I just updated the linux app to version 3.66. Let me know if there are any other issues.

Hi,

<stderr_txt>
../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.65_x86_64-pc-linux-gnu: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory
</stderr_txt>

had the same problem and after installing freeglut3 'sudo apt-get install freeglut3' in Ubuntu 14.04 it worked for me again.

Cheers, Chris

Hello Guys

I am on Debian 8 and used the following files to fix the problem (I have now had several work units complete successfully)

apt-get install freeglut3 libglu1-mesalibglu1-mesa

cheers

Yeah. Sorry for the 500 or so bad WUs rosetta admins. I was running boinc headless and hit this same issue with 3 days of units queued on two fairly powerful boxes.

On my Ubuntu box: apt-get install freeglut3
On my Arch box: pacman -Sy freeglut

That gives me the freeglut library. Can't check to see if it fixes things or not since my machine's account is limited now:

17-Oct-2015 14:26:37 [rosetta@home] Sending scheduler request: To fetch work.
17-Oct-2015 14:26:37 [rosetta@home] Requesting new tasks for CPU
17-Oct-2015 14:26:40 [rosetta@home] Scheduler request completed: got 0 new tasks
17-Oct-2015 14:26:40 [rosetta@home] No work sent
17-Oct-2015 14:26:40 [rosetta@home] (reached daily quota of 8 results)

Guess we are waiting until tomorrow.....

Hi.

The first w.u. with 3.66 app has run & returned no problems from my xeon, my other rigs have a backlog of 3.65 w.u. as I run a two days cashe they will be on it by tonight my time.

---

Yeah. Sorry for the 500 or so bad WUs rosetta admins. I was running boinc headless and hit this same issue with 3 days of units queued on two fairly powerful boxes.

On my Ubuntu box: apt-get install freeglut3
On my Arch box: pacman -Sy freeglut

That gives me the freeglut library. Can't check to see if it fixes things or not since my machine's account is limited now:

17-Oct-2015 14:26:37 [rosetta@home] Sending scheduler request: To fetch work.
17-Oct-2015 14:26:37 [rosetta@home] Requesting new tasks for CPU
17-Oct-2015 14:26:40 [rosetta@home] Scheduler request completed: got 0 new tasks
17-Oct-2015 14:26:40 [rosetta@home] No work sent
17-Oct-2015 14:26:40 [rosetta@home] (reached daily quota of 8 results)

Guess we are waiting until tomorrow.....

Was also missing libGLU.so.1

<![CDATA[
<message>
process exited with code 127 (0x7f, -129)
</message>
<stderr_txt>
../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.66_x86_64-pc-linux-gnu: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory

</stderr_txt>
]]>

To install the correct libraries that are not pulled in by package management, this is what I'm trying:

On my Ubuntu box: apt-get install freeglu3 libglu1-mesa
On my Arch box: pacman -Sy freeglut glu

Waiting yet another day as I dwell in the pit of quota confinement.

Yeah. Sorry for the 500 or so bad WUs rosetta admins. I was running boinc headless and hit this same issue with 3 days of units queued on two fairly powerful boxes.

On my Ubuntu box: apt-get install freeglut3
On my Arch box: pacman -Sy freeglut

That gives me the freeglut library. Can't check to see if it fixes things or not since my machine's account is limited now:

17-Oct-2015 14:26:37 [rosetta@home] Sending scheduler request: To fetch work.
17-Oct-2015 14:26:37 [rosetta@home] Requesting new tasks for CPU
17-Oct-2015 14:26:40 [rosetta@home] Scheduler request completed: got 0 new tasks
17-Oct-2015 14:26:40 [rosetta@home] No work sent
17-Oct-2015 14:26:40 [rosetta@home] (reached daily quota of 8 results)

Guess we are waiting until tomorrow.....

Was also missing libGLU.so.1

<![CDATA[
<message>
process exited with code 127 (0x7f, -129)
</message>
<stderr_txt>
../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.66_x86_64-pc-linux-gnu: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory

</stderr_txt>
]]>

To install the correct libraries that are not pulled in by package management, this is what I'm trying:

On my Ubuntu box: apt-get install freeglu3 libglu1-mesa
On my Arch box: pacman -Sy freeglut glu

Waiting yet another day as I dwell in the pit of quota confinement.

Good detective work and concise instructions! Nice.

I think the needed libraries vary by (possibly) distribution and version of distribution AND possibly by what graphics board drivers you have installed.

There are several tools to check that all the needed libraries on a dynamically linked executable binary exist and there should not be a "missing library" error. I usually use (out of habit) "ldd".

Rosetta@home will have to clear up the dynamic linking problem, because Baker Labs will definitely not want statically linked Rosetta binaries distributed once they understand the LGPL license will require them to freely distribute COMPLETE Rosetta source code or linkable object files. Statically linking LGPL libraries creates a LGPL "COMBINED WORK" and probably more cost legally and distribution wise than just dynamic linking.


LGPL v3.0

LGPL license v3.0 section 4.d.0 is the relevant section describing combined works and requirements.

"For the purpose of complying with the LGPL (any extant
version: v2, v2.1 or v3):

(1) If you statically link against an LGPL'd library, you must also provide your application in an object (not necessarily source) format, so that a user has the opportunity to modify the library and relink the application.
"

Hi,

<stderr_txt>
../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.65_x86_64-pc-linux-gnu: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory
</stderr_txt>

had the same problem and after installing freeglut3 'sudo apt-get install freeglut3' in Ubuntu 14.04 it worked for me again.

Cheers, Chris

Hello Guys

I am on Debian 8 and used the following files to fix the problem (I have now had several work units complete successfully)

apt-get install freeglut3 libglu1-mesalibglu1-mesa

cheers

Hi Guys

Just a follow-up - units processing normally now from the time of the adding of
freeglut3 and libglu1-mesalibglu1-mesa - barring one isolated wobble amongst 60-odd successful ones.

Thanks

---

Hi, all!

I have two 3.65 tasks stuck at 100%. Elapsed times are 32:16:03 and 14:30:21.

Please, should I let them crunch or abort?

Many thanks,
Valter Aguiar.

---

Hi, all!

I have two 3.65 tasks stuck at 100%. Elapsed times are 32:16:03 and 14:30:21.

Please, should I let them crunch or abort?

You should restart BOINC.

---

.

Hi, all!

I have two 3.65 tasks stuck at 100%. Elapsed times are 32:16:03 and 14:30:21.

Please, should I let them crunch or abort?

You should restart BOINC.

And make sure "Stop running tasks when exiting BOINC manager" is selected in the popup when you exit BOINC.

---

Hi, all!

I have two 3.65 tasks stuck at 100%. Elapsed times are 32:16:03 and 14:30:21.

Please, should I let them crunch or abort?

You should restart BOINC.

And make sure "Stop running tasks when exiting BOINC manager" is selected in the popup when you exit BOINC.

Restarted, and both WUs came to the end.

Many thanks,
Valter.

---

Outstanding!

Yet another statically linked binary. One step forward, two steps back.

We wouldn't want the users to forgo their incredibly important screen savers, right?

771051688

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x00C76BA6 read attempt to address 0x12364000

---

Outstanding!

Yet another statically linked binary. One step forward, two steps back.

We wouldn't want the users to forgo their incredibly important screen savers, right?

Can't please everyone.....

Can't please everyone.....

...just ditch the project? Hmm, sure. At least I can.

Your problem no. 1: You don't seem to have a ginormous supercomputer.
Your problem no. 2: So you have to rely on volunteers through BOINC.

Therefore, sometimes, you'll have to deal with our "input" or get yourself said ginormous super computer with no annoying users.

The lists in the "Statistics" part of this website are littered with corpses of inactive users and ancient computers - last logon in 2008.

You want to make sure that Rosetta will run on any host, no matter how old? OK, but you are wasting a lot of potential and in your drive to cater to all users, you alienate those who are willing to invest in some high-end equipment to help get the work done more quickly.

When it comes to the highly important screen saver part: rjs5 has offered help. Maybe ask him?

Not saying you should ditch projects and we are not trying to alienate anyone. We'll continue to focus on our research objectives.

Outstanding!

Yet another statically linked binary. One step forward, two steps back.

We wouldn't want the users to forgo their incredibly important screen savers, right?

Can't please everyone.....

Just a "heads up" ....

3.67 Rosetta jobs just hit my Xeon 1540D machine running Fedora22 and ..... and .... after 40 minutes compute time ..... VALIDATE ERRORS. I RESET the project and will see if that clears it up.


Task ID 771281114
Name from_phil_model20_relax_SAVE_ALL_OUT_311211_4_0
Workunit 699094937
Created 11 Nov 2015 2:24:58 UTC
Sent 11 Nov 2015 2:35:38 UTC
Received 11 Nov 2015 3:21:12 UTC
Server state Over
Outcome Validate error
Client state Done
Exit status 0 (0x0)
Computer ID 2366448
Report deadline 25 Nov 2015 2:35:38 UTC
CPU time 2343.913
stderr out <core_client_version>7.2.42</core_client_version>
<![CDATA[
<stderr_txt>
[2015-11-10 18:40:33:] :: BOINC:: Initializing ... ok.
[2015-11-10 18:40:33:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
command: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_3.67_x86_64-pc-linux-gnu -out:file:silent default.out -in:file:s 00001.pdb -frag3 00001.200.3mers -in:file:native 00001.pdb -frag9 00001.200.9mers -silent_gz 1 -ex2aro 1 -relax::default_repeats 15 -in:file:fullatom 1 -run:protocol relax -ex1 1 -in:file:boinc_wu_zip from_phil_model20_data.zip -out:file:silent default.out -silent_gz -mute all -in:file:native 00001.pdb -in:file:fullatom -in:file:s 00001.pdb -nstruct 10000 -cpu_run_time 21600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 2097500
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize() End reached
Loaded options.... ok
Processed options.... ok
Initializing random generators... ok
Initialization complete.
Setting WU description ...
Unpacking zip data: ../../projects/boinc.bakerlab.org_rosetta/minirosetta_database_b7c7d78.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/from_phil_model20_data.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
======================================================
DONE :: 99 starting structures 2343.59 cpu seconds
This process generated 99 decoys from 99 attempts
======================================================
BOINC :: WS_max 0

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down cleanly ...
called boinc_finish

</stderr_txt>
]]>


Validate state Invalid
Claimed credit 6.24573687673079
Granted credit 0
application version 3.67

We'll continue to focus on our research objectives.

And THIS is very important, but....

The lists in the "Statistics" part of this website are littered with corpses of inactive users and ancient computers - last logon in 2008.

It's a simple command in your db to clear these zombies so, why not?
I think it's VERY important the "loyalty" of your crunchers (i'm here since 2005) and some actions, like update the software server, clear the old accounts, create an optimized app, etc help the community.
I hope, in 2016, you will consider these actions

---

The machine is completing jobs after resetting.

We'll continue to focus on our research objectives.

And THIS is very important, but....

The lists in the "Statistics" part of this website are littered with corpses of inactive users and ancient computers - last logon in 2008.

It's a simple command in your db to clear these zombies so, why not?
I think it's VERY important the "loyalty" of your crunchers (i'm here since 2005) and some actions, like update the software server, clear the old accounts, create an optimized app, etc help the community.
I hope, in 2016, you will consider these actions

I can definitely do a simple house cleaning, the others are a bit more involved.

The machine is completing jobs after resetting.

Looks like that particular job was creating too many models than allowed. If this happens again, you don't have to do anything, but letting us know does help so I can tell the researcher who is running the job.