Posts by Trotador

1) Message boards : RALPH@home bug list : Rosetta_beta 4.0+ (Message 6239)
Posted 21 Nov 2017 by Trotador
Post:
I seems that there are lots of units to download but I can't downoload any in my hosts (linux), is it only for windows?
2) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6074)
Posted 23 Mar 2016 by Trotador
Post:
All WUs continue erroring in Linux. W7 seems Ok, rest of windows is a mix of failure/success
3) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6061)
Posted 19 Mar 2016 by Trotador
Post:
All units erroring in all my Linux hosts:

Some of the wus failing after finishing crunching OK with the error (these wus were donwloaded yesterday):

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>des5ralph_design5_hydrophobic32_test1_buriedtrp_S_0095_SAVE_ALL_OUT_20313_229_0_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>

Other failing after several hours or after restarting BOINC and reporting 0 seconds of time computed with the error (these ones dowloaded today):

ERROR: ERROR: Option matching -cyclic_peptide:user_set_alph_dihedral_perturbation not found in command line top-level context

I'm seing that most of the windows hosts seem to finish Ok the wu and report success, but it is not a conclusive fact.

Stopping crunching until knowing more.


4) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6060)
Posted 18 Mar 2016 by Trotador
Post:
In one of my hosts, all "des5ralph_design5" units failing after finishing crunching OK with

</stderr_txt>
<message>
upload failure: <file_xfer_error>
<file_name>des5ralph_design5_hydrophobic32_test1_buriedtrp_S_0095_SAVE_ALL_OUT_20313_229_0_0</file_name>
<error_code>-161 (not found)</error_code>
</file_xfer_error>

</message>
]]>

This host have have processing time above default, all units have been crunched during 9-12 hours and generated lot of decoys but end with this error.

Wingmen crunhing just an hour and generating few decoys are uploading OK.
5) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6051)
Posted 13 Feb 2016 by Trotador
Post:
The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation?

thanks for the info




Yes, I'm running a test of a new type of job that runs small perturbations of the protein backbone and then does a round of design. The design protocol can use a lot of memory. I realize that this will be problematic and will see if we can distribute these jobs to high memory machines. We may just not be able to run these on R@h.



I've crunched a lot of these backrub units, they are tough due to the large memory requirements. It is necessary to limit the quantity of units being simultaneously crunched and a lot of baby sitting, but it is also fun :).

Most of them don't use to go over 4 Gb but I got half a dozen reaching almost 7GB in the same host. It has 32 Gb but also 72 threads :), in short it stalled because lack of memory, So I finally had to abort them and a few more because they were nearly over the deadline.



6) Message boards : RALPH@home bug list : Win10 3.71 Unhandled Exception: Reason: Out Of Memory (backrub) (Message 6047)
Posted 7 Feb 2016 by Trotador
Post:
Quote from thread http://ralph.bakerlab.org/forum_thread.php?id=567

Trotador
The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation?

thanks for the info


Dekim

Yes, I'm running a test of a new type of job that runs small perturbations of the protein backbone and then does a round of design. The design protocol can use a lot of memory. I realize that this will be problematic and will see if we can distribute these jobs to high memory machines. We may just not be able to run these on R@h.
7) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6038)
Posted 4 Feb 2016 by Trotador
Post:
The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation?

thanks for the info




Yes, I'm running a test of a new type of job that runs small perturbations of the protein backbone and then does a round of design. The design protocol can use a lot of memory. I realize that this will be problematic and will see if we can distribute these jobs to high memory machines. We may just not be able to run these on R@h.


R@H means Rosseta, doesn`t it? It is good for the investigation you could look for ways of distributing these units. The only effective way I could think of is limiting the quantity of units downloaded, by the user as in CEP project in WCG or by the project. Distributing them only to hosts with lot of memory could just not be enough if the hosts have also a lot of available threads (like mine).

A good thing I'm seeing with these units is that Boinc/Ralph seems to take into account the amount of available system memory and limits the menory used, even limiting the quantity of units in execution below the quantity of available threads, and the systems does not stall and hang as used to happen in these cases. Is it correct ?

8) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 6035)
Posted 4 Feb 2016 by Trotador
Post:
The current Ralph WUs use huge amounts of RAM, I've seen up to 4 Gb per unit, is it on purpose? any new kind of simulation?

thanks for the info

9) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 5905)
Posted 10 Oct 2015 by Trotador
Post:
I just updated the 64bit linux app. Please let me know how it goes as there might still be compatibility issues with the glut, GL, GLU libraries etc...


3.65 is working, great!
10) Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83 (Message 5897)
Posted 9 Oct 2015 by Trotador
Post:
In Linux libglut.so.3 errors all over the place, perhaps looking in wrong directory?


me too :(
11) Message boards : RALPH@home bug list : minirosetta beta 3.50-3.52 apps (Message 5824)
Posted 5 Mar 2015 by Trotador
Post:
Validate error for all tasks returned today.

It looks like being on the server side, units crunch ok.

Suspended until solved.
12) Message boards : RALPH@home bug list : RosettaMini Beta 3.24 (Message 5491)
Posted 31 Mar 2012 by Trotador
Post:
Same here windows 7 and linux both 64 bits. All crashed with that same error.

regards
13) Message boards : RALPH@home bug list : Rosetta@Home Version 3.23 (Message 5473)
Posted 9 Mar 2012 by Trotador
Post:
Had this error on a 6 hour preference, it was completed by another volunteer with a much shorter runtime preference

See 2607010

ERROR: Fatal SOGFunc_Impl error.
ERROR:: Exit from: ..\..\..\src\core\scoring\constraints\SOGFunc_Impl.cc line: 181
BOINC:: Error reading and gzipping output datafile: default.out

Conan


Around a couple of tenths of mine have errored with this same message, all the wingmen but one also failed so far.

It is a system with windows 7 64 bits, boinc manager 6.10.58
14) Message boards : Number crunching : Milestones (Message 5454)
Posted 3 Feb 2012 by Trotador
Post:
Congratulations Conan! I take off my hat

regards
15) Message boards : RALPH@home bug list : Rosetta mini 3.18 (Message 5417)
Posted 8 Nov 2011 by Trotador
Post:
2KZU_... units are erroring just at the start

ERROR: in::file::boinc_wu_zip 4-boinc-submit/2KZU_chromodomain.zip does not exist!
ERROR:: Exit from: src/apps/public/boinc/minirosetta.cc line: 168
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


a problem with the nemae of the files
16) Message boards : RALPH@home bug list : Rosetta mini 3.18 (Message 5414)
Posted 4 Nov 2011 by Trotador
Post:
Hi

Many validation errors today, around 90 out of 320 units, most of them finish in less of 100-200 seconds with few o them reaching 600 or 1000 seconds. So far all the wingmen also failed in these workunits. Both in Linux and in W7.

Regarding the extra long units with very low scores, I think they all are TO538..., It happened firtst with the beta 3.17 (TBC) and the subsequent releases behave equally. I tend lately to abort them.

regards

Edit: I've noticed that many units with validation errors are over 200 seconds
17) Message boards : Number crunching : Can't report work, Server Error : Can't attach shared memory (Message 5249)
Posted 31 Mar 2011 by Trotador
Post:
Hi

I'm now in this situation, I can't upload finished wus for two days receiving this same mesage.

regards
18) Message boards : RALPH@home bug list : Minirosetta 2.16 (Message 5199)
Posted 24 Oct 2010 by Trotador
Post:
It seems that some tasks with validate error status are being valued by the project -> good and thanks!

Some others no, I think it is the case when the replica sent in a second step has succeeded.

regards,
19) Message boards : RALPH@home bug list : Minirosetta 2.16 (Message 5195)
Posted 22 Oct 2010 by Trotador
Post:
My errors are all in windows XP 32 bit. But I think the fault is on the servers side not in ours (from the post from TJ).

regards
20) Message boards : RALPH@home bug list : Minirosetta 2.16 (Message 5193)
Posted 22 Oct 2010 by Trotador
Post:
Hi,

After the server unavailability I notice over a 20% validate error units rate in the uploaded units in the last two or so days.

For almost 110 units uploaded just now it means a lot. Sad if it is just a problem in the servers.

regards

Edit: and it does not seem fixed






©2018 University of Washington
http://www.bakerlab.org