[Pw_forum] Distributing phonon calculations todifferent machines
Huiqun Zhou
hqzhou at nju.edu.cn
Fri Jul 9 12:24:02 CEST 2010
Andrea,
Below are what I have in q1/ directory, it includes everything, I think.
[hqzhou at c01n05 ~]$ ls -l /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/
total 405184
drwxrwxr-x 2 hqzhou hqzhou 65536 Jul 9 18:17 _ph0sill_1.04v0.phsave
drwxrwxr-x 10 hqzhou hqzhou 65536 Jul 6 07:54 sill_1.04v0.save
-rw-rw-r-- 1 hqzhou hqzhou 52060160 Jul 9 18:14 sill_1.04v0.wfc1
-rw-rw-r-- 1 hqzhou hqzhou 52224000 Jul 9 18:14 sill_1.04v0.wfc2
-rw-rw-r-- 1 hqzhou hqzhou 51773440 Jul 9 18:14 sill_1.04v0.wfc3
-rw-rw-r-- 1 hqzhou hqzhou 51814400 Jul 9 18:14 sill_1.04v0.wfc4
-rw-rw-r-- 1 hqzhou hqzhou 51855360 Jul 9 18:14 sill_1.04v0.wfc5
-rw-rw-r-- 1 hqzhou hqzhou 51363840 Jul 9 18:14 sill_1.04v0.wfc6
-rw-rw-r-- 1 hqzhou hqzhou 51896320 Jul 9 18:14 sill_1.04v0.wfc7
-rw-rw-r-- 1 hqzhou hqzhou 51609600 Jul 9 18:14 sill_1.04v0.wfc8
Thanks for your help.
huiqun zhou
@earth sciences, nanjing university, china
----- Original Message -----
From: "Dal Corso Andrea" <dalcorso at sissa.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Thursday, July 08, 2010 2:40 PM
Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
machines
> On Thu, 2010-07-08 at 11:11 +0800, Huiqun Zhou wrote:
>> Andrea,
>>
>> I checked the directory, all files are there. See below,
>>
>> ls /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/_ph0sill_1.04v0.phsave/
>> data-file.xml data-file.xml.2 data-file.xml.5 data-file.xml.8
>> data-file.xml.1 data-file.xml.3 data-file.xml.6
>> data-file.xml.1.0 data-file.xml.4 data-file.xml.7
>>
>
> what about the directory /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1 ?
> Are all the files there? and the directory
> /gpfsTMP/hqzhou/tmp/sill_1.04v0/q1/sill_1.04v0.save ?
>
> Andrea
>
>> It's a little bit insane, this error only occurred when I compute the
>> first q point (gamma). ph.x worked fine while calculating other
>> q points. You can see the script snippet in my second post in this
>> thread, I had created neccessary directories and copied all needed
>> files in advance before distributing jobs.
>>
>> Any ideas?
>>
>> huiqun zhou
>> @earth sciences, nanjing university, china
>>
>> ----- Original Message -----
>> From: "Dal Corso Andrea" <dalcorso at sissa.it>
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Sent: Wednesday, July 07, 2010 8:06 PM
>> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> machines
>>
>>
>> > On Tue, 2010-07-06 at 17:55 +0800, Huiqun Zhou wrote:
>> >> Thanks, Andrea.
>> >>
>> >> As indicated in the script below, I have copied all files and
>> >> directories
>> >> created
>> >> by pw.x run.
>> >>
>> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >> mkdir $TMP_DIR/${system}/q${i}
>> >> cp -r $TMP_DIR/${system}/${system}.* $TMP_DIR/${system}/q${i}
>> >> fi
>> >>
>> >
>> > Are the files really there? If all the files are in the directory
>> > $TMP_DIR/${system}/q${i} there is no reason why the ph.x code stops.
>> > If they are not, I cannot help you. It is not a problem of ph.x.
>> >
>> >
>> >> BTW, could you please describe more in detail about the newly added
>> >> information
>> >> in INPUT_PH.html for distributing phonon calculations to cluster? If I
>> >> set
>> >> wf_collect
>> >> to true, there should be no relation in nproc and npool between pw.x
>> >> run
>> >> and
>> >> later
>> >> two ph.x runs, right? Taking AlAs in the GRID_example as example, If I
>> >> want
>> >> to use
>> >> server with 8 CPU core to do calculations for each one q point (8
>> >> servers
>> >> in
>> >> total),
>> >> what are the values of images and pools?
>> >>
>> >>
>> > You are right, the explanation refer only to the case
>> > wf_collect=.false.. However, image parallelization of ph.x is very
>> > experimental, so be patient. At the moment it divides both q and
>> > irreps.
>> > Load balancing on q only is not implemented.
>> >
>> >
>> > Andrea
>> >
>> >
>> >
>> >> Huiqun Zhou
>> >> @Earth Sciences, Nanjing University, China
>> >>
>> >> ----- Original Message -----
>> >> From: "Dal Corso Andrea" <dalcorso at sissa.it>
>> >> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> >> Sent: Tuesday, July 06, 2010 4:14 PM
>> >> Subject: Re: [Pw_forum] Distributing phonon calculations todifferent
>> >> machines
>> >>
>> >>
>> >> > On Tue, 2010-07-06 at 12:13 +0800, Huiqun Zhou wrote:
>> >> >> Sorry, I sent an unfinished message.
>> >> >>
>> >> >> When using _ph0{prefix}.phsave, I got the error message shown in
>> >> >> the
>> >> >> previous
>> >> >> message.
>> >> >>
>> >> >> Here is the snippet of my script for distributing lsf tasks:
>> >> >>
>> >> >> ......
>> >> >> nq=`sed -n '2p' ./${system}_q${nq1}${nq2}${nq3}.dyn0`
>> >> >>
>> >> >> for ((i=1; i<=$nq; i++))
>> >> >> do
>> >> >> if test ! -d $TMP_DIR/${system}/q${i} ; then
>> >> >> mkdir $TMP_DIR/${system}/q${i}
>> >> >> cp -r $TMP_DIR/${system}/${system}.*
>> >> >> $TMP_DIR/${system}/q${i}
>> >> >> fi
>> >> >> if test ! -d $TMP_DIR/${system}/q${i}/_ph0${system}.phsave ;
>> >> >> then
>> >> >> mkdir $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> >> cp -r $TMP_DIR/${system}/_ph0${system}.phsave/*
>> >> >> $TMP_DIR/${system}/q${i}/_ph0${system}.phsave
>> >> >> fi
>> >> >> done
>> >> >>
>> >> >> for ((i=1; i<=$nq; i++))
>> >> >> do
>> >> >> cat > ${system}_q${i}.in << EOF
>> >> >> phonons of ${system}
>> >> >> &inputph
>> >> >> tr2_ph = 1.0d-13,
>> >> >> alpha_mix(1) = 0.2,
>> >> >> prefix = '${system}',
>> >> >> ldisp = .true.,
>> >> >> recover = .true.
>> >> >> nq1 = ${nq1}, nq2 = ${nq2}, nq3 = ${nq3}
>> >> >> start_q = $i, last_q = $i
>> >> >> outdir = '$TMP_DIR/${system}/q${i}',
>> >> >> fildyn = '${system}_q${nq1}${nq2}${nq3}.dyn'
>> >> >> ......
>> >> >> EOF
>> >> >> $ECHO "calculation of q point $i"
>> >> >> bsub -a intelmpi -n $processes \
>> >> >> -R "span[ptile=8]" \
>> >> >> -J ${r}q${i}anda \
>> >> >> -oo ${system}_q${i}.out \
>> >> >> -eo ${system}_q${i}.err \
>> >> >> $PH_COMMAND -input ./${system}_q${i}.in
>> >> >> done
>> >> >>
>> >> >>
>> >> >> Huiqun Zhou
>> >> >> @Earth Sciences, Nanjing University, China
>> >> >> ----- Original Message -----
>> >> >> From: Huiqun Zhou
>> >> >> To: pw_forum at pwscf.org
>> >> >> Sent: Tuesday, July 06, 2010 12:00 PM
>> >> >> Subject: [Pw_forum] Distributing phonon calculations to
>> >> >> different machines
>> >> >>
>> >> >>
>> >> >> dear developers,
>> >> >>
>> >> >> Please clarify what directory should be copied
>> >> >> for distributing phonon calculations
>> >> >> to different machines, _ph{prefix}.phsave
>> >> >> or _ph0{prefix}.phsave? The former is
>> >> >> described in the manual INPUT_PH.html, the latter is used
>> >> >> in
>> >> >> the GRID_example.
>> >> >> Although there is no _ph{prefix}.phsave existed after the
>> >> >> preparatory run with
>> >> >> start_irr=0 and last_irr=0, using the former works OK at
>> >> >> the
>> >> >> cost of redundant
>> >> >> calculations.
>> >> >>
>> >> >> Representation # 1 mode # 1
>> >> >>
>> >> >> Self-consistent Calculation
>> >> >>
>> >> >>
>> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >> >> %%%%%%%%%%%%%%%%%
>> >> >> from davcio : error # 25
>> >> >> error while reading from file
>> >> >>
>> >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >> >> %%%%%%%%%%%%%%%%%
>> >> >>
>> >> >> stopping ...
>> >> >
>> >> > Thank you for the message. I will correct the INPUT_PH
>> >> > documentation.
>> >> > The correct directory is _ph0{prefix}.phsave.
>> >> >
>> >> > This message usually means that you have not copied all the required
>> >> > files. Did you copy all the files produced by pw.x?
>> >> >
>> >> > HTH,
>> >> >
>> >> > Andrea
>> >> >
>> >> >
>> >> >
>> >> >>
>> >> >>
>> >> >> ______________________________________________________________
>> >> >>
>> >> >> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> > --
>> >> > Andrea Dal Corso Tel. 0039-040-3787428
>> >> > SISSA, Via Beirut 2/4 Fax. 0039-040-3787528
>> >> > 34151 Trieste (Italy) e-mail: dalcorso at sissa.it
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >
>> >>
>> >>
>> >> _______________________________________________
>> >> Pw_forum mailing list
>> >> Pw_forum at pwscf.org
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> > --
>> > Andrea Dal Corso Tel. 0039-040-3787428
>> > SISSA, Via Beirut 2/4 Fax. 0039-040-3787528
>> > 34151 Trieste (Italy) e-mail: dalcorso at sissa.it
>> >
>> >
>> > _______________________________________________
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://www.democritos.it/mailman/listinfo/pw_forum
>> >
>>
>>
>> _______________________________________________
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>> Pw_forum at pwscf.org
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> --
> Andrea Dal Corso Tel. 0039-040-3787428
> SISSA, Via Beirut 2/4 Fax. 0039-040-3787528
> 34151 Trieste (Italy) e-mail: dalcorso at sissa.it
>
>
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