:09:44 (1076): called boinc_finish(1)

</stderr_txt>
]]>

Result: https://boinc.bakerlab.org/rosetta/result.php?resultid=1166025891
ZN5I2D63_RiAFP_fiber_solenoid_Peralta_published_fold_SAVE_ALL_OUT_925453_948_1
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Message 95667 - Posted: 1 May 2020, 14:06:44 UTC
Last modified: 1 May 2020, 14:11:16 UTC

Regarding WinXP and memory:
I'm runnign Vista x86 and it does Rosetta work OK. So, definitely not a 32-bit restriction to available memory.
Most probably app was built against new MS SDK. And they broke (they do this regularly) process creation function for old OS. PErhaps app should be built with XP-compatibility flag turned ON.

And regarding "unpatched" and so on. Clear your minds from marketing bul...t.
Talented hacker will enter in modern Win10 just as easy :)
On each old closed backdor each new update opens dozen new ones...
Old OSes just never had exposed SO many network services as modern OSes do.
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Message 95670 - Posted: 1 May 2020, 16:33:45 UTC - in response to Message 95661.  


Rather than imposing our own wishes on Conan it was more a case of pointing out the dangers both to his own system and to the systems he connects to.
I have no way of imposing my wishes on anyone, nor would I want to.

lol win10 more dangerous with spying and unnecessary 100500 services
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Message 95673 - Posted: 1 May 2020, 17:53:18 UTC

OK, so back to the topic of the thread...
Conan, my first instinct when I see process can't start sorts of messages is that there is an authority issue, or anti-virus software in the way.
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Message 95678 - Posted: 1 May 2020, 20:28:58 UTC
Last modified: 1 May 2020, 20:35:56 UTC

I updated the rosetta app version to 4.20 for the arm, android, and mac platforms. I will update the remaining platforms in the next day or so.

Please post issues regarding this updated app version here.

This update includes:

1. extraction of the Rosetta database into the project directory with all following jobs reading from the same database rather than extracting into the slot directory for every job. This significantly reduces the disk usage per job.
2. checkpointing in the Rosetta comparative modeling protocol. This should significantly reduce wasted cpu time if jobs are preempted often, particularly for jobs that take a long time to produce models.
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Message 95701 - Posted: 1 May 2020, 23:31:52 UTC

Had a task error out with a computation error. Can be found here https://boinc.bakerlab.org/rosetta/result.php?resultid=1164088165
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Message 95702 - Posted: 1 May 2020, 23:39:27 UTC - in response to Message 95701.  
Last modified: 1 May 2020, 23:47:58 UTC

Had a task error out with a computation error. Can be found here https://boinc.bakerlab.org/rosetta/result.php?resultid=1164088165
16GB of RAM & 12 cores/threads in use, there's a good chance that will happen once or twice a day, every few days, depending on the Tasks being processed.
I limited the number of threads on one system (till i upgraded it's RAM), and increased the amount of RAM on the other, and then stopped getting those errors.

A Task that ends up needing more RAM than is available (either physically or due to your RAM settings in your Compute preferences) should just result in that (or another) Task suspending till the need for RAM drops & there's enough for all of them to run again.
Unfortunately it seems it doesn't always work that way.



EDIT- i'd also suggest reducing the size of your cache while the BOINC Manager works out the actual Estimated completion times, otherwise there's a good chance you'll start missing deadlines.
   Other	
                                Store at least 0.5 days of work
                     Store up to an additional 0.02 days of work
Give it a week or 3 to settle down & see how things go from there.
With more than one project, "Store at least 0.1 days of work" or less would probably be better still.
Grant
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Message 95706 - Posted: 1 May 2020, 23:49:27 UTC

Thanks Grant, I thought that might have been the issue. I went ahead and cut the cores used back by half just to be sure. Also set work buffers at Minimum 0.20 day(s) and additional buffer at 0.02 because I am seeing that it thinks it will take 23 hrs to finish a task. I know the watchdog won't let it go that long, but this is a brand new system so it is trying to sort itself
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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