Re: [Wien] Problem with k-parallel

Peter Blaha Wed, 09 Mar 2016 08:13:13 -0800

Just put it to /tmp.

(There was a suggestion in the mailing list that someone wanted tochange /tmp to some other directory, which is tedious in the oldversions. With a variable $tmp_dir this is "easy" to change and will beactive in the next release.



On 03/09/2016 04:27 PM, Maciej Polak wrote:

Dear Prof. Blaha,

Thank you for your answer. I found the appropriate part of my lapw2para and 
substituted it with what you suggested.
However, one of the changes that I notice here is that you changed tmp for 
$tmp_dir. This $tmp_dir is a new variable which is not recognized by my script 
(tmp_dir: Undefined variable.). What is the meaning of this variable?

Thank you again for finding the time to reply to my email.

Best regards,

Maciej Polak

P.S In case you need it, I post the unmodified part of my code:


set i = 1
while ($i <= $maxproc)
# if ($debug > 0) echo -n "$i "
  cp $def.def /tmp/.tmp.$user.$$
  #subsituting in files:
  cat <<theend >/tmp/.script.$user.$$

s/vectorso$dnup/&_$i/w /tmp/.mist.$user.$$
s/vectorso$updn/&_$i/w /tmp/.mist.$user.$$
s/vectordum$dnup/&_$i/w /tmp/.mist.$user.$$
s/vectordum$updn/&_$i/w /tmp/.mist.$user.$$
s/vector$dnup/&_$i/w /tmp/.mist.$user.$$
s/vector$updn/&_$i/w /tmp/.mist.$user.$$
s/energyso$dnup/&_$i/w /tmp/.mist.$user.$$
s/energyso$updn/&_$i/w /tmp/.mist.$user.$$
s/energydum/&_$i/w /tmp/.mist.$user.$$
s/energy$dnup/&_$i/w /tmp/.mist.$user.$$
s/energy$updn/&_$i/w /tmp/.mist.$user.$$
s/\(weigh$dnup\)'/\1_$i'/w /tmp/.mist.$user.$$
s/\(weigh$updn\)'/\1_$i'/w /tmp/.mist.$user.$$
s/\(weightaverso$updn\)'/\1_$i'/w /tmp/.mist.$user.$$
s/normso$dnup/&_$i/w /tmp/.mist.$user.$$
s/normso$updn/&_$i/w /tmp/.mist.$user.$$
s/output2${updn}$eece/&_$i/w /tmp/.mist.$user.$$
s/clmval${updn}$eece/&_$i/w /tmp/.mist.$user.$$
s/vrespval$updn/&_$i/w /tmp/.mist.$user.$$
s/dmat$updn/&_$i/w /tmp/.mist.$user.$$
s/scf2$updn/&_$i/w /tmp/.mist.$user.$$
s/help$updn/&_$i/w /tmp/.mist.$user.$$
s/almblm$updn/&_$i/w /tmp/.mist.$user.$$

theend

  sed -f /tmp/.script.$user.$$ /tmp/.tmp.$user.$$ > /tmp/.tmp1.$user.$$
  sed "s/vector_${i}dn_$i/vectordn_$i/" /tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/vector_${i}up_$i/vectorup_$i/" /tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/vector_${i}so_$i/vectorso_$i/" /tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/energy_${i}up_$i/energyup_$i/" /tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/energy_${i}dn_$i/energydn_$i/" /tmp/.tmp1.$user.$$>/tmp/.tmp2.$user.$$
  sed "s/energy_${i}so_$i/energyso_$i/" /tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$$
  sed "s/energyso_${i}dn_$i/energysodn_${i}/" /tmp/.tmp1.$user.$$>/tmp/.tmp2.$u$
  sed "s/energy_${i}dum_$i/energydum_$i/" /tmp/.tmp2.$user.$$>/tmp/.tmp1.$user.$
  sed "s/vector_${i}so_${i}dn_$i/vectorsodn_$i/" /tmp/.tmp1.$user.$$>/tmp/.tmp2$
  sed "s/vector_${i}dum_${i}dn_$i/vectordumdn_$i/" /tmp/.tmp2.$user.$$>"$def"_$$
  @ i ++
end


W dniu 09/03/16 13:45 Peter Blaha <pbl...@theochem.tuwien.ac.at> napisał:


Hi,

Yes, we had have recently also such a problem. It comes from slow disk I/O.

A fie like /tmp/.tmp2.mpolak.50255

is a temporary file created by lapw2para and is used when we modify the 
lapw2_xx.def files by a couple of sed commands.

Because of this I've reduced the sed commands in my version of lapw2para. 
Unfortunately, I cannot post the script because it will not be compatible with 
your WIEN2k version, but I can tell you what we did and since then these errors 
did not show up anymore.

Please identify the following lines in your lapw2para and modify it like shown 
below:
...
#creating def files
set i = 1
while ($i <= $maxproc)
# if ($debug > 0) echo -n "$i "
cp $def.def $tmp_dir/.tmp.$user.$$
#subsituting in files:
cat <<theend >$tmp_dir/.script.$user.$$
s/vectorso$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/vectorso$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/vectordum$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/vectordum$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/vector$dnup'/vector${dnup}_$i'/w $tmp_dir/.mist.$user.$$
s/vector$updn'/vector${updn}_$i'/w $tmp_dir/.mist.$user.$$
s/energyso$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/energyso$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/energydum/&_$i/w $tmp_dir/.mist.$user.$$
s/energy$dnup'/energy${dnup}_$i'/w $tmp_dir/.mist.$user.$$
s/energy$updn'/energy${updn}_$i'/w $tmp_dir/.mist.$user.$$
s/\(weigh$dnup\)'/\1_$i'/w $tmp_dir/.mist.$user.$$
s/\(weigh$updn\)'/\1_$i'/w $tmp_dir/.mist.$user.$$
s/\(weightaverso$updn\)'/\1_$i'/w $tmp_dir/.mist.$user.$$
s/normso$dnup/&_$i/w $tmp_dir/.mist.$user.$$
s/normso$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/output2${updn}$eece/&_$i/w $tmp_dir/.mist.$user.$$
s/clmval${updn}$eece/&_$i/w $tmp_dir/.mist.$user.$$
s/vrespval$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/dmat$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/scf2$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/help$updn/&_$i/w $tmp_dir/.mist.$user.$$
s/almblm$updn/&_$i/w $tmp_dir/.mist.$user.$$

theend

sed -f $tmp_dir/.script.$user.$$ $tmp_dir/.tmp.$user.$$ > 
$tmp_dir/.tmp1.$user.$$
mv $tmp_dir/.tmp1.$user.$$ "$def"_$i.def

# sed "s/vector_${i}dn_$i/vectordn_$i/" 
$tmp_dir/.tmp1.$user.$$>$tmp_dir/.tmp2.$user.$$
# sed "s/vector_${i}up_$i/vectorup_$i/" 
$tmp_dir/.tmp2.$user.$$>$tmp_dir/.tmp1.$user.$$
# sed "s/vector_${i}so_$i/vectorso_$i/" 
$tmp_dir/.tmp1.$user.$$>$tmp_dir/.tmp2.$user.$$
# sed "s/energy_${i}up_$i/energyup_$i/" 
$tmp_dir/.tmp2.$user.$$>$tmp_dir/.tmp1.$user.$$
# sed "s/energy_${i}dn_$i/energydn_$i/" 
$tmp_dir/.tmp1.$user.$$>$tmp_dir/.tmp2.$user.$$
# sed "s/energy_${i}so_$i/energyso_$i/" 
$tmp_dir/.tmp2.$user.$$>$tmp_dir/.tmp1.$user.$$
# sed "s/energyso_${i}dn_$i/energysodn_${i}/" 
$tmp_dir/.tmp1.$user.$$>$tmp_dir/.tmp2.$user.$$
# sed "s/energy_${i}dum_$i/energydum_$i/" 
$tmp_dir/.tmp2.$user.$$>$tmp_dir/.tmp1.$user.$$
# sed "s/vector_${i}so_${i}dn_$i/vectorsodn_$i/" 
$tmp_dir/.tmp1.$user.$$>$tmp_dir/.tmp2.$user.$$
# sed "s/vector_${i}dum_${i}dn_$i/vectordumdn_$i/" 
$tmp_dir/.tmp2.$user.$$>"$def"_$i.def
@ i ++
end

As you can see, all these additional sed commands are now commented, since 
after the modifications of the .script.xx file they are not needed anymore.


On 03/08/2016 03:44 PM, Maciej Polak wrote:

Dear WIEN2k users and developers,

I encountered a very strange problem. Sometimes (50/50 chance), the 
calculations using just k-parallel will not finish. This exact same case, when 
submitted again (it sometime takes more tries) finishes with no problem. 
Sometimes it crashes after a few iterations, sometimes after a hundred or more, 
and sometimes it just finishes successfully.

This is what I get in the output:

sed: can't read /tmp/.tmp2.mpolak.50255: No such file or directory
cp: cannot stat `.in.tmp': No such file or directory


There is also an error in stderr:

forrtl: No such file or directory
forrtl: severe (29): file not found, unit 20, file 
/lustre/scratch/tmp/pbs.1275300.achilles/MoS2_LDA/fort.20
Image PC Routine Line Source
lapw2 00000000004B3E37 Unknown Unknown Unknown
lapw2 00000000004D5BE0 Unknown Unknown Unknown
lapw2 000000000048140D MAIN__ 155 lapw2_tmp_.F
lapw2 0000000000403F0E Unknown Unknown Unknown
libc.so.6 00002B1F2CD53D5D Unknown Unknown Unknown
lapw2 0000000000403E19 Unknown Unknown Unknown


Do you have any idea what may be the cause of this? Running on just one CPU is 
always fine. There is certainly no error in my input file, because after a few 
tries this exact same case will eventually finish correctly.

Thank you for your help

Maciej Polak
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P.Blaha
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SEARCH the MAILING-LIST at:  
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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: bl...@theochem.tuwien.ac.at    WIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
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Re: [Wien] Problem with k-parallel

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