Problems and Technical Issues with Rosetta@home

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kotenok2000
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Message 107137 - Posted: 8 Oct 2022, 2:59:03 UTC - in response to Message 107136.  

Does it run all 8 cores on one frequency or is it like those new intel cpus with half cores with half power?
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Sid Celery

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Message 107138 - Posted: 8 Oct 2022, 3:06:52 UTC - in response to Message 107136.  

I have 2 Androids who were told no tasks available 2, 7, and 9 hours ago. So for some reason there aren't many of them.
I can't answer that. I have a Samsung 10 with Android 12 if that makes a difference and I'm definitely running 2 tasks right now, with 2 recently completed
here
I have a Samsung A10 with Android 11 and a VKWorld Mix Plus with Android 7. I guess you got lucky. I normally get quite a few tasks on both of them.

P.S. what projects can you run on your phone? I've found the later Android versions prevent most projects running due to over the top security. All I can run on the Samsung is Einstein, LHC, Rosetta, Universe.

Most obviously, WCGrid. I seem to always get tasks when the Project is up. Mapping Cancer Markers, mainly.
My newer phone stopped doing those, it kept crashing the OS. That was before and after I upgraded it from Android 9 to 11. No idea why this happened. Only thing is it has a very small amount of RAM. In fact I can only do 4 Einsteins at once, on its 8 cores. The others do Universe. Can't find anything else with a good supply of work.

I don't understand phones at all, so I can't help as to why.
Generally speaking, WCG tasks seem to be less resource intensive so it does seem odd if you can run other projects ok.
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hadron

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Message 107139 - Posted: 8 Oct 2022, 3:46:03 UTC - in response to Message 107112.  

You are beginning to remind me of the people I've fought with over the past few years, who actually believe that H.264 and x.264 are different video codecs.
But on to the present, and your apparent attention deficit disorder.

[quote]... SSDs suck, I use NVME.

You might benefit from a good google search on NVMe. It's not what you seem to think it is.
I know exactly what they are and have several, they're much faster. An SSD over SATA is far too slow, because of the SATA.

Are you from the Android forum?

Well, clearly you do not know, or you would not be suggesting that NVMe is some kind of storage device. It is not. NVMe is a host controller interface specification, the same as SATA. Thus, one might well imagine that some day, we might also see HDDs with a NVMe interface, just as we now have SSDs with a NVMe interface.
I'm not interested in your OCD. I know perfectly well how all disks work and have been in the business since 1997. Please learn basic English. Here is a helper for you:

Hard disk/rust spinner = mechanical drive connected via SATA, previously IDE. Now gets up to about 170MB/s.

SSD = solid state drive connected via SATA, limited by SATA to about 550MB/s.

NVME = solid state drive connected directly to the motherboard using PCI express, gets up to 7000MB/s.

I prefer 7000 to 550.

Thanks for the history lesson, but I actually don't need it. I've been in this game since the IBM/XT was born. I've done my stint in IT, back when ethernet was barely a rumour and ARCnet was all the rage. A colleague at the time was all hot about ethernet, as the rumours suggested that ethernet would be capable of a whole 2 Mbps whereas ARCnet could only do 1!! Talk about progress!!

BTW, you forgot to mention SCSI, and SATA was not "previously IDE" -- SATA means "serial ATA", while another name for IDE is "parallel ATA".

So, once again -- SSD simply means the device uses solid state electronics as its storage medium. it absolutely does NOT refer to the device/host interface, which must be specified separately.
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UBT - wbiz

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Message 107141 - Posted: 8 Oct 2022, 5:39:30 UTC - in response to Message 107112.  

I know perfectly well how all disks work and have been in the business since 1997. Please learn basic English. Here is a helper for you:

Hard disk/rust spinner = mechanical drive connected via SATA, previously IDE. Now gets up to about 170MB/s.

SSD = solid state drive connected via SATA, limited by SATA to about 550MB/s.

NVME = solid state drive connected directly to the motherboard using PCI express, gets up to 7000MB/s.

I prefer 7000 to 550.



As I understand it ....

The underlying speed difference of the SSD chips is probably not that much different, NVME speed relies heavily on dram cache inside the SSD package, if a similar cache system was built into the CPU motherboard and a SATA drive used, would the performance of the system be similar to NVME?

Basically NVME vs SATA is measuring speed at a different point in the chain.

Going one step further, do any motherboards have a dedicated disk-cache system built in? If not, why not? It would appear to be a terrible waste having every SSD containing components that could be located on the motherboard where more flexible choices could be included.
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Profile Grant (SSSF)

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Message 107142 - Posted: 8 Oct 2022, 6:36:09 UTC - in response to Message 107141.  
Last modified: 8 Oct 2022, 6:36:51 UTC

As I understand it ....

The underlying speed difference of the SSD chips is probably not that much different, NVME speed relies heavily on dram cache inside the SSD package, if a similar cache system was built into the CPU motherboard and a SATA drive used, would the performance of the system be similar to NVME?

The short answer is no- NVMe devices use the PCIe bus which offers up to 64GB/s, whereas SATA devices use the SATA interface and SATA III is limited to 600MB/s.
Grant
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Message 107143 - Posted: 8 Oct 2022, 7:57:02 UTC

Dropped WCG. Seems the GPU server can't do it's job handing out tasks properly.
Everything stalls with transient errors.
Oh well...something else then.
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Sid Celery

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Message 107145 - Posted: 8 Oct 2022, 9:40:28 UTC - in response to Message 107143.  

Dropped WCG. Seems the GPU server can't do it's job handing out tasks properly.
Everything stalls with transient errors.
Oh well...something else then.

Not sure why you need to drop it. You're not getting runnable tasks anyway...
But I sympathise. I'm getting the same thing and it's driving me nuts.

On the plus side, while Rosetta has some tasks, hits on WCG have reduced and it's not <quite> as bad as it has been.
Still terrible though, I accept
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Profile [VENETO] boboviz

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Message 107146 - Posted: 8 Oct 2022, 11:39:14 UTC - in response to Message 107145.  

Meantime, the validator and the assimilator seem to be freezed
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Mr P Hucker
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Message 107147 - Posted: 8 Oct 2022, 13:37:52 UTC - in response to Message 107137.  
Last modified: 8 Oct 2022, 13:38:27 UTC

Does it run all 8 cores on one frequency or is it like those new intel cpus with half cores with half power?
It is "big/little" with different frequencies, but they're only marginally different. Something like 1.4 and 1.8. 2 small 6 large. But strangely they tend to all run at the same speed, perhaps it can't use all 8 at full power at once or it would overheat. Probably I could run 6 of 1.8 or 8 of 1.4.

But since WCG is single core, I don't see why this would matter.
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Mr P Hucker
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Message 107148 - Posted: 8 Oct 2022, 13:41:54 UTC - in response to Message 107139.  

You are beginning to remind me of the people I've fought with over the past few years, who actually believe that H.264 and x.264 are different video codecs.
But on to the present, and your apparent attention deficit disorder.

Thanks for the history lesson, but I actually don't need it. I've been in this game since the IBM/XT was born. I've done my stint in IT, back when ethernet was barely a rumour and ARCnet was all the rage. A colleague at the time was all hot about ethernet, as the rumours suggested that ethernet would be capable of a whole 2 Mbps whereas ARCnet could only do 1!! Talk about progress!!

BTW, you forgot to mention SCSI, and SATA was not "previously IDE" -- SATA means "serial ATA", while another name for IDE is "parallel ATA".

So, once again -- SSD simply means the device uses solid state electronics as its storage medium. it absolutely does NOT refer to the device/host interface, which must be specified separately.
ROTFPMSL. Let me explain again, I'm talking about what people call them, not precise OCD terminology. Again, would you tell me you've just bought a car or you've just bought a Ferrari?

Anyone saying they have an SSD clearly has a SATA attached one, or they would say NVME, just take a look at the ads for new computers containing them. You don't undersell what you're advertising.

SATA was IDE. It was the successor to it. They made it faster and serial.
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Mr P Hucker
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Message 107149 - Posted: 8 Oct 2022, 13:43:36 UTC - in response to Message 107145.  

Dropped WCG. Seems the GPU server can't do it's job handing out tasks properly.
Everything stalls with transient errors.
Oh well...something else then.

Not sure why you need to drop it. You're not getting runnable tasks anyway...
But I sympathise. I'm getting the same thing and it's driving me nuts.
Huh? I was getting almost 3 million credit per day running 12 GPUs on it 24/7. You need to configure Boinc better....
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Mr P Hucker
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Message 107150 - Posted: 8 Oct 2022, 13:45:01 UTC - in response to Message 107146.  

Meantime, the validator and the assimilator seem to be freezed
Does it matter? The tasks are coming through and we can return them. The little job of validating will take place very quickly once someone comes into the office on Monday and kicks the server. Are you that desperate for your credits?
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Message 107152 - Posted: 8 Oct 2022, 15:10:20 UTC - in response to Message 107150.  

Are you that desperate for your credits?

If you know me, the credits are the last of my thoughts.
But if the validator has problems, the work could be lost: so no science and wasted work.
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Message 107153 - Posted: 8 Oct 2022, 15:12:46 UTC

Bad batch of RB tasks, perhaps?
rb_10_07_420543_416291_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_03_06_2919833_26_0
<core_client_version>7.20.2</core_client_version>
<![CDATA[
<message>
Incorrect function.
 (0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe @rb_10_07_420543_416291_ab_t000__robetta_FLAGS -in::file::fasta t000_.fasta -jumps:pairing_file t000_.fasta.bbcontacts.jumps -jumps:random_sheets 1 -constraints::cst_file t000_.fasta.CB.cst -constraints:cst_weight 5.0 -constraints::cst_fa_file t000_.fasta.MIN.cst -constraints:cst_fa_weight 5.0 -in:file:boinc_wu_zip rb_10_07_420543_416291_ab_t000__robetta.zip -frag3 rb_10_07_420543_416291_ab_t000__robetta.200.3mers.index.gz -fragA rb_10_07_420543_416291_ab_t000__robetta.200.6mers.index.gz -fragB rb_10_07_420543_416291_ab_t000__robetta.200.3mers.index.gz -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 2145106
Using database: database_357d5d93529_n_methylminirosetta_database

[ ERROR ]: Caught exception:


File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)
 ------------------------ Begin developer's backtrace ------------------------- 
BACKTRACE:
 ------------------------- End developer's backtrace -------------------------- 


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.



</stderr_txt>
]]>

rb_09_03_406077_401241__t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_2917054_4409_1
<core_client_version>7.20.2</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code 3221225477 (0xc0000005)</message>
<stderr_txt>
command: projects/boinc.bakerlab.org_rosetta/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting @flags_rb_09_03_406077_401241__t000__0_C1_robetta -silent_gz -mute all -out:file:silent default.out -in:file:boinc_wu_zip input_rb_09_03_406077_401241__t000__0_C1_robetta.zip -max_registry_shift 3 -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 1826313
Using database: database_357d5d93529_n_methylminirosetta_database


Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x0000000000000000 

Engaging BOINC Windows Runtime Debugger...



********************


BOINC Windows Runtime Debugger Version 7.9.0


Dump Timestamp    : 10/08/22 10:00:20
Install Directory : C:Program FilesBOINC
Data Directory    : B:BOINC
Project Symstore  : https://boinc.bakerlab.org/rosetta/symstore
LoadLibraryA( B:BOINCdbghelp.dll ): GetLastError = 126
Loaded Library    : dbghelp.dll
LoadLibraryA( B:BOINCsymsrv.dll ): GetLastError = 126
LoadLibraryA( symsrv.dll ): GetLastError = 126
LoadLibraryA( B:BOINCsrcsrv.dll ): GetLastError = 126
LoadLibraryA( srcsrv.dll ): GetLastError = 126
LoadLibraryA( B:BOINCversion.dll ): GetLastError = 126
Loaded Library    : version.dll
Debugger Engine   : 4.0.5.0
Symbol Search Path: B:BOINCslots5;B:BOINCprojectsboinc.bakerlab.org_rosetta;srv*B:BOINCprojectsboinc.bakerlab.org_rosettasymbols*http://msdl.microsoft.com/download/symbols;srv*B:BOINCprojectsboinc.bakerlab.org_rosettasymbols*https://boinc.bakerlab.org/rosetta/symstore
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Mr P Hucker
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Message 107154 - Posted: 8 Oct 2022, 15:19:47 UTC - in response to Message 107152.  

Are you that desperate for your credits?

If you know me, the credits are the last of my thoughts.
But if the validator has problems, the work could be lost: so no science and wasted work.
Work doesn't tend to get lost unless there's some catastrophic disk error. If you look at the specs of Rosetta's Servers, I very much doubt that would happen. Look, it's just crashed, someone restarts the validator program on Monday and it goes through them in 20 minutes.
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Message 107155 - Posted: 8 Oct 2022, 15:23:48 UTC - in response to Message 107154.  

Work doesn't tend to get lost unless there's some catastrophic disk error. If you look at the specs of Rosetta's Servers, I very much doubt that would happen.


Don't speak about R@H server.
They are VERY old, not updated, etc
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Message 107156 - Posted: 8 Oct 2022, 15:28:08 UTC - in response to Message 107155.  

Work doesn't tend to get lost unless there's some catastrophic disk error. If you look at the specs of Rosetta's Servers, I very much doubt that would happen.


Don't speak about R@H server.
They are VERY old, not updated, etc
WTF? From their server status page, 72TB of SSD, show me another project with that, and I've never seen Rosetta slow or overloaded, unlike almost every other project out there that can't keep up:


Web servers:
Rack mounted 1U SuperMicro server
Specs: Intel Xeon CPU E3-1270 v5 @ 3.60GHz, 32 GB RAM, X11SSH-TF, 10 GbE
Storage: 256GB SSD for OS
File system: ZFS on Linux v0.7
OS: Ubuntu Server 16.04
Primary file server:
Rack mounted 4U SuperMicro server
Specs: Dual Intel Xeon E5-2640 v4 @ 2.40GHz, 256 GB RAM, X10DRD-IT, 2 x 10 GbE
Storage: 72 x 1TB SSD via LSI SAS 9207-8i
File system: ZFS on Linux v0.7 (raidz2, 9 vdevs with 8 disks) served via NFSv4
OS: Ubuntu Server 16.04
Backup file server:
Rack mounted 4U SuperMicro server
Specs: Intel Xeon E5-1650 v4 @ 3.60GHz, 128 GB RAM, X10SRM-TF, 2 x 10 GbE
Storage: 24 x 10TB HGST drives via LSI SAS 9300-8i
File system: ZFS on Linux v0.7 (raidz2, 2 vdevs with 12 disks)
OS: Ubuntu Server 16.04
Database servers:
Rack mounted 1U SuperMicro server
Specs: Intel Xeon CPU E3-1270 v6 @ 3.80GHz, 64 GB RAM, X11SSH-TF, 10 GbE
Storage: 2 x 1TB SSD
File system: ZFS on Linux v0.7 (mirror)
OS: Ubuntu Server 16.04
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Message 107157 - Posted: 8 Oct 2022, 15:30:43 UTC - in response to Message 107156.  
Last modified: 8 Oct 2022, 15:30:57 UTC

Ubuntu 16.04 will recieve Extended Security Maintenance up to 2026
https://ubuntu.com/about/release-cycle
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Message 107158 - Posted: 8 Oct 2022, 15:32:28 UTC - in response to Message 107157.  

Ubuntu 16.04 will recieve Extended Security Maintenance up to 2026
https://ubuntu.com/about/release-cycle


For a fee.
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Message 107159 - Posted: 8 Oct 2022, 15:35:32 UTC - in response to Message 107156.  

WTF? From their server status page, 72TB of SSD, show me another project with that, and I've never seen Rosetta slow or overloaded, unlike almost every other project out there that can't keep up:

Web servers:
Rack mounted 1U SuperMicro server
.................


All this HW and SW are, almost, 10 year old.
Ehy, It's not a problem, i have customers with over 12 years old server. But you can't say it's all up to date.
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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