Posts by manalog

1) Message boards : Rosetta@home Science : Alphafold and CASP14 in the news (Message 99998)
Posted 11 Dec 2020 by manalog
Post:
Directly from the December Update of the Microbiome Immunity Project (which uses Rosetta) on World Community Grid:

New technology announced

A few weeks ago, the researchers participated in a biennial protein structure predication conference (CASP14). This year, they heard about a brand new technology that may have a major impact on the protein structure prediction problem and the study of protein shapes in general. It is very exciting to see such progress in the field which is going to benefit all of us in the long run.

Over the coming months, the researchers will learn more about this technology, if and how to use it, and how computationally feasible it is at the scale they are working on. They'll let us know if/when the Microbiome Immunity Project would embrace it.

obviously they are referring to DeepFold ;) perhaps it could be possible for us to crunch such workunits sometime in the future

Source: https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=672[/url]
2) Message boards : Predictor of the day : Predictor of the day: Congratulations to grcpool.com-2 (Team Gridcoin) for predicting the (Message 99268)
Posted 8 Oct 2020 by manalog
Post:
These "graft" workunits are issued since end August if I remember well. While the very first weeks I thought it was a mistake and so no science was done, now, after two month and after many more workunits with different names but always with "graft" in the name and always with the same message in the stderr, I am starting thinking that actually it is not a mistake but just a characteristic of these type of experiment and they are doing science even with the error message. A lot of time has passed and I really hope that the scientists aren't wasting so much computing power (especially considering the high quality of science they are doing). Even though, I still have some bad feelings when I see workunits with so much errors in the stderr and I don't like that, despite many people on this forum pointed out this problem, nobody answered. Just a three words sentence is fine "Everything is working fine". Why leaving volunteers with this doubt?
when i take a look at the rosetta screensaver, i can see some "non-continuous drawing" with 2 or more proteins not connected between them ...
very interesting, it's a pity I cannot see the screensaver on Linux. It would be wonderful to have an explanation for the science behind each type of WU![/quote]
3) Message boards : Predictor of the day : Predictor of the day: Congratulations to grcpool.com-2 (Team Gridcoin) for predicting the (Message 99256)
Posted 7 Oct 2020 by manalog
Post:
Finally someone predicts the lowest energy for a "graft" workunits.

Perhaps it's not work wasted?
These workunits, as noted in the forum by many users, produce a lot of bad errors in the stderr. None of the staff answered, so to be safe that my energy is not wasted I abort all of these workunits when they come. Then, annoyed from the fact that after more than a month nobody told us that yes, they are producing work despite the errors, I stopped supporting Rosetta despite it is my favourite projects with regard to science. I really cannot understand why people from the staff do not realize that we are spending energy, time and a lot of money to help them. A short message about those workunits full of errors it's the minimum we can ask.
4) Message boards : News : Coronavirus update from David Baker. Thank you all for your contributions! (Message 99087)
Posted 22 Sep 2020 by manalog
Post:
David, thank you so much for this update.
You are a great, great scientist... I've read a lot in these months about your works and biography and I am sure the work you are doing together with all the people working at IPD will do revolutionary things for everyone in the next years.
Actually I got so passionate about this field that I am seriously considering to move my study path toward bioinformatics... It's not an easy move from a bachelor in Philosopy but it could be done :)
This LCB1 protein looks very promising, I hope that this work could defeat this terrible pandemic. It would be childish to believe that this will be 100% the first and revolutionary cure against coronavirus: it still has to be tested on human beings and this will takes months and potentially adverse effects could arise; nonetheless, the chance that it will works are good. In the case it will function and it will be the first, then you will get an incredible media coverage. In this (incredible lucky) case, please remember to mention several times Rosetta@Home and Foldit to the media... Boinc could pass from a niche phenomenon to a mass and global case, with benefits for everyone :)
Thank you again in the name of everyone.
5) Message boards : Number crunching : Invalid pointer issue (Message 98460)
Posted 10 Aug 2020 by manalog
Post:
That's weird, on Linux I can also change the preferred runtime of a task during its execution: just change the preference, issue an 'update' and then restart the client. If a task is let's say at 4 hours and was set to 8hrs, then if you change it to 2 and restart the client it will finish the last decoys and send it to the server
6) Message boards : Number crunching : Invalid pointer issue (Message 98449)
Posted 9 Aug 2020 by manalog
Post:
Hi all,
I observed a couple of weeks ago that some tasks processed by my Intel T7250 laptop had in the stderr (visible from the task page on the website) error messages such as these:
*** Error in `../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu': free(): invalid pointer: 0x00000000067bd783 ***

repeated hundreds of time. I thought it was a laptop's problem, so I turned it on other projects. Some days ago I tried again to crunch Rosetta on that laptop. It ran two tasks over a night, 8 hours, no suspensions nor restart of boinc-client: the (valid) tasks shown a correct stderr with a good number of decoy. The day after I needed to turn the laptop off but there were two tasks at 4 hours. Thus, I changed Rosetta runtime preference to 2 hours, issued an update on the laptop and restarted the boinc client via /etc/init.d/boinc-client restart.
When the tasks were sent to the server, I checked the stderr on the webpage and the "invalid pointer issue" was again present. Nonetheless, the tasks were considered valid and had a correct number of decoys (around 30 for a JHR that is a sound number for 4 hours of work on a T7250 core).
I have another host running Rosetta, and old iMac running Debian with a T7200 processor. It ran, before with Windows 7 and since a week with Debian, Rosetta H24 for a month without any issue of this kind, always set to 8 hours. While it was running Debian, I do not remember if I restarted boinc-client until today, but I am pretty much sure I suspended the tasks a couple of time.
Today I restarted the boinc-client on this machine and then checked the stderr of the running rosetta processes via
cat /proc/(PID)/fd/2
and... Invalid pointer again! Same issue as the laptop!
So now I know that this is not an issue isolated to my laptop but it can be replicated on other hosts, so perhaps it could be dangerous for the science of the project and I think we as volunteers should do a bit of debug.

1) This invalid pointer error in stderr does not affect the validation of the tasks, nor the credit, nor the number of decoys. It could be that it is just a bug giving a warning message that can be ignored, but it could also be that it generates results that are believed to be valid but that then are not actually valid. Only someone from the staff could answer this, and I think it is important, because if this problem causes issues on the results it is dangerous.
2) It seems to affect only the 64 bit version of rosetta for linux. I tried to restart the boinc-client on a Pentium 4 32 bit and cat /proc/(PID)/fd/2 shown a correct stderr with only the command issued by the boinc-manager
3) I am not sure how to replicate it but my guess is that it could be caused:
a) by a suspension of the task (unlikely)
b) by a change in the runtime preferences during the execution of the task, followed by a restart of the boinc-client
c) by a restart of the boinc-client while tasks are running
d) randomly

Please I ask some volunteer running Linux (problem appeared both in Mint (laptop) and in Debian (iMac)) to try to do the a, b and c step separately and then in combination, always checking as soon as the task starts again if the stderr (cat /proc/pid/fd/2) shows some invalid pointer error message.
Thank you :)
7) Message boards : Number crunching : ARM Compute Raspberry Pi4 with Ubuntu Mate 20.04 beta1 (Message 98409)
Posted 3 Aug 2020 by manalog
Post:
4 rosetta workunits on 4GB sometimes works, sometimes not (leaving one core unused because the boinc client doesn't switch to another job if one is stuck "waiting for memory"... this is something not well designed in boinc client and I'd like to signal to the developer).
Safe number of Rosetta WUs on 4GB of Ram is 2, but also 3 will usually works (the era of ram-eating "COVID scaffold" workunits has ended). If you are new to Boinc, I suggest you to use 2 or 3 cores for Rosetta and then use the other core with a project that uses a very little amount of RAM such as Tn-Grid. You could also try OpenPandemics but I do not remember exactly how much RAM it takes. Tn-Grid uses really a very small amount of RAM, something around 70MB if i remember well. Considered you are new in the Boinc world, if you want I'd be happy to explain you how to set your Raspi to run 3 rosetta Wus and 1 Tn-Grid wu ;)

Ah, very important things: if you don't use the graphic environment in your RPI, then close it because it takes a lot of RAM. Go in the console and type service lightdm stop or service gdm3 stop or whatever login manager are you using. Be sure there are no other tasks sucking memory and cpu if you run "top". Then set the boinc-manager to use 95% of Ram if your Rpi is dedicated only for Boinc.
8) Message boards : Rosetta@home Science : Besides "de novo protein design" are we doing also a lot of benchmarks? (Message 98408)
Posted 3 Aug 2020 by manalog
Post:
Hi all,
during these months of quarantine I read a lot about Rosetta@Home and the science grounding it. Of course my knowledge is very limited, but I am starting having a general intuitive understanding of what we are doing here.
I follow the names of the workunits sometimes, and I search on the internet for more informations about the proteins we are working on (when the WU name is explicative, which is not always the case).
Sometimes we work on proteins with no references at all on the Internet, such as JHR, b4k, b3x... Other times, I realized that we are working on well known proteins: bpmr (1,3), cd86, activin receptor, tgfr... If I look for a PDP structure of these proteins, I always found the crystal structure of them (and usually it was discovered several years ago). So I have some questions:
1) are we working on these proteins because the crystal structure is in some way incomplete and we need to improve it computationally?
1b) perhaps we need some kind of rosetta-model of these structures in order to work on them for example by designing proteins capable of binding to them?
2) are we doing benchmarks to see if and how fast the Rosetta algorithms can predict the actual structure?
3) are scientists manually tuning the algorithm in order to match with the already known structure?
4) is there already a kind of AI that analyze the results from Rosetta@Home and improves the algorithm so it needs to work also on already known crystal structures to train itself?

I am asking this just to understand how much are we working on "new" things, that is: de novo protein design, solving unknown crystal structures, protein-protein docking etc... and how much are we instead trying to improve the Rosetta algorithm and if scientists are doing it manually or by using an AI.

Reading a bit about the history of Rosetta@Home, I understood (perhaps wrongly) that during the very first years of the project the main goal were (2) and (3). Then, around 2017 if I don't misremember, David Baker announced a "breakthrough", that the Rosetta algorithm is now very precise and we can successfully design de-novo proteins.

Another small doubt: usually I cannot see the screensaver because it doesn't working on Linux. Now (and for a short period of time) I have a Windows 7 computer just beside me and sometimes I can see the screensaver. I noticed that for the cd86 workunits there was no "Native" box, while that box was present for the "JHR" workunits... and this was counterintuitive for me, because the cd86 native structure is solved while there are no reference at all on the Internet about JHR.

Thank you to answer my curiosity and sorry for my English :)
9) Message boards : Number crunching : No decoys on an old Pentium 4. Just a curiosity: why? (Message 98407)
Posted 3 Aug 2020 by manalog
Post:
I answer just to tell you how this experiment is going (if anyone is curious about it). After having successfully crunched 178 hours of WCG's MIP (which uses an older version of Rosetta), I decided to switch the old computer on Rosetta@Home again. Now it is working properly, and after 150 hours it never got stuck again on a WU. I realized that "JHR" workunits crunch very well on this P4; on the other hand, yesterday a cd86 workunit arrived and, after 4 hours of elaboration, no decoys were made. Now it is suspended, deadline is tomorrow and probably I am going to abort it. That's weird, because a similar WU on the core of another machine fast only twice of the P4 computed more than 700 decoys in 8 hours.
So I'm wondering if the problem with such an old computer is not in the speed of the process of decoys-making in itself rather than just a kind of intolerance with some WUs which on other computers run even faster than the JHR ones that my P4 loves. RAM is not an issue at it got 2GB of RAM per core, that's a very good amount for Rosetta. Bah. By the way, I am going to turn it off in no longer than one or two weeks. Crunching on a 2.8 P4 is just a completely waste of power: with a rapid proportion, I realized that this computer is 4 times slower than a single core of a mid-range i5 laptop, laptop that is quad core, thus, 16 times slower than a computer (not even brand new) that uses half electricity!
I don't know if overclock it a bit, even if it is summer and here in Rome is very hot. I remember that several years ago I ran this P4 2.8 at 3.06 Ghz and it was very stable.
10) Message boards : Number crunching : Why are my 'Remaining' time estimates so far off? (Message 98135)
Posted 16 Jul 2020 by manalog
Post:
Which runtime did you set on your preferences?
Default is 8 hours, but you could modified it to one day. The other option is that your computer is taking 24 hours just for the first decoy, but this is very unlikely (in particular given your host's performances)
11) Message boards : Number crunching : No decoys on an old Pentium 4. Just a curiosity: why? (Message 97993)
Posted 10 Jul 2020 by manalog
Post:
No, CPU was always doing R@H and nothing else. Even the desktop environment was shut down. Now it is running WCG-MIP workunits and the CPU time is almost the same as the elapsed time. I am waiting for my wingman's result, then I will try another workunit, choosing a task that usually produces hundres of decoys in few time on a faster cpu.
12) Message boards : Number crunching : No decoys on an old Pentium 4. Just a curiosity: why? (Message 97970)
Posted 8 Jul 2020 by manalog
Post:
Indeed, CPU was around 99,8 all the time, with some slight drop and reprise some time but in the order of few point. The process was alive, for sure, my only worry was that it could have been stuck in some loop. 15 hours with no decoys is very strange, even with a Pentium 4. Now it is crunching MIP; it still has to finish its first workunit, but timing seems not too different from a single core of a old dual core laptop I succesfully used on Rosetta and that produced several decoys in eight hours (unles, of course, for the COVID workunits of April, but that was an exceptional case).
I am checking other host: [url]https://boinc.bakerlab.org/rosetta/workunit.php?wuid=1091797531[url]; it is a very powerful computer and it's set on 8 hours runtime. We will see; probably I'll give another try of Rosetta on this host.
13) Message boards : Number crunching : No decoys on an old Pentium 4. Just a curiosity: why? (Message 97963)
Posted 8 Jul 2020 by manalog
Post:
Hi all,
I am totally aware that crunching on a Pentium 4 is extremely inefficient and contributes as a drop in an ocean. Nonetheless, I will be for some days (probably less than a week) in an house where is present an old Pentium 4 2,8; I do not pay the electricity and it comes from certified renewable source. Considered that I am going to do this only for a short period of time, I don't see any issue, I am doing it just for fun and to give some "glory" to this old machine.
The computer runs (very smoothly actually) Debian 7; all the hardware is in very good condition and it has 2GB of Ram. Yesterday I attached it to Rosetta@Home and it started crunching a
bmpr1_attempt3_0_SAVE_ALL_OUT_IGNORE_THE_REST_0se1zv2k_951179_2
workunit; default runtime: 8hrs.
This morning the Wu was at 98.9% of progress, after more than 15 hours of elaboration and no checkpoints were made, that is, no decoy was computed. The process was running, 100% cpu usage, 20% ram usage and, when I checked the /proc/PID/fd/2 file I saw that it was sending signal with its runtime. I killed the WU and now it started another one,
tgfbR2_1_SAVE_ALL_OUT_IGNORE_THE_REST_6th1hn7q_951729_3
. 16471 seconds have passed and still no checkpoint/decoy.
Now, I know that the processor is old (2003) and slow (single core 2.8Ghz) BUT the absence of decoys still looks very inconsistent to me. BMPR and TGFBR2 WUs are very "easy" one and a single core of my Xeon L5420 completes hundreds of decoys in the same time. I know that the IPC of a Pentium 4 is much lower than the one of Core2Duo, but I tried to do some proportions and this behavior is just impossible. Ok, it is slower, but not one hundred time slower! More like 50% and in case I expect half decoys, not no decoys!
Just for curiosity, why? Is it related to the 32 bit architecture? Moreover I have found a couple of old P4/Xeon/Celeron Family 15 in the accounts of "Fold for Covid" and "Grcpool" and they are still working. I am just curious because this thing is puzzling me.
Any suggestion to a project where switching this machine for these days? Tn-Grid no because in order to support P4 with SSE2 is required a recompilation; I have done it but the binary is in another computer I cannot access it and I cannot recompile it now because yesterday in trying to update from Debian 7 to 10 I broken apt and i do not want to fix it, thus I can not install the dependencies required to compile Tn-Grid for SSE2 and I do not want to crunch it without SIMD as a matter of principle. WCG's MIP?
Thank you.[/code]
14) Message boards : News : Rosetta's role in fighting coronavirus (Message 97666)
Posted 27 Jun 2020 by manalog
Post:
https://twitter.com/RosettaAtHome/status/1276324129390555136
We have some BIG NEWS: Researchers @UWproteindesign
have succeeded in creating antiviral proteins that neutralize the new coronavirus in the lab. (These experimental drugs are being optimized for animal trials now)

THANK YOU for helping out!

Join in: http://boinc.bakerlab.org
15) Message boards : Number crunching : no new tasks? (Message 97548)
Posted 24 Jun 2020 by manalog
Post:
Just got some new tasks with this name:
DL_TrR_PSSM_plus_rosetta1998881_0001_0001_fragments_abinitio_SAVE_ALL_OUT_950049_595_0


DeepLearning TrRosetta.
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14042
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13921
PSSM: https://en.wikipedia.org/wiki/Position_weight_matrix
IMHO prepare for a breakthrough in R@h after this pseudo-break ;)
16) Message boards : Number crunching : no new tasks? (Message 97536)
Posted 23 Jun 2020 by manalog
Post:
Put them on tn-grid https://gene.disi.unitn.it/test it works very well on arm even if 32 bit (if I remember correctly). If you want, you could compile the source for your platform and share the binary with the others. It's extremely easy. Other projects for arm are: wcg opn , universe, lhc sixtrack, einstein
EDIT: I've just checked and there is a 64 bit arm version of tn-grid actually
17) Message boards : Rosetta@home Science : Is Rosetta coming to an end? (Message 97470)
Posted 19 Jun 2020 by manalog
Post:
Very interesting, thank you
18) Message boards : Rosetta@home Science : Is Rosetta coming to an end? (Message 97334)
Posted 11 Jun 2020 by manalog
Post:
Now, it is obvious that Rosetta@Home is contributing in some way to this new TrRosetta, just look at the name of a WU I have just received:
DL_energy_landscape_trR_vanilla_5435432132001074_0002_62_fragments_abinitio_SAVE_ALL_OUT_947046_413
It does not require much fantasy to recognize in this name the words "DeepLearning" and "trRosetta".
So I'm curious and I'd like to ask an admin: in which way are we contributing in the development of this new and very promising software?

Good catch. I am sure they are up to something.


You have some of them too ;) https://boinc.bakerlab.org/rosetta/result.php?resultid=1200970479


But the news since COVID has actually been more than normal. In other words, don't expect an answer anytime soon.
But they are working on it. It is a good project.


Ok, it's good to hear this because I have read many users complaining about the lack of news so I thought that the project was going to be abandoned.[/url]
19) Message boards : Rosetta@home Science : Is Rosetta coming to an end? (Message 97332)
Posted 11 Jun 2020 by manalog
Post:
Hi all,
admins are being silent since a lot of time, despite in this period Rosetta@Home is benefiting from a never seen computational power given by a lot of new volunteers due to the coronavirus crisis. It's sad that the community who is contributing with so much effort , time and money spent for equipment and energy has been left alone without any news on how the work is going on, especially the work related to the COVID-19 Workunits.
But there is a glimmer of hope that could explain this silence: is this a preparation for a breakthrough in the future of Rosetta and Rosetta@Home?

I have read something about TrRosetta, and it looks like that the Baker Lab is putting a lot of effort in the development of this new software that will merge the expertise coming from years working for Rosetta and the immense power of Deep Learning (don't forget about the power shown by AlphaFold during the last CASP). This software looks much more powerful than the standard Rosetta, and perhaps this could be the key for a radical revolution in de novo protein design, the dream of David Baker and the IPD.
Now, it is obvious that Rosetta@Home is contributing in some way to this new TrRosetta, just look at the name of a WU I have just received:
DL_energy_landscape_trR_vanilla_5435432132001074_0002_62_fragments_abinitio_SAVE_ALL_OUT_947046_413
It does not require much fantasy to recognize in this name the words "DeepLearning" and "trRosetta".
So I'm curious and I'd like to ask an admin: in which way are we contributing in the development of this new and very promising software?

Moreover, I have a couple more questions:
1) Once the development of TrRosetta will be completed, will this software be considered as a substitute for the classic Rosetta and will the latter became just surpassed or there will be some kind of tasks requesting the classic Rosetta and so eventually the Rosetta@Home infrastructure?
2) If TrRosetta will substitute Rosetta, will Rosetta@Home be shut off or will it be used to run the new software?

So, to sum up: is there any future for Rosetta? Is the Rosetta@Home adventure coming to an end?

Thank you.
20) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 97179)
Posted 3 Jun 2020 by manalog
Post:
for two work units I got very little credit

https://boinc.bakerlab.org/rosetta/result.php?resultid=1193838376

https://boinc.bakerlab.org/rosetta/result.php?resultid=1193967941

can anyone tell me why


Maybe I've figured out your problem.
Look at the stderr of your low-credit WUs:

======================================================
DONE ::     1 starting structures    28571 cpu seconds
This process generated    107 decoys from     107 attempts
======================================================
BOINC :: WS_max 3.3083e+08
09:29:24 (1807): called boinc_finish(0)
======================================================
DONE ::     1 starting structures  28798.1 cpu seconds
This process generated      1 decoys from       1 attempts
======================================================
BOINC :: WS_max 1.61755e+08
09:39:51 (18194): called boinc_finish(0)


and

======================================================
DONE ::     1 starting structures  10694.4 cpu seconds
This process generated     64 decoys from      64 attempts
======================================================
BOINC :: WS_max 0
11:53:27 (15922): called boinc_finish(0)
======================================================
DONE ::     1 starting structures    10791 cpu seconds
This process generated      1 decoys from       1 attempts
======================================================
BOINC :: WS_max 0
11:59:28 (20970): called boinc_finish(0)


It looks like there is a duplicate declaration of how many decoys were computed (don't ask me why); so my hypothesis is that since the credit system is based on the number of decoys computed it sees only the second declaration of your wu ignoring the first one.
I don't know if this problems affects only credits or also science done by the wu.[/quote]


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