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" <[email protected]> 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 >> > >> >> >> _______________________________________________ >> 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 >
