The problem started 1 day ago. I am running the latest Boinc 64-bit for Linux. All other projects upload and download fine, only Rosetta is still pending the upload.

Sun 31 May 2009 03:12:57 PM EDT||Starting BOINC client version 6.4.5 for x86_64-pc-linux-gnu
Sun 31 May 2009 03:12:57 PM EDT||log flags: task, file_xfer, sched_ops
Sun 31 May 2009 03:12:57 PM EDT||Libraries: libcurl/7.18.0 OpenSSL/0.9.8g zlib/1.2.3 c-ares/1.5.1
Sun 31 May 2009 03:12:57 PM EDT||Data directory: /home/angel/BOINC
Sun 31 May 2009 03:12:57 PM EDT|SETI@home|Found app_info.xml; using anonymous platform
Sun 31 May 2009 03:12:57 PM EDT||Processor: 2 GenuineIntel Intel(R) Core(TM)2 Duo CPU E6750 @ 2.66GHz [Family 6 Model 15 Stepping 11]
Sun 31 May 2009 03:12:57 PM EDT||Processor features: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall lm constant_tsc arch_perfmon pebs bts rep_good nopl pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr lahf
Sun 31 May 2009 03:12:57 PM EDT||OS: Linux: 2.6.27.24-170.2.68.fc10.x86_64
Sun 31 May 2009 03:12:57 PM EDT||Memory: 3.87 GB physical, 1.95 GB virtual
Sun 31 May 2009 03:12:57 PM EDT||Disk: 212.89 GB total, 200.61 GB free
Sun 31 May 2009 03:12:57 PM EDT||Local time is UTC -4 hours
Sun 31 May 2009 03:12:57 PM EDT||Not using a proxy
Sun 31 May 2009 03:12:57 PM EDT||No CUDA devices found
Sun 31 May 2009 03:12:57 PM EDT||No coprocessors
Sun 31 May 2009 03:12:57 PM EDT|Einstein@Home|URL: http://einstein.phys.uwm.edu/; Computer ID: 1960450; location: home; project prefs: default
Sun 31 May 2009 03:12:57 PM EDT|SETI@home|URL: http://setiathome.berkeley.edu/; Computer ID: 4959391; location: home; project prefs: default
Sun 31 May 2009 03:12:57 PM EDT|World Community Grid|URL: http://www.worldcommunitygrid.org/; Computer ID: 951249; location: (none); project prefs: default
Sun 31 May 2009 03:12:57 PM EDT|rosetta@home|URL: https://boinc.bakerlab.org/rosetta/; Computer ID: 1079399; location: home; project prefs: default
Sun 31 May 2009 03:12:57 PM EDT||General prefs: from rosetta@home (last modified 30-Apr-2009 19:37:21)
Sun 31 May 2009 03:12:57 PM EDT||Computer location: home
Sun 31 May 2009 03:12:57 PM EDT||General prefs: no separate prefs for home; using your defaults
Sun 31 May 2009 03:12:57 PM EDT||Preferences limit memory usage when active to 3845.61MB
Sun 31 May 2009 03:12:57 PM EDT||Preferences limit memory usage when idle to 3964.54MB
Sun 31 May 2009 03:12:57 PM EDT||Preferences limit disk usage to 100.00GB
Sun 31 May 2009 03:12:58 PM EDT|Einstein@Home|Restarting task p2030_53694_73276_0030_G44.35-01.37.N_0.dm_446_0 using einsteinbinary_ABP1 version 104
Sun 31 May 2009 03:12:58 PM EDT|rosetta@home|Restarting task lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0 using minirosetta version 171
Sun 31 May 2009 05:13:35 PM EDT|rosetta@home|Computation for task lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0 finished
Sun 31 May 2009 05:13:35 PM EDT|SETI@home|Restarting task ap_28au08af_B2_P0_00030_20090529_03458.wu_0 using astropulse_v5 version 503
Sun 31 May 2009 05:13:37 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:16:38 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:16:38 PM EDT|rosetta@home|Backing off 1 min 0 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:17:38 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:20:39 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:20:39 PM EDT|rosetta@home|Backing off 1 min 0 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:21:39 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:24:41 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:24:41 PM EDT|rosetta@home|Backing off 1 min 0 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:25:41 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:28:41 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:28:41 PM EDT|rosetta@home|Backing off 1 min 0 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:29:41 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:32:43 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:32:43 PM EDT|rosetta@home|Backing off 1 min 34 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:34:18 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:37:18 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:37:18 PM EDT|rosetta@home|Backing off 4 min 0 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:41:20 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:43:02 PM EDT|World Community Grid|Restarting task ml572_00090_18 using hpf2 version 603
Sun 31 May 2009 05:44:20 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:44:20 PM EDT|rosetta@home|Backing off 9 min 1 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:53:23 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 05:56:25 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 05:56:25 PM EDT|rosetta@home|Backing off 4 min 53 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 06:01:19 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 06:04:20 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 06:04:20 PM EDT|rosetta@home|Backing off 51 min 45 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 06:17:47 PM EDT|rosetta@home|Started upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0
Sun 31 May 2009 06:20:47 PM EDT|rosetta@home|Temporarily failed upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0: HTTP error
Sun 31 May 2009 06:20:47 PM EDT|rosetta@home|Backing off 2 hr 40 min 23 sec on upload of lb_alnmatrix_threading_alncap__hb_t288__IGNORE_THE_REST_12566_738_0_0

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I have been able to upload all of my WU's this week without any issues. There seems to be no problems on the Rosetta side, all of the servers are running correctly (https://boinc.bakerlab.org/rosetta/rah_status.php).
Have you tried restarting the machine or BOINC? Sometimes it just gets a bit "confused"!! Also make sure that you do not have any personal firewalls which my be blocking the Rosetta@Home application.

I have found the problem. I am running the latest Smoothwall firewall and i checked the logs of my Intrusion Protection System a.k.a[Snort] and found where the Rosetta servers were trying to ping me too much and Guardian blocked the Rosetta IP.

SmoothWall guardian log
Date: 1 June

00:38:27 '1' 222.82.249.235->6%.229.*.* [1:2050:14] SQL version overflow attempt - Blocked till 3-Jun-2009 00:38:27
00:38:27 * '2' 222.82.249.235->6%.229.%.% [1:2003:12] SQL Worm propagation attempt - Updated till 3-Jun-2009 00:38:27
03:47:54 '1' 218.4.149.124->6%.229.*.* [1:2050:14] SQL version overflow attempt - Blocked till 3-Jun-2009 03:47:54
03:47:54 * '2' 218.4.149.124->6%.229.*.* [1:2003:12] SQL Worm propagation attempt - Updated till 3-Jun-2009 03:47:54
08:37:07 ? Alert filename changed. Reopening /var/log/snort/alert
09:48:40 Received notice from GUI : unblock 218.4.149.124 : OK
09:48:40 * Rebuilding manual ipblock IPs hash and CIDR netblocks array...
09:51:56 '1' 218.23.37.51->6%.229.*.* [1:2050:14] SQL version overflow attempt - Blocked till 3-Jun-2009 09:51:56
09:51:56 * '2' 218.23.37.51->6%.229.*.* [1:2003:12] SQL Worm propagation attempt - Updated till 3-Jun-2009 09:51:56

ROSETTA IP>>>>>>>>>140.142.20.111
09:53:56 '3' 140.142.20.111->6%.229.*.* [1:486:5] ICMP Destination Unreachable Communication with Destination Host is Administratively Prohibited - Blocked till 3-Jun-2009 09:53:56
09:53:56 * '3' 140.142.20.111->6%.229.*.* [1:486:5] ICMP Destination Unreachable Communication with Destination Host is Administratively Prohibited - Updated till 3-Jun-2009 09:53:56
09:55:05 Received notice from GUI : unblock 140.142.20.111 : OK
09:55:05 * Rebuilding manual ipblock IPs hash and CIDR netblocks array...

I unblocked it for now but maybe a system admin would like to comment on the necessity of the ICMP ping. Why ping me when I'm already connected to you downloading/uploading work?

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My guess is the pings are caused by the schedular as your BOINC constantly updates itself by contacting the Rosetta servers.

Rosetta servers never initiate contact to your machine. It is always your machine that initiates contact to the project. I mention this for future readers because the direction of the connection is often needed to setup firewalls.

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Rosetta Moderator: Mod.Sense

Edit -- Deleted

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