[Wien] scp error

[Laurence Marks]

I meant "may not be too hard" to setup a script.

Too early in the morning, not enough coffee.

On Tue, Jun 4, 2013 at 7:42 AM, Laurence Marks <L-marks at northwestern.edu> wrote:
> Let me add a couple of clarifications to what Peter suggested, since I
> often get caught by the ".process" and ".process2" files. I just did a
> quick search of the UG and they do not appear to be described
> (suggestion to Peter to add). Their format is somewhat self
> explanatory (although they do not seem to be constructed to be very
> human readable, i.e. no comments on the right.)
>
> The shell scripts create these files during a -p run so, for instance,
> lapw2 can run in parallel on the same nodes that lapw1 used and
> therefore SCRATCH and other files which might only be in temporary
> storage are consistent. When you run under PBS or several other
> similar job control codes which nodes you use are dynamically
> allocated and are then stored within these files. If you now run a
> second job or interactive task to do some analysis you are likely to
> have a different set of nodes allocated to you which can then create
> problems.
>
> If you are running interactively you can adjust these files for the
> nodes that you have. Alternatively you can do a single -p pass
> although unfortunately -it might switch to non-iterative because the
> setup uses the .process file to cp the old vector file.
>
> I suspect that it may be too hard to construct a shell script (or csh)
> to set these up properly for a given .machines file by extracting the
> relevant section from lapw1para, perhaps a good mini project for
> someone.
>
> On Tue, Jun 4, 2013 at 7:04 AM, Peter Blaha
> <pblaha at theochem.tuwien.ac.at> wrote:
>> -it does not have an effect for lapw2 since there is no diagonalization.
>>
>> The problem is most likely that you need a proper .processes file to run
>>      x lapw2 -p. Most PBS-scripts create only   .machines and run_lapw
>> will then generate later on .processes.
>>
>> My suggestion:  First check if you have the vector files in "case":
>>
>> cd /home/my_username/wien2k/case
>> ls -alsrt *vector*
>>
>> If they look ok (size and date !!!)
>>
>> use   join_vectorfiles
>>
>> to combine them to a single "non-parallel" vector and then
>> submit   x lapw2 -qtl   (without -p)
>>
>> Note: in "QTL-mode", lapw2 always runs only on a single core and the -p
>> option is only used to let the code know about the parallel vector files.
>>
>>
>> On 06/04/2013 12:06 PM, Yundi Quan wrote:
>>> Thank Stefaan and Michael for your prompt replies.
>>>
>>> My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
>>> that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
>>> option -it tells WIEN2k to use iterative diagonalization, which should
>>> not be a problem. In uplapw2_1.def, it says that
>>> 10,'./case.vectorup_1', 'unknown','unformatted',9000
>>>
>>> I think this line tells lapw2 where to find the vector. But again, ./
>>> seems to mean my home directory rather than my working directory.
>>>
>>> I tried making a new scratch directory and set the $SCRATCH to that
>>> directory as suggested by Michael. I hope it works.
>>>
>>>
>>>
>>> Yundi
>>>
>>>
>>>
>>> On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan <yquan at ucdavis.edu> wrote:
>>>>
>>>>
>>>> ---------- Forwarded message ----------
>>>> From: Yundi Quan <quanyundi at gmail.com>
>>>> Date: Tue, Jun 4, 2013 at 2:19 AM
>>>> Subject: [Wien] scp error
>>>> To: A Mailing list for WIEN2k users <wien at zeus.theochem.tuwien.ac.at>
>>>>
>>>>
>>>> Hi,
>>>> I'm working on a cluster 8 quadcore nodes. Nodes are called n001,
>>>> n002, n003, n004... I use torque PBS queue system. When I submit a job
>>>> using a bash file, the default directory is always my home directory.
>>>> Therefore, at the beginning of my bash file, I always add a line 'cd
>>>>  '. This works for scf calculations.
>>>> However, when I use x lapw2 -qtl -band -p to calculate the band
>>>> structure or x lapw2 -qtl -p to calculate the DOS, I always encounter
>>>> the following error message:
>>>> scp: .//case.vector_1 not found
>>>> scp: .//case.vector_2 not found
>>>> ...
>>>>
>>>> It seems scp is looking for case.vector_1 in my home directory rather
>>>> than my working directory, even though I've added the line 'cd
>>>> /home/my_username/case' in my bash file. This problem only occurs with
>>>> using x lapw2 -qtl -p. I used to do scf calculation in serial and then
>>>> use x lapw2 -qtl. But I'm wondering whether there is a workaround.
>>>>
>>>>
>>>> Thanks.
>>>> _______________________________________________
>>>> Wien mailing list
>>>> Wien at zeus.theochem.tuwien.ac.at
>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>> SEARCH the MAILING-LIST at:
>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>>
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>
>>
>> --
>>
>>                                        P.Blaha
>> --------------------------------------------------------------------------
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
>> Email: blaha at theochem.tuwien.ac.at    WWW:
>> http://info.tuwien.ac.at/theochem/
>> --------------------------------------------------------------------------
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:  http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
>
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu 1-847-491-3996
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi



-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
"Research is to see what everybody else has seen, and to think what
nobody else has thought"
Albert Szent-Gyorgi