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mikkyo · May 30, 2002, 03:15 PM

So here is what I am using for launching distribfold..

My foldit script looks like this
nohup ./foldtrajlite -f protein -n native -p -20 -g 0 -qt &

The p sets the priority to -20 and the g sets the progress logging to off (less disk access).

Anyone else have anything to add to speed things up?

Oh, I looked but could not find an old thread that mentioned how to upload orphaned structures. I swear I read something somewhere about how to get specific .bz2 files uploaded after a crash.

rkadowns · May 30, 2002, 03:46 PM

<blockquote>quote:<hr />Originally posted by mikkyo:
So here is what I am using for launching distribfold..

My foldit script looks like this
nohup ./foldtrajlite -f protein -n native -p -20 -g 0 -qt &

The p sets the priority to -20 and the g sets the progress logging to off (less disk access).

Anyone else have anything to add to speed things up?

Oh, I looked but could not find an old thread that mentioned how to upload orphaned structures. I swear I read something somewhere about how to get specific .bz2 files uploaded after a crash.<hr /></blockquote>I use the -u t option to do this however it has not uploaded the files under circumstances which I have not been able to determine. In other words, the process has crashed and the -u t option has worked, AND, the process has crashed and the -u t option has NOT worked.

Go figure. <img border="0" alt="[Skeptical]" title="" src="graemlins/bugeye.gif" />

RIP

reader50 · May 30, 2002, 04:52 PM

<blockquote>quote:<hr />Originally posted by mikkyo:
...
Oh, I looked but could not find an old thread that mentioned how to upload orphaned structures. I swear I read something somewhere about how to get specific .bz2 files uploaded after a crash.<hr /></blockquote>It was a thread on the project forum, now buried some pages back.

<a href="http://bane.free-dc.org/forum/showthread.php3?threadid=583" target="_blank">http://bane.free-dc.org/forum/showthread.php3?threadid=583</a>

To mirror the most relevant info here...

<blockquote>quote:<hr />Originally posted by Brian the Fist:
How to upload orphaned files {Advanced users only}

We do not recommend the use of this procedure and would prefer you just ignore/delete any *.log.bz2 or *.val.bz2 files left on your machine from failed uploads, buggy client versions, etc.

But there are those of you who are going to try it whether I tell you to or not so I may as well tell you how to do it properly. Here is what to do.

First make sure the software is NOT running.
If it doesn't already exist, create a plain text file called 'filelist.txt'.
If it's already there, edit it.

Get a list of all your *.val.bz2 and *.log.bz2 files.
These come in pairs. If you just have one or the other, they cannot be uploaded and should be removed.
The fold*.log.bz2 contains a number in its name. Find the *.val.bz2 file with a number just slightly bigger than this {usually within 5000 or 10000} and definitely smaller than the number in any other log.bz2 file. This is a file pair.

An example would be:
fold_xxxxxxxx_589180_protein.log.bz2
xxxxxxxx_protein_0593960.val.bz2

where xxxxxxxx is your handle.
The important thing is 593960>589180 and 593960-589180<10000 {get out your calculators}

You must pair up all your orphaned files and anything left is cyber-trash and must be deleted or ignored. Only file pairs will be uploaded successfully.
Now simply add the names of the file pairs to filelist.txt, one per line. the ORDER is important - first the fold*log.bz2, then the paired *.val.bz2
Continue to do this for all the pairs. It does not matter which pair you add first, second, etc., only the ordering within the pair is critical. Make sure the file names are all correct.

Lastly, if you just created filelist.txt, add a final line which says:

CurrentStruc #####

Where #### is some number less than 10 million {it is arbitrary}
If you are editing an existing filelist.txt, this line shoudl already be there - make sure it is the last line of the file.

Now save filelist.txt and exit, then restart the program. If you did it right, your files will be uploaded and removed from your machine!

Remember, this is not recommended for the faint of heart

__________________
Howard Feldman

<hr /></blockquote>

[ 05-30-2002, 05:07 PM: Message edited by: reader50 ]

mikkyo · May 30, 2002, 07:13 PM

<blockquote>quote:<hr />Originally posted by reader50:
Get a list of all your *.val.bz2 and *.log.bz2 files.
These come in pairs. If you just have one or the other, they cannot be uploaded and should be removed.
<hr /></blockquote>Funny I have no log.bz2 files on any of my machines..
I guess all the proteins are orphaned then. Strange.
The current protein I received today doesn't have a log.bz2 file either..
hmmm

Shaktai · May 30, 2002, 08:22 PM

<blockquote>quote:<hr />Originally posted by mikkyo:
 <blockquote>quote:<hr />Originally posted by reader50:
Get a list of all your *.val.bz2 and *.log.bz2 files.
These come in pairs. If you just have one or the other, they cannot be uploaded and should be removed.
<hr /></blockquote>Funny I have no log.bz2 files on any of my machines..
I guess all the proteins are orphaned then. Strange.
The current protein I received today doesn't have a log.bz2 file either..
hmmm<hr /></blockquote>The work unit in progress won't have it until it is completed. At least that is the way it has worked on my Macs.