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Bug reports for Ralph 5.24

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Message boards : RALPH@home bug list : Bug reports for Ralph 5.24

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Rhiju
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Message 1842 - Posted 19 Jun 2006 3:28:38 UTC

    We\'ve added a couple features:

    (1) We can now use prior predictions for which parts of the chain are buried or exposed to guide the Rosetta search.

    (2) We can efficiently assemble predefined domains of the protein chain into a whole structure.

    If this round of ralph goes well, we\'ll probably update the application on Rosetta@home later this week!
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    Message 1845 - Posted 19 Jun 2006 14:11:01 UTC

      id love to run 5.24, but i am getting \"no work from project\".
      i thought there was supposed to be work available at any time now? :)
      server status page is all green, it only shows no WUs ready to send.

      Profile feet1st

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      Message 1846 - Posted 19 Jun 2006 18:49:42 UTC

        Still no work.
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        bt1228

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        Message 1847 - Posted 19 Jun 2006 23:39:14 UTC

          I just received this error:

          2006-Jun-19 7:34:43 pm|ralph@home|Requesting 366120 seconds of new work
          2006-Jun-19 7:34:48 pm|ralph@home|Scheduler request succeeded
          2006-Jun-19 7:34:48 pm|ralph@home|Message from server: No work sent
          2006-Jun-19 7:34:48 pm|ralph@home|Message from server: (reached daily quota of 1 results)

          Is there actually a quota of one (1) result per day ?

          I do have one 5.24 WU in my current task list.

          --- bt

          doc :)

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          Message 1848 - Posted 20 Jun 2006 1:03:44 UTC

            no clue how your quota got that low, i got mine by 18 right now, after a couple of errors.
            finally got some 5.24 work, all of them that got their turn so far errored out with incorrect function.
            all had names like t299_LOOPRELAX_hom00X_S_000XX_000XXXX_0_727_1_X and i was not the only one where those failed.
            the result page contains the following error:

            <stderr_txt>
            ERROR:: Unable to obtain sequence information.
            fasta file must be provided.
            ERROR:: Exit at: .\\initialize.cc line:236

            </stderr_txt>

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            Message 1849 - Posted 20 Jun 2006 3:25:54 UTC

              9 jobs with this error on Windows and 2 jobs on Linux

              process exited with code 1 (0x1)
              </message>
              <stderr_txt>
              Graphics are disabled due to configuration...
              ERROR:: Unable to obtain sequence information.
              fasta file must be provided.
              ERROR:: Exit at: initialize.cc line:236

              I am somewhat lazy by now to provide a link for each WU -;

              So, a link to 1 on Linux
              http://ralph.bakerlab.org/result.php?resultid=187655
              and a link to 1 on Windows
              http://ralph.bakerlab.org/result.php?resultid=187566

              Thanks


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              Deborah Goldsmith

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              Message 1850 - Posted 20 Jun 2006 6:07:02 UTC

                Mac OS X (Intel), failed immediately on running the application:
                2006-06-19 16:59:46 [ralph@home] Starting task t299_LOOPRELAX_hom004_S_00018_0004609_0_728_2_0 using rosetta_beta version 524
                2006-06-19 16:59:48 [ralph@home] Unrecoverable error for result t299_LOOPRELAX_hom004_S_00018_0004609_0_728_2_0 (process exited with
                code 1 (0x1))
                2006-06-19 16:59:48 [ralph@home] Unrecoverable error for result t299_LOOPRELAX_hom004_S_00018_0004609_0_728_2_0 (process exited with
                code 1 (0x1))
                2006-06-19 16:59:48 [---] Rescheduling CPU: application exited

                It did this 12 times in a row before exhausting the daily quota.

                5.24 is working fine on my PPC machines. 5.23 worked fine on my Intel machine. This failure appears to be Intel-specific and 5.24-specific.

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                [B^S] suguruhirahara

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                Message 1851 - Posted 20 Jun 2006 10:13:55 UTC

                  http://ralph.bakerlab.org/result.php?resultid=187639

                  <stderr_txt>
                  ERROR:: Unable to obtain sequence information.
                  fasta file must be provided.
                  ERROR:: Exit at: .\\initialize.cc line:236

                  </stderr_txt>

                  ____________

                  Profile feet1st

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                  Message 1852 - Posted 20 Jun 2006 14:16:09 UTC

                    6 failed in a row upon startup. Same Fasta file not found error.
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                    Message 1853 - Posted 20 Jun 2006 15:05:23 UTC

                      just a little update, after those failures i had with my first couple of 5.24s i have some successes now (they are out of another WU batch as far as i can tell though, 731 instead of 727 in my case, so it was probably just a bad batch of WUs)

                      Rhiju
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                      Message 1854 - Posted 20 Jun 2006 21:36:48 UTC - in response to Message 1853.

                        Thanks for posting. I think it was just all the simultaneous downloading produced some strain on our fileserver and some users got incomplete jobs. Once things settled down, we don\'t seem to be seeing many errors!

                        just a little update, after those failures i had with my first couple of 5.24s i have some successes now (they are out of another WU batch as far as i can tell though, 731 instead of 727 in my case, so it was probably just a bad batch of WUs)


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                        Rhiju
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                        Message 1855 - Posted 20 Jun 2006 21:41:12 UTC - in response to Message 1845.

                          We tried the \"continuous work for ralph\" for a week or so, but our turnaround time for testing new WUs was just too slow! It would take about 24 hours for computers to free up, accept new WUs, and give back initial results -- we want the tunaround time to be less than 12 hours. Hope that\'s a reasonable explanation!

                          My advice is to crunch for both rosetta@home and ralph, if you haven\'t already... the good news is that we\'re setting up the debugging stuff over on rosetta@home, so we\'ll be hopefully be getting a steady stream of callstacks from whatever errors are going on over there too!

                          id love to run 5.24, but i am getting \"no work from project\".
                          i thought there was supposed to be work available at any time now? :)
                          server status page is all green, it only shows no WUs ready to send.


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                          Message 1856 - Posted 20 Jun 2006 22:14:22 UTC - in response to Message 1855.

                            ...we want the tunaround time to be less than 12 hours.


                            This doesn\'t leave you much time to test running the WUs for 24hrs then. Nor much time to test running in environments where you aren\'t the only application.

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                            Message 1857 - Posted 20 Jun 2006 22:30:46 UTC

                              Looking back in my messages, I see that I did complete a download of a fasta file prior to the 6 WUs that failed on startup.

                              6/19/2006 6:45:30 PM|ralph@home|Started download of file nterm_nohelix3_hom001_t299_.fasta.gz
                              6/19/2006 6:45:31 PM|ralph@home|Finished download of file nterm_nohelix3_hom001_t299_.fasta.gz

                              I see no failed attempts to download any other fasta files when those WUs came down. It seems there may be more to the story then a busy server.
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                              Rhiju
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                              Message 1858 - Posted 20 Jun 2006 23:18:33 UTC - in response to Message 1857.

                                Hmm, thanks for checking on this. I\'ll look at those WUs more carefully...

                                Looking back in my messages, I see that I did complete a download of a fasta file prior to the 6 WUs that failed on startup.

                                6/19/2006 6:45:30 PM|ralph@home|Started download of file nterm_nohelix3_hom001_t299_.fasta.gz
                                6/19/2006 6:45:31 PM|ralph@home|Finished download of file nterm_nohelix3_hom001_t299_.fasta.gz

                                I see no failed attempts to download any other fasta files when those WUs came down. It seems there may be more to the story then a busy server.


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                                Rhiju
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                                Message 1859 - Posted 20 Jun 2006 23:26:34 UTC - in response to Message 1858.

                                  Last modified: 20 Jun 2006 23:27:15 UTC

                                  OK, I checked those jobs. Looks like those work units all failed for the same known reason (a problem in the submitter\'s submission script), and then were fixed and sent out again. The second round went well. Phew. It wasn\'t the app!

                                  By the way, its pretty great that we had so many postings -- its very useful to get this continuous feedback .

                                  Hmm, thanks for checking on this. I\'ll look at those WUs more carefully...

                                  Looking back in my messages, I see that I did complete a download of a fasta file prior to the 6 WUs that failed on startup.

                                  6/19/2006 6:45:30 PM|ralph@home|Started download of file nterm_nohelix3_hom001_t299_.fasta.gz
                                  6/19/2006 6:45:31 PM|ralph@home|Finished download of file nterm_nohelix3_hom001_t299_.fasta.gz

                                  I see no failed attempts to download any other fasta files when those WUs came down. It seems there may be more to the story then a busy server.



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                                  Message 1860 - Posted 21 Jun 2006 3:04:58 UTC - in response to Message 1855.

                                    Last modified: 21 Jun 2006 3:06:36 UTC

                                    We tried the \"continuous work for ralph\" for a week or so, but our turnaround time for testing new WUs was just too slow! It would take about 24 hours for computers to free up, accept new WUs, and give back initial results -- we want the tunaround time to be less than 12 hours. Hope that\'s a reasonable explanation!

                                    My advice is to crunch for both rosetta@home and ralph, if you haven\'t already... the good news is that we\'re setting up the debugging stuff over on rosetta@home, so we\'ll be hopefully be getting a steady stream of callstacks from whatever errors are going on over there too!

                                    id love to run 5.24, but i am getting \"no work from project\".
                                    i thought there was supposed to be work available at any time now? :)
                                    server status page is all green, it only shows no WUs ready to send.



                                    I make a new host, venue school , connect to network every second , running *only* ralph@home

                                    *This one should download only 1 job at a time, crunch and upload, report
                                    and then download the next -:) and on and on

                                    However my WUs are failing on them !

                                    May be a host setup problem ?
                                    -or- just bad WUs ?

                                    Exit status -1073741684 (0xffffffffc000008c)
                                    http://ralph.bakerlab.org/result.php?resultid=190094
                                    http://ralph.bakerlab.org/result.php?resultid=190240
                                    http://ralph.bakerlab.org/result.php?resultid=190262

                                    any help appreciated -> this host owns a virtual CPU
                                    and had crunched simap and einstein , with no problems -:)

                                    my host specs
                                    Average upload rate 0.53 KB/sec
                                    Average download rate 9.59 KB/sec
                                    Average turnaround time 0 days

                                    Also was able to meet TANPAKU deadline of 1 hour

                                    Thanks
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                                    Message 1861 - Posted 21 Jun 2006 14:38:27 UTC - in response to Message 1860.

                                      We tried the \"continuous work for ralph\" for a week or so, but our turnaround time for testing new WUs was just too slow! It would take about 24 hours for computers to free up, accept new WUs, and give back initial results -- we want the tunaround time to be less than 12 hours. Hope that\'s a reasonable explanation!

                                      My advice is to crunch for both rosetta@home and ralph, if you haven\'t already... the good news is that we\'re setting up the debugging stuff over on rosetta@home, so we\'ll be hopefully be getting a steady stream of callstacks from whatever errors are going on over there too!

                                      id love to run 5.24, but i am getting \"no work from project\".
                                      i thought there was supposed to be work available at any time now? :)
                                      server status page is all green, it only shows no WUs ready to send.



                                      I make a new host, venue school , connect to network every second , running *only* ralph@home

                                      *This one should download only 1 job at a time, crunch and upload, report
                                      and then download the next -:) and on and on

                                      However my WUs are failing on them !

                                      May be a host setup problem ?
                                      -or- just bad WUs ?

                                      Exit status -1073741684 (0xffffffffc000008c)
                                      http://ralph.bakerlab.org/result.php?resultid=190094
                                      http://ralph.bakerlab.org/result.php?resultid=190240
                                      http://ralph.bakerlab.org/result.php?resultid=190262

                                      any help appreciated -> this host owns a virtual CPU
                                      and had crunched simap and einstein , with no problems -:)

                                      my host specs
                                      Average upload rate 0.53 KB/sec
                                      Average download rate 9.59 KB/sec
                                      Average turnaround time 0 days

                                      Also was able to meet TANPAKU deadline of 1 hour

                                      Thanks


                                      Found the problem, and fixed it. was a corrupted NTFS virtual FileSystem

                                      Now the problem is another

                                      Outcome Client error
                                      Client state Downloading
                                      Exit status -186 (0xffffffffffffff46


                                      I looked at the download progress,
                                      and before all files of the WU has finished downloading,
                                      the job started to run, and imediatelly got this error.
                                      http://ralph.bakerlab.org/result.php?resultid=190486

                                      I am believing on a ralph server problem, or my ISP had some glitch with my Link
                                      Anyway the job (WU) should not start to run before all files downloaded

                                      Now,
                                      I\'ll wait there is work again ... Xlab (backup project)
                                      is downloading / crunching / uploading 100% OK ;)

                                      I select Xlab to \"backup project\" cause their WUs crunch in 9 minutes
                                      so, when there is work, immediattely the vpc switch to ralph.

                                      Thanks
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                                      [B^S] sTrey
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                                      Message 1862 - Posted 22 Jun 2006 3:05:43 UTC

                                        Last modified: 22 Jun 2006 3:07:22 UTC

                                        Errored out on t299__CASP7_ABRELAX_SAVE_ALL_OUT_TEST_ASSEMBLE_hom001__753_34_0 with -161
                                        <file_xfer_error>
                                        <file_name>t299__CASP7_ABRELAX_SAVE_ALL_OUT_TEST_ASSEMBLE_hom001__753_34_0_0
                                        </file_name>
                                        <error_code>-161</error_code>

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                                        Message 1863 - Posted 22 Jun 2006 13:52:16 UTC

                                          Last modified: 22 Jun 2006 13:52:32 UTC

                                          Error -WARNING! attempt to gzip file .\\xxt299.out failed: file does not exist.
                                          on this wu http://ralph.bakerlab.org/result.php?resultid=191298

                                          Anders n
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                                          dainenyu

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                                          Message 1864 - Posted 22 Jun 2006 17:45:54 UTC - in response to Message 1863.

                                            Error -WARNING! attempt to gzip file .\\xxt299.out failed: file does not exist.
                                            on this wu http://ralph.bakerlab.org/result.php?resultid=191298


                                            Same error on this result: http://ralph.bakerlab.org/result.php?resultid=192118. It also happened to the other user who crunched this WU: http://ralph.bakerlab.org/result.php?resultid=191496.
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                                            Message 1865 - Posted 22 Jun 2006 19:36:48 UTC

                                              Rosetta_beta 5.24 Linux

                                              WARNING! attempt to gzip file ./xxt299.out failed: file does not exist.

                                              http://ralph.bakerlab.org/result.php?resultid=192080

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                                              Message 1866 - Posted 22 Jun 2006 19:45:24 UTC

                                                Last modified: 22 Jun 2006 19:46:26 UTC

                                                Phantom WU
                                                http://ralph.bakerlab.org/result.php?resultid=189881

                                                I dont have this WU on this pc to crunch !

                                                Thanks
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                                                Message 1868 - Posted 23 Jun 2006 4:44:27 UTC - in response to Message 1861.

                                                  Last modified: 23 Jun 2006 4:55:04 UTC

                                                  We tried the \"continuous work for ralph\" for a week or so, but our turnaround time for testing new WUs was just too slow! It would take about 24 hours for computers to free up, accept new WUs, and give back initial results -- we want the tunaround time to be less than 12 hours. Hope that\'s a reasonable explanation!

                                                  My advice is to crunch for both rosetta@home and ralph, if you haven\'t already... the good news is that we\'re setting up the debugging stuff over on rosetta@home, so we\'ll be hopefully be getting a steady stream of callstacks from whatever errors are going on over there too!

                                                  id love to run 5.24, but i am getting \"no work from project\".
                                                  i thought there was supposed to be work available at any time now? :)
                                                  server status page is all green, it only shows no WUs ready to send.



                                                  I make a new host, venue school , connect to network every second , running *only* ralph@home

                                                  *This one should download only 1 job at a time, crunch and upload, report
                                                  and then download the next -:) and on and on

                                                  However my WUs are failing on them !

                                                  May be a host setup problem ?
                                                  -or- just bad WUs ?

                                                  Exit status -1073741684 (0xffffffffc000008c)
                                                  http://ralph.bakerlab.org/result.php?resultid=190094
                                                  http://ralph.bakerlab.org/result.php?resultid=190240
                                                  http://ralph.bakerlab.org/result.php?resultid=190262

                                                  any help appreciated -> this host owns a virtual CPU
                                                  and had crunched simap and einstein , with no problems -:)

                                                  my host specs
                                                  Average upload rate 0.53 KB/sec
                                                  Average download rate 9.59 KB/sec
                                                  Average turnaround time 0 days

                                                  Also was able to meet TANPAKU deadline of 1 hour

                                                  Thanks


                                                  Found the problem, and fixed it. was a corrupted NTFS virtual FileSystem

                                                  Now the problem is another

                                                  Outcome Client error
                                                  Client state Downloading
                                                  Exit status -186 (0xffffffffffffff46


                                                  I looked at the download progress,
                                                  and before all files of the WU has finished downloading,
                                                  the job started to run, and imediatelly got this error.
                                                  http://ralph.bakerlab.org/result.php?resultid=190486

                                                  I am believing on a ralph server problem, or my ISP had some glitch with my Link
                                                  Anyway the job (WU) should not start to run before all files downloaded

                                                  Now,
                                                  I\'ll wait there is work again ... Xlab (backup project)
                                                  is downloading / crunching / uploading 100% OK ;)

                                                  I select Xlab to \"backup project\" cause their WUs crunch in 9 minutes
                                                  so, when there is work, immediattely the vpc switch to ralph.

                                                  Thanks


                                                  Finally I got my host working properly. (in reallity I setup two hosts
                                                  to have a fast turnaroud -> One Linux and another Windows

                                                  These are my turnaroud times
                                                  1) Linux
                                                  Average turnaround time 0.07 days
                                                  *By now 14 Jobs sucessfull under this turnaroud.
                                                  ->thanks fast Internet Link 2gbit
                                                  2) Windows
                                                  Average turnaround time 0.2 days
                                                  *By now 5 sucessfull jobs under this turnaroud.
                                                  No thanks to my dialup speed 28800 bps

                                                  Everyone wanting to to get a fast turnaround too do the following.

                                                  1) Must have a permanent -or- quasi permanent Internet connection
                                                  eg: a Dialup conneted 24/hours by day.

                                                  2) using a unused venue. eg: school
                                                  setup the following:
                                                  Leave applications in memory while preempted? yes
                                                  Switch between applications every 17 minutes
                                                  Write to disk at most every 14 seconds
                                                  Connect to network about every 0.0000100 days

                                                  3) Assign that venue to a pc with > 500 mhz
                                                  and attach that pc to ralph@home

                                                  4) On ralph preferences
                                                  Target CPU run time 1 hour

                                                  *cause ralph@home does not ever has work to crunch
                                                  Attach a second project too, to that pc
                                                  This second project must have(fast WUs) that is: less than a half hour to crunch

                                                  *Suitable projects to use as a second project, (that I know, by now)
                                                  XtremLab,
                                                  Leiden Classic,
                                                  Hash Clash,
                                                  Prime Grid,
                                                  Tanpaku.

                                                  And enjoy a ralph@home turnaround time of less than 12 hours -:)

                                                  ps: dont forget to join my team (on ralph@home)
                                                  http://ralph.bakerlab.org/team_join_form.php?id=52

                                                  Thanks

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                                                  Message 1869 - Posted 23 Jun 2006 19:24:17 UTC

                                                    Rosetta_beta_5.24 Linux

                                                    WARNING! attempt to gzip file ./xxt299.out failed: file does not exist

                                                    http://ralph.bakerlab.org/result.php?resultid=192840

                                                    Bjarke

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                                                    Message 1871 - Posted 25 Jun 2006 9:56:29 UTC

                                                      Last modified: 25 Jun 2006 10:01:49 UTC

                                                      24-06-2006 13:20:42||Starting BOINC client version 5.4.9 for windows_intelx86
                                                      24-06-2006 13:20:42||libcurl/7.15.3 OpenSSL/0.9.8a zlib/1.2.3
                                                      24-06-2006 13:20:42||Data directory: C:\\Program Files\\BOINC
                                                      24-06-2006 13:20:42||Processor: 1 GenuineIntel Intel(R) Pentium(R) M processor 1.73GHz
                                                      24-06-2006 13:20:42||Memory: 502.42 MB physical, 1.20 GB virtual
                                                      24-06-2006 13:20:42||Disk: 55.88 GB total, 16.94 GB free
                                                      24-06-2006 13:20:42|rosetta@home|URL: http://boinc.bakerlab.org/rosetta/; Computer ID: 165598; location: ; project prefs: default
                                                      24-06-2006 13:20:42|ralph@home|URL: http://ralph.bakerlab.org/; Computer ID: 1597; location: ; project prefs: default
                                                      24-06-2006 13:20:42||General prefs: from rosetta@home (last modified 2006-03-30 08:46:27)
                                                      24-06-2006 13:20:42||General prefs: using your defaults
                                                      24-06-2006 13:20:42||Local control only allowed
                                                      24-06-2006 13:20:42||Listening on port 31416

                                                      [...]

                                                      25-06-2006 11:15:37|ralph@home|Computation for task t299__CASP7_ABRELAX_SAVE_ALL_OUT_hom001__NT5_CT1_762_10_2 finished
                                                      25-06-2006 11:15:38|ralph@home|Unrecoverable error for result t299__CASP7_ABRELAX_SAVE_ALL_OUT_hom001__NT5_CT1_762_10_2 (<file_xfer_error> <file_name>t299__CASP7_ABRELAX_SAVE_ALL_OUT_hom001__NT5_CT1_762_10_2_0</file_name> <error_code>-161</error_code></file_xfer_error>)

                                                      running 71,43% rosetta and 28,57% RALPH, not sure if it has any effect

                                                      Result:http://ralph.bakerlab.org/result.php?resultid=195882
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                                                      RAC: 0
                                                      Message 1873 - Posted 25 Jun 2006 22:31:26 UTC

                                                        25.06.2006 23:24:26|ralph@home|Unrecoverable error for result t330__CASP7_ABRELAX_SAVE_ALL_OUT_ncap_hom002__776_50_0 (Unzulässige Funktion. (0x1) - exit code 1 (0x1))


                                                        Result
                                                        ____________

                                                        Bones

                                                        Joined: Feb 16 06
                                                        Posts: 2
                                                        ID: 107
                                                        Credit: 3,850
                                                        RAC: 0
                                                        Message 1874 - Posted 26 Jun 2006 11:19:39 UTC

                                                          Last modified: 26 Jun 2006 11:20:23 UTC

                                                          Resultid 195909
                                                          Resultid 195910

                                                          WARNING! attempt to gzip file .\\xxt299.out failed: file does not exist.
                                                          26/06/2006 7:43:58 PM|ralph@home|Unrecoverable error for result t299__CASP7_ABRELAX_SAVE_ALL_OUT_hom001__NT5_CT4_762_10_1 (<file_xfer_error> <file_name>t299__CASP7_ABRELAX_SAVE_ALL_OUT_hom001__NT5_CT4_762_10_1_0</file_name> <error_code>-161</error_code> <error_message></error_message></file_xfer_error>)


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