Posts by manalog

21) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 97171)
Posted 2 Jun 2020 by manalog
Post:
It is not the first time that I see in the stderr of the completed workunit error messages like this:

Error in `../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu': free(): invalid pointer: 0x00000000067bd783 


Nonetheless, at the end of the stderr there is the number of decoys computed, example:
======================================================
DONE ::     1 starting structures  7183.36 cpu seconds
This process generated     38 decoys from      38 attempts
======================================================

And credits are given.

The problematic WUs of today were:
dongrz_42_42_out_file_0527_d1a75a_4AS_pb_ASW0_TERM14_length60_0095_fragments_abinitio_SAVE_ALL_OUT_942476_1285_0
and
f833377c4525b0718d971c3d5b05283b_fold_SAVE_ALL_OUT_939475_49_0

All the others computed by this host today were free of error.

Are the results still useful or will they be discarded?
I do not want to waste computing power, so if my old laptop is the problem (Intel T7250, 4GB Ram, year 2007) i will use it for other projects where it does not give any error.
Thank you.
22) Message boards : Rosetta@home Science : Two less known DC-projects working on Sars-Cov2 (Message 96589)
Posted 17 May 2020 by manalog
Post:
Hello,
I'd like to share also here a post I published on World Community Grid's forum, perhaps it can be useful also here:

Hi all,
I assume Scripps' researchers are aware of the existence of other distributed-computing projects participating in this fight against this invisible enemy: Rosetta@Home, Folding@Home, Ibercivis. I am aware that each one of those is doing research with a different approach, that everything helps, and I assume that the researchers behind OPN1 knows if they need some data from these projects and how to contact them. In science verification is important, but mere replication without communication is obviously a waste of precious resources.
I would like to show in brief two other projects that are working on Covid: they are less know, and perhaps OPN's researches does not know them. Perhaps they know them, in case ignore my post :)

The first is TN-Grid, from the University of Trento, Italy. They are running a project, gene@home, that is doing "gene network expansion" with an algorithm called PC-IM. They looks like a small but very serious project, with a good number of publication and very precise in the work they are doing. They did this "gene expansion" thing for many genes involved in some human pathologies but, during this outbreak, they expanded all the genes related to Sars-Cov2 according to recent papers, as can be seen in this forum post. Onestly, I do not know what a gene expansion is, but I am sure Scripps' researchers does. They completed this part of the research (1242 genes in 730296 WUs), and they are ok with sharing the data with the scientific community as soon as they need them. So, if this kind of research can be of any use for the purpose of OPN1, you should contact them!

The second is called Quarantine@Home and it is maintained by researchers from the University of California, San Francisco, as can be seen in this reddit post. This project is really new and much less known than Tn-Grid. But I think it can be interesting for Scripps' researchers to see what they are doing because:
1) They are performing Autodock simulations between molecules from the ZINC database and three Sars-Cov2's targets: mpro-1, spike-1, spike-2;
2) Their software runs also on Nvidia GPU's on a docker, and I have seen that it runs very well, with a speed way faster than the one of OPN1 on CPU (of course);
3) Despite being very "spartan" their website is outstanding: results are updated real time and you can see all the binding energy calculated by users in a public database! So the data are immediately available to everyone, including your researchers of course. The best binding energy they've found so far is -14,8
Perhaps it could be very useful for you to compare their results with yours.

Let me know if this post was useful even if just a tiny bit in this fight.
Thank you for your job!


This is the link to the original post: https://www.worldcommunitygrid.org/forums/wcg/viewthread_thread,42403

Let me know if it can be useful here :)
Cheers, good job!
23) Message boards : Cafe Rosetta : Older MOBO's with processors to donate (EU/UK Only) (Message 96481)
Posted 14 May 2020 by manalog
Post:
Hi, I don't know if you still have the computers after a year. In case, I am interested in the Ryzen machine. It would be used h24 to crunch on Boinc projects. I live in Italy; it's a pity I didn't read your message a year ago because I was doing an Erasmus in Leven and I also had a car :( let me know!
24) Message boards : Number crunching : All tasks failed : finish file present too long (Message 95367)
Posted 25 Apr 2020 by manalog
Post:
I am facing the same problem of Raistmer,: a "warming up" lasting several minutes (30-40) before tasks start.
I dedicated a Xeon L5420 24/24 on Rosetta but I do not have an hard disk to use and so its only storage unity is a 16GB thumb drive (USB 2.0). I was thinking too about the Ram disk: which are the files Rosetta needs to access more frequently? If they are, let's say, 400MB big, then we could move them on a ram disk without problems.
totale 727M
-rwxr-xr-x 1 boinc boinc 485M apr 23 19:23 database_357d5d93529_n_methyl.zip
-rw-r--r-- 1 boinc boinc  701 apr 25 21:17 flags_il6r3
-rw-r--r-- 1 boinc boinc  343 apr 25 22:11 jgHE_b02_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2qo6vn6b.flags
-rw-r--r-- 1 boinc boinc 151K apr 25 22:11 jgHE_b02_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_2qo6vn6b.zip
-rw-r--r-- 1 boinc boinc   12 apr 25 22:11 jgHE_b02.flags
-rwxr-xr-x 1 boinc boinc 345K apr 23 19:13 LiberationSans-Regular.ttf
-rw-r--r-- 1 boinc boinc 3,9K apr 25 22:11 Mini_Protein_binds_IL6R_COVID-19_1p9m_v2_0_SAVE_ALL_OUT_IGNORE_THE_REST_9iu9zq9t.flags
-rw-r--r-- 1 boinc boinc 1,9M apr 25 22:11 Mini_Protein_binds_IL6R_COVID-19_1p9m_v2_0_SAVE_ALL_OUT_IGNORE_THE_REST_9iu9zq9t.zip
-rw-r--r-- 1 boinc boinc 3,0K apr 25 21:21 Mini_Protein_binds_IL6R_COVID-19_1p9m_v2_4_SAVE_ALL_OUT_IGNORE_THE_REST_0pa6ea9e.flags
-rw-r--r-- 1 boinc boinc 1,8M apr 25 21:20 Mini_Protein_binds_IL6R_COVID-19_1p9m_v2_4_SAVE_ALL_OUT_IGNORE_THE_REST_0pa6ea9e.zip
-rw-r--r-- 1 boinc boinc 170K apr 25 21:21 r3x_3934_data.zip
-rw-r--r-- 1 boinc boinc 181K apr 25 22:10 r4k_11675_data.zip
-rw-r--r-- 1 boinc boinc 177K apr 25 22:11 r4k_13116_data.zip
-rwxr-xr-x 1 boinc boinc 120M apr 23 19:15 rosetta_4.15_x86_64-pc-linux-gnu
-rwxr-xr-x 1 boinc boinc 118M apr 25 21:24 rosetta_graphics_4.15_x86_64-pc-linux-gnu


Is the database the one that causes trouble? How often is the database file updated?


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