[Wien] scp error
Laurence Marks
L-marks at northwestern.edu
Tue Jun 4 16:18:25 CEST 2013
To err is human, to make slly name/spelling errors takes a Prof.
Yes, I should have written .processes etc, sorry.
On Tue, Jun 4, 2013 at 9:08 AM, Peter Blaha
<pblaha at theochem.tuwien.ac.at> wrote:
> I guess I also have to add some clarifications, because there is no
> .process or .process2 file, ....
>
>
> For parallel calculations the main file of interest is
>
> .machines
>
> And this file is used by lapw0para and lapw1para as input.
>
> However, lapw1para produces
>
> .processes
>
> (because you may have more parallel jobs then specified in .machines
> (because of "non-integer k-point/core ratio) and in particular because
> we allow explicitly to modify .machines during run_lapw (changing the
> parallelization by hand for the next iterations in case a machine is
> overloaded on a cluster).
>
> The following parallel scripts (lapwso, lapw2) therefore read from
> .processes (and not from .machines). (Also vec2old and vec2pratt need
> .processes and this may cause eventually problems, although if you
> change the number of cores ot use a non-local $SCRATCH, it cannot do -it
> at the very beginning anyway).
>
> This is (at least to some extend) documented in the UG (search eg. for
> processes).
>
> These are usually the only 2 files of interest for a user.
> There are no .process or .process2 files; and other ".machineXX or
> .processesXX files are internal only.
>
> I'm sometimes using PBS-scripts which do generate .processes, but the
> easiest thing would be to add a flag to lapw1para, so that it does not
> execute lapw1, but just generates the .processes file.
>
>
>
> On 06/04/2013 02:42 PM, Laurence Marks 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
>>>>>
>>>> _______________________________________________
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>>>
>>> --
>>>
>>> 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
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>>
>>
>>
>
> --
>
> 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/
> --------------------------------------------------------------------------
> _______________________________________________
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--
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
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