Message boards : RALPH@home bug list : Rosetta mini beta and/or android 3.61-3.83
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dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
This application update includes an improved and optimized energy function developed mainly by Frank DiMaio and Hahnbeom Park, and others which improves on all scientific benchmarks. This is an exciting development which we would like to push out and test further. This update also includes new protocols since it uses current Rosetta source. At this point I have included a 64bit linux version but did not compile with SSE optimizations as it will require more testing. I did turn on SSE for the windows app. Please post bugs/issues here regarding the 3.61 minirosetta_beta app update. |
Chilean Send message Joined: 31 Jul 09 Posts: 12 Credit: 38,068 RAC: 0 |
Awesome! I have my i7 fully stocked on ralph WUs. So far 3 errors, 2 of them failed immediately, the other @ 1000 secs. I'm currently running 6 WUs around the 25 min mark (1600 secs) so far with no errors though. WUs that failed: https://ralph.bakerlab.org/workunit.php?wuid=3003399 https://ralph.bakerlab.org/workunit.php?wuid=3006069 https://ralph.bakerlab.org/workunit.php?wuid=3006096 |
Chilean Send message Joined: 31 Jul 09 Posts: 12 Credit: 38,068 RAC: 0 |
Just finished 3 WUs successfully, but there are plenty that fail right at the start: <core_client_version>7.6.6</core_client_version> <![CDATA[ <message> (unknown error) - exit code -1 (0xffffffff) </message> <stderr_txt> [2015- 8-28 16:50:38:] :: BOINC:: Initializing ... ok. [2015- 8-28 16:50:38:] :: 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/ralph.bakerlab.org/minirosetta_beta_3.61_windows_x86_64.exe -run:protocol relax -ex1 -ex2aro -in:file:boinc_wu_zip FFF_939e816d73e5d4a3e6faf001ad588d96_hh5_Wed_Jun__3_15_28_03_PDT_2015.zip -in:file:s 00001.pdb -in:file:native 00001.pdb -in:file:fullatom -relax::default_repeats 15 -out:file:silent default.out -out:file:silent_struct_type score -silent_gz -relax:cyclic_peptide -mute all -nstruct 10000 -cpu_run_time 3600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3184233 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 ERROR: Option matching -relax:cyclic_peptide not found in command line top-level context </stderr_txt> ]]> |
Felix Kaeufer Send message Joined: 10 Aug 12 Posts: 1 Credit: 13,566 RAC: 0 |
So far I received two work units. One of them finished correctly, the other one failed with the following error: ERROR: Option matching -relax:cyclic_peptide not found in command line top-level context. |
Dr. Merkwürdigliebe Send message Joined: 12 Jun 15 Posts: 16 Credit: 23,473 RAC: 0 |
Yeah, I received this error, too. Task ID 3404721 <core_client_version>7.4.23</core_client_version> <![CDATA[ <message> process exited with code 255 (0xff, -1) </message> <stderr_txt> [2015- 8-29 11:29:13:] :: BOINC:: Initializing ... ok. [2015- 8-29 11:29:13:] :: 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/ralph.bakerlab.org/minirosetta_beta_3.61_x86_64-pc-linux-gnu -run:protocol relax -ex1 -ex2aro -in:file:boinc_wu_zip FFF_939e816d73e5d4a3e6faf001ad588d96_hh5_Wed_Jun__3_15_28_03_PDT_2015.zip -in:file:s 00001.pdb -in:file:native 00001.pdb -in:file:fullatom -relax::default_repeats 15 -out:file:silent default.out -out:file:silent_struct_type score -silent_gz -relax:cyclic_peptide -mute all -nstruct 10000 -cpu_run_time 3600 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -run::rng mt19937 -constant_seed -jran 3184272 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 ERROR: Option matching -relax:cyclic_peptide not found in command line top-level context </stderr_txt> ]]> |
Mumps [MM] Send message Joined: 10 Mar 15 Posts: 2 Credit: 11,258,633 RAC: 0 |
Yup. Most are good on my linux hosts, with a handful of immediate compute errors. stderr out My guess is something strange in the configuration on those particular WU's. Maybe the -relax:cyclic_peptide option is missing a required parameter there? |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 908 Credit: 1,892,541 RAC: 294 |
At this point I have included a 64bit linux version but did not compile with SSE optimizations as it will require more testing. I did turn on SSE for the windows app. From rosetta forum: 1) Please, insert brief description of app in Applications Page, like this. |
dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors. |
Chilean Send message Joined: 31 Jul 09 Posts: 12 Credit: 38,068 RAC: 0 |
For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors. Errors in addition to the "Option matching -relax:cyclic_peptide not found in command line top-level context" ?? |
trigggl Send message Joined: 24 Apr 09 Posts: 1 Credit: 98,061 RAC: 0 |
So far, so good on 64-bit Linux. |
Sysadm@Nbg Send message Joined: 9 Dec 09 Posts: 7 Credit: 225,112 RAC: 0 |
For the 3.62 update, I reverted the windows application back to the 32bit non-sse build, and also reverted the linux application to the 32bit build (for the 64bit apps). There was a significant fraction of errors which prompted the change. We will do another update soon related to the "Option matching -relax:cyclic_peptide not found in command line top-level context" errors. on Linux-64 got some
where the error string is a little bit different to yours eg this workunit |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 908 Credit: 1,892,541 RAC: 294 |
on Linux-64 got some Seems to be the same error of 3.54 version |
Ed Send message Joined: 3 Sep 15 Posts: 2 Credit: 1,042 RAC: 0 |
Hello, As a general software engineering/debugging principal, I would not recommend mixing cpu optimizations and new code in the same build. If a WU fails, what caused it to fail? The new code or one of the optimizations? Instead, make as many branches as you need off the branch of the latest stable build in production, and start testing the optimizations one at a time. Test against work units that have already been run successfully on the stable code base without the optimizations. By following this procedure, you will only be testing one change at a time, for instance enabling SSE or SSE2. So, debugging will be far more straightforward in the case of any WU failures. Cheers, Ed |
dekim Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 20 Jan 06 Posts: 250 Credit: 543,579 RAC: 0 |
The protocol code for the majority of jobs (and all the test jobs) hasn't changed. BUT, for this cyclic peptide error, the developer did not check his code into the main source repo as he should have long ago. In an effort to save time a while ago, we incorporated his code before he checked it in under the understanding he would check it in soon after, which he didn't. But on a positive note, he is busy trying to make and characterize his cyclic peptide designs now. |
Chilean Send message Joined: 31 Jul 09 Posts: 12 Credit: 38,068 RAC: 0 |
The protocol code for the majority of jobs (and all the test jobs) hasn't changed. BUT, for this cyclic peptide error, the developer did not check his code into the main source repo as he should have long ago. In an effort to save time a while ago, we incorporated his code before he checked it in under the understanding he would check it in soon after, which he didn't. But on a positive note, he is busy trying to make and characterize his cyclic peptide designs now. What kind of errors was the SSE extension giving then? Remember that improving performance directly improves scientific benchmarks. There is lots of compute power in RALPH to bug-out any problems that come from using SSE/SSE2 (thought technically there shouldn't be any, since 99% of users are using SSE2 capable CPUs). |
Ed Send message Joined: 3 Sep 15 Posts: 2 Credit: 1,042 RAC: 0 |
Thanks, David. So, to be clear, would the following release notes reflect the version of 3.62 that went to production? Improvements: - Improved and optimized energy function developed mainly by Frank DiMaio and Hahnbeom Park and others which improves on all scientific benchmarks - This update also includes new protocols since it uses current Rosetta source (Ed - What are the *new* protocols that were not in 3.59?) Not Changed: - reverted the windows application back to the 32bit non-sse build - reverted the linux application to the 32bit build (for the 64bit apps), non-sse build |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 908 Credit: 1,892,541 RAC: 294 |
Not Changed: I cannot understand if rosetta's admins are working together with rjs5, sesef or other volunteers expert on optimization. |
Chilean Send message Joined: 31 Jul 09 Posts: 12 Credit: 38,068 RAC: 0 |
Any news regarding the 3.63 version? |
[VENETO] boboviz Send message Joined: 9 Apr 08 Posts: 908 Credit: 1,892,541 RAC: 294 |
Any news regarding the 3.63 version? New exe, new screensaver, new db. Optimizations or only bugfixes? |
Dirk Broer Send message Joined: 7 Aug 14 Posts: 15 Credit: 139,340 RAC: 28 |
In Linux libglut.so.3 errors all over the place, perhaps looking in wrong directory? |
Message boards :
RALPH@home bug list :
Rosetta mini beta and/or android 3.61-3.83
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