How to upload orphaned files (Advanced users only)

[Brian the Fist]

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

[IronBits]

Thanks Howard!

Would you take a look at Team Stir Fry's FAQ here, http://tsf.dbestern.net/faq.php
2nd paragraph begins the relevant information.
Do you see anything wrong with that method so they can update their FAQ if need be? I especially like the explanation of the DIR command line switches for DOS to aid in 'file pairing'.

[pointwood]

Yes, thanks Howard!

And thanks IronBits - I'll fix our FAQ quickly if there is something wrong with it.

[IronBits]

Hey PW, I don't believe there is anything wrong with your FAQ.
Worked for me many times, and I'm sure there were others.

[pointwood]

I'll just blame Creep - he was the one that wrote it

[Scoofy12]

Originally posted by Brian the Fist
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.

Howard, you are the man. This is one reason why this is such a great project. Like any, (especially a young one), it has its glitches but the dedication and willingness of you guys to listen to, interact with, and respond to your contributors really makes me feel like my cpu time is going to a great cause. keep up the good work

[Chris Wolfe]

This works in both the text client and the screensaver.

[Brian the Fist]

Re the Stir Fry FAQ,
it is fairly correct but be sure to emphasize that the numbers in file paris must correspond and be withing 10000 numbers of each other, or else they are not paired correctly. USUALLY the way you describe will work fine though.
Also, you should add the Currentstruc line to the end of the file (see my initial post in this thread) with a number slightly larger than any other number in the filenames in this file.

Aslo note on UNIX, you can do

ls -t *.bz2 > filelist.txt

to replace the DOS DIR command in your FAQ!
Thanks.

[Gunslinger]

Thanks for the instructions Howard.

Unfortunately I still had some problems. I got this error message after the first six pairs were uploaded:

========================[ Apr 10, 2002  8:15 PM ]========================
ERROR: [001.001] {foldtrajlite.c, line 598} Too many files to send, some have been lost

I sent the remainder four pairs at a time.

What is the actual limit on the number of file pairs? (For obvious reasons I didn't want to experiment )

[pointwood]

Thanks Howard.

I'll update our FAQ in a few days when I get home from my parents

[Brian the Fist]

I think I forgot to mention.. If you want to upload more than 6 pairs, make sure you are using the -df option in foldit.bat.
Otherwise everything exceeding the 6th pair will be deleted (oops). This is intended behaviour.

[pointwood]

Originally posted by Brian the Fist
I think I forgot to mention.. If you want to upload more than 6 pairs, make sure you are using the -df option in foldit.bat.
Otherwise everything exceeding the 6th pair will be deleted (oops). This is intended behaviour.

Could you explain why that is intended behaviour?

[[Ars]KD5MDK]

I don't suppose this applies to people who had files leftover after a protein change right?

[ColinT]

No, those are Dead.

[Paratima]

No need to sugar-coat it, Colin! Tell it like it is.

[Brian the Fist]

If you want to buffer more than 6 file pairs, you must use the -df option, that's why it is the intended behaviour. Its just the way it is. Kind of like asking 'why is the sky blue?', except not really I guess since that is because the upper atmosphere absorbs the other light frequencies befor ethey reach us at the angle the sun is normally at in the sky But I digress. Anyways, that's why I said this is for Advanced Users only, we do not endorse doing this unless you really know what you're doing. Or you really have a lot of unuploaded files. Like days worth. But then you can get someone who's Advanced to help you at least.

[pointwood]

Originally posted by Brian the Fist
If you want to buffer more than 6 file pairs, you must use the -df option, that's why it is the intended behaviour. Its just the way it is. Kind of like asking 'why is the sky blue?', except not really I guess since that is because the upper atmosphere absorbs the other light frequencies befor ethey reach us at the angle the sun is normally at in the sky But I digress. Anyways, that's why I said this is for Advanced Users only, we do not endorse doing this unless you really know what you're doing. Or you really have a lot of unuploaded files. Like days worth. But then you can get someone who's Advanced to help you at least.

Just because you have configured the client to not crunch more than 6 file pairs, doesn't neccesarily mean that you don't have more than 6 file pairs to upload. Why have that limitation? That is why I don't see it as a "why is the sky blue" question It's a behaviour that potentially can delete *a lot* of work if you're not careful!

You could be in a situation where you want to upload a lot of work from another PC or maybe several PC's and you end up uploading 6 pairs and getting the rest deleted

I'll bet that you sooner, rather than later will get an angry post here in the forum about exactly that.

[Michelle]

Thanks for this info, Howard.

I was almost doing it properly

[Brian the Fist]

You could be right. However the assumption is that if you do not use the -df option, you do not want to keep more than 6 pairs on your hard drive, to conserve hard drive space. I think it is pretty clear already in the README but Ill make it a bit clearer just in case. As for people who don't read the readme ( You know who you are), they may indeed have to find out the hard way but that will always be a problem no matter what the default behaviour may be.

I understand everyone has different preferences and different ideas, and we welcome any suggestions to improve the software. We have designed the default behaviour to be that which we believe will both suit the largest number of people while at the same time honoring the privacy of the user. In this case, the default is not -df for example, because we do not wish to litter your hard drive with Megs of data unless you give your explicit permission with the -df option. We take this sort of thing very seriously or we wouldn't have gone to the trouble of digitally encrypting update files, encrypting your e-mails and passwords in our user accounts, and so on.

Thus we will in all likelihood not change any default behaviours as they have all been carefully thought out beforehand and are the way they are for a good reason, unless you can make a very convincing argument that does not go against our original intentions.

Again, we certainly do not want to stifle your creative suggestions - if it were not for some of the great suggestions from users, the client would not have developed to be as flexible as it now is. But the software now seems to be very stable (on all 10 platforms!) and is working well for the majority of users. So changes that would benefit just a small portion of the population will probably be postponed since what helps some people may hinder others.

Sorry for the long rant but I just wanted to make clear that we are still open to suggestions but will hopefully leave the client "as is" for the next little while and see how things go as we are happy with its present state.

[IronBits]

[quote]But the software now seems to be very stable (on all 10 platforms!) [quote]

Quite an accomplishment to! Three cheers !!!
You should be *very* proud of what you have done in such a short time frame!