Posts by [AF>Libristes] Dudumomo

1) Message boards : Number crunching : Computation error - WS_max (Message 90549)
Posted 22 Mar 2019 by Profile [AF>Libristes] Dudumomo
Post:
Hello,
I am having a lot of errors on many machines. The compute time is set per default (8hr) and out of 500 results, I got 200 failing, quite massive for me....

It is always the same error, on different machines, with Rosetta v4.08 x86_64-pc-linux-gnu

<core_client_version>7.8.3</core_client_version>
<![CDATA[
<message>
finish file present too long</message>
<stderr_txt>
command: ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.08_x86_64-pc-linux-gnu @rb_03_20_1958_2097_ab_t000__h001_robetta_FLAGS -in::file::fasta t000__h001.fasta -psipred_ss2 t000__h001.spider3_ss2 -kill_hairpins t000__h001.nobuformat.spider3_ss2 -abinitio::use_filters true -in:file:boinc_wu_zip rb_03_20_1958_2097_ab_t000__h001_robetta.zip -frag3 rb_03_20_1958_2097_ab_t000__h001_robetta.200.3mers.index.gz -fragA rb_03_20_1958_2097_ab_t000__h001_robetta.200.4mers.index.gz -fragB rb_03_20_1958_2097_ab_t000__h001_robetta.200.7mers.index.gz -nstruct 10000 -cpu_run_time 28800 -watchdog -boinc:max_nstruct 600 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3837233
Starting watchdog...
Watchdog active.
======================================================
DONE ::     1 starting structures    28077 cpu seconds
This process generated     25 decoys from      25 attempts
======================================================
BOINC :: WS_max 2.82124e+08

BOINC :: Watchdog shutting down...
05:08:52 (30439): called boinc_finish(0)

</stderr_txt>
]]>


Any idea how to fix this?

Thank you
2) Message boards : Number crunching : IBM z900 for Crunching (Message 64817)
Posted 5 Jan 2010 by Profile [AF>Libristes] Dudumomo
Post:
As Rosetta doesn\'t have a GPU app, you may just want to buy a big CPU farm.
What about a V16 V32 ? etc..
Buy a tyan mobo for example, with 4 quad xeon or opteron. It would be a good computer too. 16 real core.

Or why not building your own supercomputer, with X mobo, X processors, etc...

Can be nice too !
3) Message boards : Number crunching : Make Boinc a standard on operating systems... (Message 64815)
Posted 5 Jan 2010 by Profile [AF>Libristes] Dudumomo
Post:
I seriously doubt about a future integration of BOINC in any OS.
First of all It can only be a link and not directly installed on the OS (For update problem, firstly)

But also, BOINC can reduce the life length of a computer if this one is not well design.
For a laptop, as it is the same OS usually than for desktop, using BOINC can cause a lot of trouble.
Furthermore, using BOINC, can increase the loudness of the computer (Because of the fans)
Using BOINC can even slow down the computer (if not enough RAM)

For all these reasons and much more, I think BOINC will never be implemented in any OS.

The user/admin and only him, has to install BOINC on his computer.

But a link is a good choice as Windows 7 or Linux.

Unfortunatly I guess it would be difficult to add this link in Seven.
(Because, then what not adding a link for this software or that one, etc..)
But if there is a real demand, may be they can do something...
4) Message boards : Number crunching : Minirosetta 2.00 (Message 64037)
Posted 13 Nov 2009 by Profile [AF>Libristes] Dudumomo
Post:
Okay thanks !
I let my second computer running these WUs.
5) Message boards : Number crunching : Minirosetta 2.00 (Message 64034)
Posted 13 Nov 2009 by Profile [AF>Libristes] Dudumomo
Post:
I got linux 64b too.
I guess there is something wrong with our lib...?

My second laptop with Linux 64b as well, does not have any error calculation...

Do we have to install a particular lib ? Or what is wrong ?

Thanks
6) Message boards : Number crunching : Minirosetta 2.00 (Message 64031)
Posted 12 Nov 2009 by Profile [AF>Libristes] Dudumomo
Post:
Hi.
I got a lot of errors too :
lr5_dun08_it04_A_rlbd_4icb_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_439_0
<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-12 17:51:35:] :: BOINC:: Initializing ... ok.
[2009-11-12 17:51:35:] :: 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.
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_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_4icb.out.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Fullatom mode ..
# cpu_run_time_pref: 86400
Fullatom mode ..
..
..
..
Fullatom mode ..
SIGSEGV: segmentation violation
Stack trace (27 frames):
[0x9667f13]
.
.
.
[0x8048121]

Exiting...

</stderr_txt>
]]>

And also :

lr5_dun08_it04_A_rlbd_1ugh_SAVE_ALL_OUT_IGNORE_THE_REST_DECOY_15799_445_0
<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)
</message>
<stderr_txt>
[2009-11-12 19:16:30:] :: BOINC:: Initializing ... ok.
[2009-11-12 19:16:30:] :: 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.
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_rev33769.zip
Unpacking WU data ...
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/yfsong_lr5_dun08_it04_A.zip
Unpacking data: ../../projects/boinc.bakerlab.org_rosetta/lr5_1wdv.out.zip
Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
Fullatom mode ..
# cpu_run_time_pref: 86400
Fullatom mode ..
Fullatom mode ..
Fullatom mode ..
*** glibc detected *** free(): invalid next size (fast): 0xef219138 ***
SIGABRT: abort called
Stack trace (30 frames):
[0x9667f13]
.
.
.
[0x8048121]

Exiting...

</stderr_txt>
]]>

Any idea why ?

And I got a lr5_dun08 blocked at 0.310% after 24h...I\'m gonna cancel it I guess.






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