[Wien] Problem with k-parallel

Wed Mar 9 16:27:02 CET 2016

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 <pblaha at 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
> >_______________________________________________
> >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 WIEN2k: http://www.wien2k.at
> WWW: http://www.imc.tuwien.ac.at/staff/tc_group_e.php
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