2.14 is the latest program version that will be put on your computer automatically with the workunit(s) you download.

As to your other question, I know buried somewhere in this forum is a thread that gives the link to a website where you can enter a protein name and get information about it. I don't recall where that post is, maybe Mod remembers.

hi, sorry to post this here, but ive been searching for a while, still i cant find the answers as simple as they may be.

1 - how do i update to the 2.14 version?

2 - how can i get some info about the workunit im working on? like what are they related to

as a suggestion i would say it would be nice if the users could pick their path, choosing the way their computer time is spent.

2 - how can i get some info about the workunit im working on? like what are they related to

In the protein name somewhere there will be a sequence of 4 characters bracketed by underscores (e.g. 1mvo ). Paste this sequence into the search field at

http://www.rcsb.org/pdb/home/home.do

and it'll tell you about the protein

HTH

thank u greg

thank u vincent

1 - how do i update to the 2.14 version?

Looking at your most recent completed jobs, you're already running 2.14 WUs.

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gunn_fragments_SAVE_ALL_OUT_-1wtyA__20675_2524
gunn_fragments_SAVE_ALL_OUT_-1lveA__20675_212

ERROR: ct == final_atoms
ERROR:: Exit from: src/core/scoring/rms_util.cc line: 410
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

rb_05_13_148_531_rs_stg0_lrlx_t000__casp9_SAVE_ALL_OUT.IGNORE_THE_REST_B_20583_1252

ERROR: CORE ERROR: You must use the ThreadingJobInputter with the LoopRelaxThreadingMover - did you forget the -in:file:template_pdb option?
ERROR:: Exit from: ....srcprotocolsloopsLoopRelaxThreadingMover.cc line: 80
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

Task 342193444 (int2_centerfirst2b_1fAc_2bmv_ProteinInterfaceDesign_23May2010_21231_77_1) failed immediately on Mac OS X

ERROR: Cannot open patchdock file: 1fAc_2bmv.patchdock
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/read_patchdock.cc line: 101
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

A previous cruncher had the same problem on Windows Vista

Task 341066734 (lrm_jorj_combined_torsion_it06_run01_A_rlbn_1bmg_SAVE_ALL_OUT_IGNORE_THE_REST_NATIVE_NOCON_21225_6_1) failed on W7

ERROR: Unable to open weights. Neither ./dslf_weights.wts nor dslf_weights.wts nor minirosetta_databasescoring/weights/dslf_weights.wts exist
ERROR:: Exit from: ....srccorescoringScoreFunctionFactory.cc line: 178
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

A wingman also had the same problem

This task was only 8% through after 15 hours of computation: Task 342533081 int2_centerfirst2b_1fAc_2hhz_ProteinInterfaceDesign_23May2010_21231_149_0

I am only on the default runtime which I believe is 3 hours. Occasionally workunits take up to 6-7 hours to complete but I leave them be, this however had around 30 hours or so remaining on it so I aborted it.

In the task details it says it only had 1485 seconds of CPU time which is only 25 minutes... Odd.

I run a dual core CPU on win7 x86 and other rosetta tasks have been crunching fine on the other core and collatz tasks been running fine on GPU.

No red error messages in message log.

int2_centerfirst2b_1fAc_2oc5_ProteinInterfaceDesign_23May2010_21231_163_1

This one errored out after 12 seconds as my Firewall challenged it. For some reason it was trying to ask for more access than a normal 2.14 unit. No other Rosetta work unit has triggered a Firewall alert for me this year.

According to my firewall logs the file causing the problem was minirosetta_2.14_windows_intelx86.exe.

Looking at the work unit, it crashed for the previous cruncher after 10 seconds.

---

When a task encounters a crash, it may directly attempt to pull the symbol table from the Rosetta website to aid in preparing the crash report. Normally all file downloads would be done by BOINC Manager, not minirosetta, but in some error scenarios minirosetta does attempt to do direct internet access. If it is not available, it returns a crash report without the detail possible with the symbol table.

So, I believe it was because the task crashed that it attempted to do a fairly unusual internet access which was trapped by your firewall. However, the resulting failure shouldn't have caused any further problem.

I'm trying to say that a failure caused the firewall trip, and that the fact that the firewall denied access was not the cause of a failure. I hope that makes sense.

---

Rosetta Moderator: Mod.Sense

I hope that makes sense.

That makes perfect sense. Thank you for the explanation.

---

It was suggested that I post this information here - it is sort of a duplication of the information I posted in a separate thread "Error opening file - anyone else?"

I have had six of these failures in the past few days across five systems. It is always the patchdoc file reported as having the error. It is not always the same exact filename. Three of my systems did not see this error at all. Several hundred work units were processed without error during the same time frame.

All of these systems are dedicated to BOINC and run 64 bit Linux on AMD Phenom II processors.

If the failure occurs, it is always seen during the first few seconds of processing.

Here is a list of the failures - I prepended my hostnames to each record to aid me in "getting back there" on case there were further questions about any specific incident.

Popeye: ERROR: Cannot open patchdock file: 1fAc_2j44.patchdock
Proteus: ERROR: Cannot open patchdock file: 1fAc_2odh.patchdock
Neptune: ERROR: Cannot open patchdock file: 1fAc_2vg9.patchdock
Poseidon: ERROR: Cannot open patchdock file: 1fAc_2vg9.patchdock
Poseidon: ERROR: Cannot open patchdock file: 1fAc_2boo.patchdock
Sinbad: ERROR: Cannot open patchdock file: 1fAc_2j44.patchdock

Chris, I happend to stumple on a host with such errors and confirmed that the same error occurred on the next machine the tasks were sent to. This would be great confirmation that there is no problem specific to your machines. Rather something must be up with how these tasks were created.

Here are two such links:
int2_centerfirst2b_1fAc_2j44_ProteinInterfaceDesign_23May2010_21231_274
int2_centerfirst2b_1fAc_2huj_ProteinInterfaceDesign_23May2010_21231_252

---

Rosetta Moderator: Mod.Sense

Your "wingman" (another machine that had been sent the same task and then due to his validate error another copy was generated and it was sent to you) had only 5 models as well. It is possible that batch of tasks was created with a 5 decoy limit rather then the 99.

---

Rosetta Moderator: Mod.Sense

I got one of these too. 8 hour runtime, 40 mins CPU time, 5 models only. Similar job-type.

rs_stg0_lrlx_t415__casp8_SAVE_ALL_OUT_20790_2334_0

---

Task 343301757 (td-only-2-BcR103A_9-15_20163_36_0) failed on Mac OS X

ERROR: rsd_type_list.size()
ERROR:: Exit from: src/core/fragment/Frame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

I'm seeing a lot of these lately in my results. Anything to worry about?


ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: ....srcprotocolsProteinInterfaceDesignmoversPlaceUtils.cc line: 281
called boinc_finish

---

I'm seeing a lot of these lately in my results. Anything to worry about?


ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: ....srcprotocolsProteinInterfaceDesignmoversPlaceUtils.cc line: 281
called boinc_finish

I'm getting them here too - so I am going to guess that it is not a problem with your system. Interesting that they are declared a "success" even though they end with an error.

Task 343850781

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


Task 343814609

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


I am running X64 Linux on systems based on AMD Phenom II CPUs

Thanks for your posts! It looks like a problem with the MDMX protocol that I put up earlier. I've now eliminated these jobs from the queue until I figure out what's wrong with these (but some jobs might still be rolling out on your machines). I'll let you know once I figure this out!

Thanks again, Sarel.

I'm seeing a lot of these lately in my results. Anything to worry about?


ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: ....srcprotocolsProteinInterfaceDesignmoversPlaceUtils.cc line: 281
called boinc_finish

I'm getting them here too - so I am going to guess that it is not a problem with your system. Interesting that they are declared a "success" even though they end with an error.

Task 343850781

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


Task 343814609

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


I am running X64 Linux on systems based on AMD Phenom II CPUs

---

I found the problem, it was an error in one of the input files that would sporadically show up (so it didn't come up on my local tests). I've now fixed it and tested it locally and will gradually resubmit the jobs to the queue (the new jobs will be dated 6Jun2010 rather than 4Jun2010). Please let me know if you have more problems with these new jobs.

Thanks for mentioning the specific task that gave you problems! It made tracking down the problem very easy.

Best, Sarel.

Thanks for your posts! It looks like a problem with the MDMX protocol that I put up earlier. I've now eliminated these jobs from the queue until I figure out what's wrong with these (but some jobs might still be rolling out on your machines). I'll let you know once I figure this out!

Thanks again, Sarel.

I'm seeing a lot of these lately in my results. Anything to worry about?


ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: ....srcprotocolsProteinInterfaceDesignmoversPlaceUtils.cc line: 281
called boinc_finish

I'm getting them here too - so I am going to guess that it is not a problem with your system. Interesting that they are declared a "success" even though they end with an error.

Task 343850781

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


Task 343814609

ERROR: ERROR: Residue not supported by Placement coordinate constraint machinery
ERROR:: Exit from: src/protocols/ProteinInterfaceDesign/movers/PlaceUtils.cc line: 281


I am running X64 Linux on systems based on AMD Phenom II CPUs

---