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I just downloaded a Gromacs p2106. Below is a copy of my log. I keep getting the "timered checkpoint triggerd" entry. It doesn't seem to be processing beyond step 48790. Would you know anything about this. I've done17 other units, and none has ever behaved like this one. Does the checkpoint message mean that there's no folding going on?

[00:19:48]

[00:19:48] Folding@Home Gromacs Core
[00:19:48] Version 1.86 (August 28, 2005)
[00:19:48]
[00:19:48] Preparing to commence simulation
[00:19:48] - Assembly optimizations manually forced on.
[00:19:48] - Not checking prior termination.
[00:19:48] - Expanded 79074 -> 419621 (decompressed 530.6 percent)
[00:19:48]
[00:19:48] Project: 2106 (Run 79, Clone 12, Gen 3)
[00:19:48]
[00:19:48] Assembly optimizations on if available.
[00:19:48] Entering M.D.
[00:20:08] (Starting from checkpoint)
[00:20:08] Protein: p2106_lambda_5way_melt_4_10011
[00:20:08]
[00:20:08] Writing local files
[00:20:08] Using table 3
[00:20:08] Completed 48790 out of 10000000 steps (0)
[00:20:09] Testing CPU type...
[00:20:09] Done testing.
[00:20:09] Extra AltiVec boost OK.
[00:26:09] Timered checkpoint triggered.
[00:32:09] Timered checkpoint triggered.
[00:38:09] Timered checkpoint triggered.
[00:44:08] Timered checkpoint triggered.
[00:50:08] Timered checkpoint triggered.

Clara, checkpointing doesn't necessarily mean no folding is occuring. Do you have it set for 6 minutes?

It's entirely possible that you've got such a bear, and those 5waymelts are that it's taking a long time and checkpointing before hitting the next reporting step.

Every core reports slightly differently but a recent log for one of those looks like this to me.

Folding@Home Gromacs Core
[15:33:19] Version 1.86 (August 28, 2005)
[15:33:19]
[15:33:19] Preparing to commence simulation
[15:33:19] - Looking at optimizations...
[15:33:19] - Created dyn
[15:33:19] - Files status OK
[15:33:19] - Expanded 76362 -> 419621 (decompressed 549.5 percent)
[15:33:19] - Starting from initial work packet
[15:33:19]
[15:33:19] Project: 2106 (Run 93, Clone 23, Gen 0)
[15:33:19]
[15:33:19] Assembly optimizations on if available.
[15:33:19] Entering M.D.
[15:33:25] Protein: p2106_lambda_5way_melt_4_10011
[15:33:25]
[15:33:25] Writing local files
[15:33:25] Using table 3
[15:33:25] Extra SSE boost OK.
[15:33:25] Writing local files
[15:33:25] Completed 0 out of 10000000 steps (0)
[15:54:47] Writing local files
[15:54:47] Completed 100000 out of 10000000 steps (1)
[16:16:13] Writing local files
[16:16:13] Completed 200000 out of 10000000 steps (2)

Notice, it's 22 minutes for 100,000 steps. This is on an AMD 64 4000+ cpu with 2gb ram. In other words, it's a pretty hefty burden and if you're running much less CPU, you could take 2-3 times to finish the same unit and with checkpointing at 6 minutes, it's just reporting in.

The timered checkpoint is a backup save frequency that you can set in the configuration menu. It probably doesn't seem to have progressed in the log file because it is such a large job that it won't report the progress until probably 100,000 steps are completed. It's only been about 30 min in that log, I would give it another hour and check on it. My computer is running the corresponding p2107 job with 20,000,000 steps reporting every 200,000 steps in the log file about every 20 minutes. Your computer is saving the progress (see your beginning step value in the log file showing you'd restarted the program and it picked up folding that job at ~49,000) but just not displaying it to you.

These are whopping huge WU, mine won't wrap up for at least 3 more days.

I also noticed something mine reports that your's does not.

[15:33:25] Extra SSE boost OK.

What CPU are you running? If it doesn't have SSE or it's disabled for some reason(can occur if a protein errors out), completion times are going to be much longer than my 22 minutes.