[Wien] Changes in case_xx.def files
Laurence Marks
L-marks at northwestern.edu
Thu Jul 29 13:14:45 CEST 2010
2010/7/28 Marcos Veríssimo Alves <marcos.verissimo.alves at gmail.com>:
> Hi Laurence,
> I will try all you have said. I didn't know about the -assu buff option - I
> suppose it is valid for ifort, right?
Yes, it is a standard ifort option. From the man page:
"Some compiler options have the form -name keyword. Both -name and
keyword can be abbreviated. It is recommended that you use the
first 4 characters of each. For example, -assume buffered_io can
be specified as -assu buff"
assume buffered_io Tells the compiler to accumu-
late records in a buffer. This
sets the default for opening
sequential output files to
BUFFERED='YES', which also
occurs if the FORT_BUFFERED
run-time environment variable
is specified. When this option
is specified, the internal
buffer is filled, possibly by
many record output statements
(WRITE), before it is written
to disk by the Fortran run-time
system. If a file is opened for
direct access, I/O buffering is
ignored. Using buffered writes
usually makes disk I/O more
efficient by writing larger
blocks of data to the disk less
often. However, if you request
buffered writes, records not
yet written to disk may be lost
in the event of a system fail-
ure. The OPEN statement
BUFFERED specifier applies to a
specific logical unit. In con-
trast, the assume
[no]buffered_io option and the
FORT_BUFFERED environment vari-
able apply to all Fortran
units.
> My scratch is already set. In fact, it was one of the variables I had the
> care to set, because I saw the size of the vector files (scary...)
> Finally, no problem with slowing down things a little. I'd rather have
> things slowed down a few seconds than have two hours lost (that is roughly
> the time it takes for running lapw1 -up/dn for my system) plus the hours
> when nothing happen until I realize the job has died... And I stil have to
> include U and spin-orbit after that!
> Thanks a lot,
> Marcos
>
> On Wed, Jul 28, 2010 at 9:00 PM, Laurence Marks <L-marks at northwestern.edu>
> wrote:
>>
>> This could be quite a lot of work. Some simpler suggestions:
>>
>> 1) In param.inc in SRC_lapw[0-2] change to
>> PARAMETER (restrict_output= 1)
>> This will reduce the size of the log files
>>
>> 2) Use -assu buff in your compilation options -- this writes data in
>> big chunks not line-by-line and is much
>> friendlier on file servers.
>>
>> 3) Set the environmental variable SCRATCH (export it from bash should
>> work) so large data files such
>> as the case.vector_X are local.
>>
>> 4) In $WIENROOT/parallel_options add (or edit)
>> set sleepy = XX # additional sleep before checking
>> set delay = YY
>>
>> where XX, YY are adjusted to try and reduce AFS problems ( 0.5 ? --
>> this will slow things down but...)
>>
>>
>> 2010/7/28 Marcos Veríssimo Alves <marcos.verissimo.alves at gmail.com>:
>> > Hi all,
>> > I have managed to run Wien2k in our cluster, with k-point
>> > parallelization.
>> > However, it looks like our NFS system (which is actually an AFS one) is
>> > still a bit unstable, since the cluster has been upgraded and
>> > re-assembled
>> > very recently. Problem is, the sysadmins have gone on vacations, so I'll
>> > have to find a way of getting around this the best I can until the
>> > beginning
>> > of next month.
>> > My current problem is that looks like some nodes of our cluster have
>> > been
>> > losing connection with the AFS server intermittently, and from what I
>> > see
>> > (please correct me if I'm wrong) all the writing is done over the
>> > network to
>> > the home directory. So, during the writing of the energy_up files, if
>> > the
>> > connection is lost then lapw2 will crash. Indeed, one of the instances
>> > of
>> > lapw1 resulted in an energyup file, in the end, with 0 size. This in
>> > turn
>> > made lapw2 crash, and this has happened overnight.
>> > My question is, I would like to make a small (I guess) change in the
>> > scripts, wherever needed. Instead of writing some files (only the ones
>> > that
>> > are critical for the execution of the next code) to the home, which
>> > would be
>> > done over AFS, they would be done in the scratch directory, which is
>> > local.
>> > Then, at the end of the execution, they would be copied to the home
>> > directory, possibly with a check on the success of the operation. I
>> > don't
>> > know if this would be better, but at least the problems with network
>> > load
>> > would be much more punctual, and it could also be more prone to error
>> > control.
>> > Since I do not have much knowledge of csh programming (I'm mostly a bash
>> > guy) and the Wien2k scripts are pretty complex beasts to which I am not
>> > very
>> > acquainted, could you give your opinions on the feasibility of my
>> > suggestions, and if they are not too complex to implement, possible
>> > changes
>> > and/or places to be changed in the scripts?
>> > Best regards,
>> > Marcos
>> > _______________________________________________
>> > Wien mailing list
>> > Wien at zeus.theochem.tuwien.ac.at
>> > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> >
>> >
>>
>>
>>
>> --
>> Laurence Marks
>> Department of Materials Science and Engineering
>> MSE Rm 2036 Cook Hall
>> 2220 N Campus Drive
>> Northwestern University
>> Evanston, IL 60208, USA
>> Tel: (847) 491-3996 Fax: (847) 491-7820
>> email: L-marks at northwestern dot edu
>> Web: www.numis.northwestern.edu
>> Chair, Commission on Electron Crystallography of IUCR
>> www.numis.northwestern.edu/
>> Electron crystallography is the branch of science that uses electron
>> scattering and imaging to study the structure of matter.
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
>
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>
--
Laurence Marks
Department of Materials Science and Engineering
MSE Rm 2036 Cook Hall
2220 N Campus Drive
Northwestern University
Evanston, IL 60208, USA
Tel: (847) 491-3996 Fax: (847) 491-7820
email: L-marks at northwestern dot edu
Web: www.numis.northwestern.edu
Chair, Commission on Electron Crystallography of IUCR
www.numis.northwestern.edu/
Electron crystallography is the branch of science that uses electron
scattering and imaging to study the structure of matter.
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