Re: phonon calculation for large system (Huiqun Zhou)
Maybe i can give it to you, but i do not know your email.<br><br><br>在2009-04-30，pw_forum-request@pwscf.org 写道：<br> <BLOCKQUOTE id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><PRE>Send Pw_forum mailing list submissions to
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Today's Topics:
1. Re: problem with installing Quantum ESPRESSO CVS version
(Paolo Giannozzi)
2. Re: electron-phonon coupling within rigid band approximation
(Paolo Giannozzi)
3. Re: can't read wavefunction and coords (Gabriele Sclauzero)
4. Re: phonon calculation for large system (Gabriele Sclauzero)
5. Re: phonon calculation for large system (Paolo Giannozzi)
6. Re: phonon calculation for large system (Gabriele Sclauzero)
7. Re: phonon calculation for large system (Huiqun Zhou)
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Message: 1
Date: Thu, 30 Apr 2009 09:16:33 +0200
From: Paolo Giannozzi <GIANNOZZ Subject:="" Re:="" problem="" with="" installing="" Quantum="" ESPRESSO="" CVS="" version="" To:="" infoshruba="" PWSCF="" Forum=""><PW_FORUM Message-ID:=""><DEB12955-9EDF-4861-8391-2428BD079614 Content-Type:="" text="" plain="" charset="us-ascii" On="" Apr="" at="" shruba="" wrote:="" apps="" intel="" fce="" lib="" libimf.so:="" warning:="" warning:="" feupdateenv="" is="" not="" implemented="" and="" will="" always="" fail="" not="" a="" problem="" opt="" intel="" mkl="" lib="" em64t="" libmkl_lapack.so:="" undefined="" reference="" to="" in="" your="" make.sys="" you="" should="" have="" LDFLAGS="-i-static" BLAS_LIBS="-L" opt="" intel="" mkl="" lib="" em64t="" LAPACK_LIBS="and" no="" when="" I="" contacted="" to="" the="" cluster="" management="" they="" suggested="" me="" to="" check="" weather="" CVS="" version="" is="" compatible="" with="" version="" of="" the="" intel="" mkl="" of="" course="" it="" is="" and="" it="" works="" on="" all="" machines="" I="" have="" tried.="" If="" you="" find="" why="" it="" doesn="" in="" your="" case="" please="" report.="" Most="" likely="" the="" version="" of="" the="" intel="" compiler="" found="" by="" configure="" is="" either="" old="" V.9=""><giannozz Giannozzi="" Paolo="" From:="" Apr="" Thu="" Date:="" Message:="" attachment-0001.htm="" ec2611ad="" attachments="" pw_forum="" pipermail="" www.democritos.it="" http:="" URL:="" scrubbed...="" was="" attachment="" HTML="" An="" part="" next="" Italy="" Udine="" of="" University="" and="" Democritos="" Giannozzi="" reason.="" obscure="" some="" for="" recognized="" correctly="" not="" or="">
Subject: Re: [Pw_forum] electron-phonon coupling within rigid band
approximation
To: PWSCF Forum <PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" charset="us-ascii" On="" Apr="" at="" asubedi="" wrote:="" I="" am="" trying="" to="" calculate="" electron-phonon="" coupling="" of="" an="" insulator="" which="" is="" not="" possible="" with="" QE.="" However="" can="" I="" do="" it="" by="" fixing="" the="" Fermi="" energy="" so="" that="" it="" crosses="" the="" valence="" bands="" I="" guess="" you="" can="" but="" is="" this="" what="" you="" want="" Paolo="" Paolo="" Giannozzi="" Democritos="" and="" University="" of="" Udine="" Italy="" next="" part="" An="" HTML="" attachment="" was="" scrubbed...="" URL:="" http:="" www.democritos.it="" pipermail="" pw_forum="" attachments="" a4593525="" attachment-0001.htm="" Message:="" Date:="" Thu="" Apr="" From:="" Gabriele="" Sclauzero=""><SCLAUZER Subject:="" Re:="" can="" read="" wavefunction="" and="" coords="" To:="" PWSCF="" Forum=""><PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" charset="us-ascii;" format="flowed" Jonas="" Baltrusaitis="" wrote:="" OK="" this="" time="" I="" have="" a="" tricky="" one.="" Fixed="" bash="" issues="" mistake="" Now="" my="" fil.dos="" and="" all="" PDOS="" files="" have="" only="" one="" line:="" E="" dos="" Int="" dos="" Seems="" like="" it="" all="" starts="" with="" file="" which="" is="" not="" complete="" either.="" No="" crash="" error="" is="" produced="" Are="" you="" sure="" of="" your="" choice="" of="" Emin="" Emax="" What="" is="" the="" highest="" KS="" eigenvalue="" you="" obtained="" from="" pw.x="" You="" should="" have="" a="" look="" a="" the="" output="" produced="" at="" the="" intermediate="" steps.="" It="" is="" not="" wise="" to="" do="" everything="" blindly="" and="" simply="" hope="" that="" at="" the="" end="" you="" will="" get="" the="" correct="" result...="" GS="" DOS="" calculation="" for="" sih4="" cat="" sih4.dos.in="" EOF="" calculation="nscf" prefix="sih4" pseudo_dir="$PSEUDO_DIR/" outdir="$TMP_DIR/" ibrav="2," celldm="" nat="5," ntyp="2," ecutwfc="16.0" mixing_mode="plain" mixing_beta="0.7," conv_thr="1.0d-8" ATOMIC_SPECIES="" Si="" Si.vbc.UPF="" H="" H.vbc.UPF="" K_POINTS="" EOF="" cat="" atpos.tmp="" sih4.dos.in="" cat="" sih4.dos2.in="" EOF="" outdir="$TMP_DIR/" prefix="sih4" fildos="sih4.dos" Emin="5.0," Emax="25.0," DeltaE="0.1," ngauss="1," degauss="0.02" EOF="" running="" DOS="" calculation="" for="" sih4...="" sih4.dos.in="" sih4.dos.out="" sih4.dos2.in="" sih4.dos2.out="" done="" cat="" sih4.pdos.in="" EOF="" outdir="$TMP_DIR/" prefix="sih4" Emin="5.0," Emax="25.0," DeltaE="0.1," ngauss="1," degauss="0.02" EOF="" running="" PDOS="" calculation="" for="" Ni...="" sih4.pdos.in="" sih4.pdos.out="" done="" done="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" o="" o="" Gabriele="" Sclauzero="" PhD="" Student="" c="" o:="" SISSA="" CNR-INFM="" Democritos="" via="" Beirut="" Trieste="" email:="" sclauzer="" phone:="" skype:="" gurlonotturno="" o="" o="" Message:="" Date:="" Thu="" Apr="" From:="" Gabriele="" Sclauzero=""><SCLAUZER Subject:="" Re:="" phonon="" calculation="" for="" large="" system="" To:="" PWSCF="" Forum=""><PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" charset="ISO-8859-1;" format="flowed" zq="" wu="" wrote:="" Dear="" pwscf="" users="" I="" need="" to="" do="" phonon="" calculation="" for="" large="" system="" hundreds="" atoms="" per="" cell="" Since="" i="" can="" use="" lots="" of="" processors="" I="" plan="" to="" submit="" many="" jobs="" each="" of="" which="" will="" calculate="" phonon="" mode.="" But="" i="" do="" not="" know="" whether="" it="" is="" available="" to="" get="" final="" dynamic="" matrix="" from="" these="" separate="" runs="" and="" how="" to="" do="" it.="" Can="" any="" one="" help="" me="" Currently="" phonon="" modes="" are="" calculated="" one="" by="" one="" in="" sequence="" in="" phonon="" calculation.="" Can="" we="" do="" some="" parallelization="" here="" Can="" we="" divide="" the="" processors="" into="" several="" groups="" and="" let="" each="" group="" take="" care="" of="" one="" or="" more="" modes="" in="" a="" way="" similar="" to="" K-points="" parallelization="" I="" think="" that="" the="" parallel="" efficeincy="" for="" modes="" parallelization="" should="" also="" be="" close="" to="" K-points="" parallelization="" since="" the="" phonon="" modes="" calculation="" is="" independent="" of="" each="" other.="" The="" modes="" parallelization="" should="" be="" very="" useful="" for="" system="" with="" large="" numbers="" of="" atoms.="" Does="" anyone="" have="" the="" idea="" how="" hard="" it="" is="" to="" do="" the="" modes="" parallelization="" If="" I="" correctly="" understood="" i="" think="" that="" this="" kind="" of="" parallelization="" has="" already="" been="" exploited="" in="" the="" latest="" versions="" of="" CVS="" in="" order="" to="" use="" ph.x="" on="" the="" GRID.="" I="" don="" know="" if="" all="" the="" related="" problems="" have="" been="" fixed="" at="" this="" stage="" they="" Paolo="" but="" you="" can="" try="" to="" download="" the="" CVS="" and="" use="" the="" keywords="" start_q="" last_q="" start_irr="" last_irr="" INPUT_PH="" to="" split="" your="" job="" in="" many="" independent="" jobs.="" Sorry="" I="" don="" know="" the="" details="" but="" at="" least="" now="" you="" aware="" that="" there="" is="" this="" possibility="" available="" not="" extensively="" tested="" I="" think="" so="" use="" _with_="" _care_="" and="" help="" debugging="" please="" HTH="" GS="" Thanks="" Zhongqing="" CACS="" University="" of="" Southern="" California="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" o="" o="" Gabriele="" Sclauzero="" PhD="" Student="" c="" o:="" SISSA="" CNR-INFM="" Democritos="" via="" Beirut="" Trieste="" email:="" sclauzer="" phone:="" skype:="" gurlonotturno="" o="" o="" Message:="" Date:="" Thu="" Apr="" From:="" Paolo="" Giannozzi=""><GIANNOZZ Subject:="" Re:="" phonon="" calculation="" for="" large="" system="" To:="" PWSCF="" Forum=""><PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" charset="US-ASCII;" delsp="yes;" format="flowed" On="" Apr="" at="" Gabriele="" Sclauzero="" wrote:="" i="" think="" that="" this="" kind="" of="" parallelization="" has="" already="" been="" exploited="" in="" the="" latest="" versions="" of="" CVS="" in="" order="" to="" use="" ph.x="" on="" the="" GRID.="" I="" don="" know="" if="" all="" the="" related="" problems="" have="" been="" fixed="" at="" this="" stage="" they="" have="" but="" I="" am="" not="" sure="" you="" can="" run="" hundreds="" of="" atoms="" on="" the="" grid:="" the="" single-q="" single-mode="" calculation="" has="" to="" fit="" into="" the="" memory="" of="" each="" node.="" P.="" Paolo="" Giannozzi="" Democritos="" and="" University="" of="" Udine="" Italy="" Message:="" Date:="" Thu="" Apr="" From:="" Gabriele="" Sclauzero=""><SCLAUZER Subject:="" Re:="" phonon="" calculation="" for="" large="" system="" To:="" PWSCF="" Forum=""><PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" charset="us-ascii;" format="flowed" Paolo="" Giannozzi="" wrote:="" On="" Apr="" at="" Gabriele="" Sclauzero="" wrote:="" i="" think="" that="" this="" kind="" of="" parallelization="" has="" already="" been="" exploited="" in="" the="" latest="" versions="" of="" CVS="" in="" order="" to="" use="" ph.x="" on="" the="" GRID.="" I="" don="" know="" if="" all="" the="" related="" problems="" have="" been="" fixed="" at="" this="" stage="" they="" have="" but="" I="" am="" not="" sure="" you="" can="" run="" hundreds="" of="" atoms="" on="" the="" grid:="" the="" single-q="" single-mode="" calculation="" has="" to="" fit="" into="" the="" memory="" of="" each="" node.="" Of="" course="" you="" are="" right.="" Anyway="" I="" think="" you="" can="" use="" this="" parallelization="" level="" even="" on="" a="" cluster="" so="" that="" you="" do="" not="" have="" to="" do="" modes="" and="" irreps="" sequentially="" but="" you="" can="" split="" them="" in="" concurrently="" running="" jobs="" so="" that="" you-ll="" have="" an="" actual="" speed-up.="" Or="" are="" you="" forced="" to="" use="" a="" single="" processor="" in="" order="" to="" exploit="" this="" start_q="" last_q="" keywords="" GS="" P.="" Paolo="" Giannozzi="" Democritos="" and="" University="" of="" Udine="" Italy="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" o="" o="" Gabriele="" Sclauzero="" PhD="" Student="" c="" o:="" SISSA="" CNR-INFM="" Democritos="" via="" Beirut="" Trieste="" email:="" sclauzer="" phone:="" skype:="" gurlonotturno="" o="" o="" Message:="" Date:="" Thu="" Apr="" From:="" Zhou=""><HQZHOU Subject:="" Re:="" phonon="" calculation="" for="" large="" system="" To:="" Forum=""><PW_FORUM Message-ID:="" Content-Type:="" text="" plain="" format="flowed;" charset="iso-8859-1" reply-type="original" Gabriele="" I="" just="" downloaded="" the="" CVS="" version="" two="" days="" ago="" but="" found="" no="" INPUT_PH="" in="" Doc.="" Should="" you="" please="" post="" one="" or="" let="" me="" know="" how="" to="" generate="" it="" Huiqun="" Zhou="" Sciences="" Nanjing="" University="" China="" Original="" Message="" From:="" Sclauzero=""><SCLAUZER To:="" Forum=""><PW_FORUM Sent:="" Thursday="" April="" PM="" Subject:="" Re:="" phonon="" calculation="" for="" large="" system="" zq="" wu="" wrote:="" Dear="" pwscf="" users="" I="" need="" to="" do="" phonon="" calculation="" for="" large="" system="" hundreds="" atoms="" per="" cell="" Since="" i="" can="" use="" lots="" of="" processors="" I="" plan="" to="" submit="" many="" jobs="" each="" of="" which="" will="" calculate="" phonon="" mode.="" But="" i="" do="" not="" know="" whether="" it="" is="" available="" to="" get="" final="" dynamic="" matrix="" from="" these="" separate="" runs="" and="" how="" to="" do="" it.="" Can="" any="" one="" help="" me="" Currently="" phonon="" modes="" are="" calculated="" one="" by="" one="" in="" sequence="" in="" phonon="" calculation.="" Can="" we="" do="" some="" parallelization="" here="" Can="" we="" divide="" the="" processors="" into="" several="" groups="" and="" let="" each="" group="" take="" care="" of="" one="" or="" more="" modes="" in="" a="" way="" similar="" to="" K-points="" parallelization="" I="" think="" that="" the="" parallel="" efficeincy="" for="" modes="" parallelization="" should="" also="" be="" close="" to="" K-points="" parallelization="" since="" the="" phonon="" modes="" calculation="" is="" independent="" of="" each="" other.="" The="" modes="" parallelization="" should="" be="" very="" useful="" for="" system="" with="" large="" numbers="" of="" atoms.="" Does="" anyone="" have="" the="" idea="" how="" hard="" it="" is="" to="" do="" the="" modes="" parallelization="" If="" I="" correctly="" understood="" i="" think="" that="" this="" kind="" of="" parallelization="" has="" already="" been="" exploited="" in="" the="" latest="" versions="" of="" CVS="" in="" order="" to="" use="" ph.x="" on="" the="" GRID.="" I="" don="" know="" if="" all="" the="" related="" problems="" have="" been="" fixed="" at="" this="" stage="" they="" Paolo="" but="" you="" can="" try="" to="" download="" the="" CVS="" and="" use="" the="" keywords="" start_q="" last_q="" start_irr="" last_irr="" INPUT_PH="" to="" split="" your="" job="" in="" many="" independent="" jobs.="" Sorry="" I="" don="" know="" the="" details="" but="" at="" least="" now="" you="" aware="" that="" there="" is="" this="" possibility="" available="" not="" extensively="" tested="" I="" think="" so="" use="" _with_="" _care_="" and="" help="" debugging="" please="" HTH="" GS="" Thanks="" Zhongqing="" CACS="" University="" of="" Southern="" California="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" o="" o="" Gabriele="" Sclauzero="" PhD="" Student="" c="" o:="" SISSA="" CNR-INFM="" Democritos="" via="" Beirut="" Trieste="" email:="" sclauzer="" phone:="" skype:="" gurlonotturno="" o="" o="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" _______________________________________________="" Pw_forum="" mailing="" list="" Pw_forum="" http:="" www.democritos.it="" mailman="" listinfo="" pw_forum="" End="" of="" Pw_forum="" Digest="" Vol="" Issue=""></PW_FORUM></SCLAUZER></PW_FORUM></HQZHOU></PW_FORUM></SCLAUZER></PW_FORUM></GIANNOZZ></PW_FORUM></SCLAUZER></PW_FORUM></SCLAUZER></PW_FORUM></giannozz></DEB12955-9EDF-4861-8391-2428BD079614></PW_FORUM></GIANNOZZ></PRE></BLOCKQUOTE><br><!-- footer --><br><span title="neteasefooter"/><hr/>
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