[Pw_forum] problem with ph.x
On Thursday 12 January 2006 16:47, Gabriele Sclauzero wrote: > I tried to patch as you gently suggested, Paolo, but one of the two > hungs was rejected: [...] I suppose it's because the row to be > substituted in my distribution (3.0) is: >USE control_flags, ONLY : restart, lphonon, tr2, & >mixing_beta, lscf, david, isolve, modenum oops...my patch was against a more recent version > Is it OK if I add manually in the ONLY list that "wg_set" from the > patch, and should I leave "modenum" where it is? yes it is. "modenum" is actually never used there. P. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale SuperiorePhone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy
[Pw_forum] execution error
On Thursday 12 January 2006 17:53, Aritz Leonardo wrote: > mpirun C -np $NPROCS /scratch/aritz/pw_root/bin/pw.x < $a.scf.in >> $a.scf.out why "mpirun C" ? Anyway: computers are deterministic objects, even if sometimes it is really hard to believe that. If you cannot run your script, there is either something in your input data that the code doesn't like (check for invisible control characters, & in the first column, / vs , missing end-of-line; all these are real-life cases); or the code is not reading the input data (check option -inp 'file'); or the code is not running under the same environment of the example that works (environmental variables, library path, batch vs interactive, whatever) P. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale SuperiorePhone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy
[Fwd: Re: [Pw_forum] execution error]
Dear Aritz, On 12 Jan 2006, at 6:37 PM, Aritz Leonardo wrote: > Thanks for the reply Marino > > 2 short questions: > > 1.- Did you have any problem with the slash sign? Apparently not > 2.- Did you use the compiler XLF? > Yes. m. > thanks again > > From: Marino Vetuschi Zuccolini > Date: 12 January 2006 6:13:46 PM CET > To: Aritz Leonardo > Subject: Re: [Pw_forum] execution error > > > Dear Aritz, > some time ago I did the same problem and the only solution was for me > to re-type the file, or to use without modify it, the file which is > output of the PWSCFGui. > Try to see the input file with vi, maybe some char at the end of line > can be visible. But I cannot hide my faithful act... > > Good luck > > m. > > On 12 Jan 2006, at 6:12 PM, Aritz Leonardo wrote: > >> Hello Gerardo. Thanks a lot for the reply. >> >> YES I compiled ESPRESSO with XLF, and what you told me is very >> helpful. >> But the rarest thing is that I am able to run example01 of espresso >> and >> not the script that I previously sent. >> >> thanks a lot again >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > *** > Marino Vetuschi Zuccolini > zucco at dipteris.unige.it > PhD / Geochemist > Laboratory of Geochemistry > http://www.dipteris.unige.it/geochimica > > Visit our BAXEICO computing cluster homepage > http://qed.dipteris.unige.it/ganglia -- out of service > > DIPartimento per lo studio della TErra e delle sue RISorse - > Universit? di Genova > Tel. ++39 010 3538136 Fax. ++39 010 352169 > Corso Europa 26, 16132 - Genova - Italy > > > *** Marino Vetuschi Zuccolini zucco at dipteris.unige.it PhD / Geochemist Laboratory of Geochemistry http://www.dipteris.unige.it/geochimica Visit our BAXEICO computing cluster homepage http://qed.dipteris.unige.it/ganglia -- out of service DIPartimento per lo studio della TErra e delle sue RISorse - Universit? di Genova Tel. ++39 010 3538136 Fax. ++39 010 352169 Corso Europa 26, 16132 - Genova - Italy -- next part -- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2724 bytes Desc: not available Url : /pipermail/attachments/20060112/8608dacf/attachment.bin
[Fwd: Re: [Pw_forum] execution error]
Thanks for the reply Marino 2 short questions: 1.- Did you have any problem with the slash sign? 2.- Did you use the compiler XLF? thanks again -- next part -- An embedded message was scrubbed... From: Marino Vetuschi Zuccolini <zu...@dipteris.unige.it> Subject: Re: [Pw_forum] execution error Date: Thu, 12 Jan 2006 18:13:46 +0100 Size: 4395 Url: /pipermail/attachments/20060112/7b917c7d/attachment.eml
[Pw_forum] execution error
Hello Gerardo. Thanks a lot for the reply. YES I compiled ESPRESSO with XLF, and what you told me is very helpful. But the rarest thing is that I am able to run example01 of espresso and not the script that I previously sent. thanks a lot again
[Pw_forum] execution error
Dear Axel and Paolo:
thanks a lot for the reply. This is the script that crashes
#!/bin/sh
###
#PBS -q parallel
#PBS -l pmem=2gb
#PBS -l nodes=1:ppn=1
#PBS -l cput=200:00:00
PATH=$PATH:/software/lam-7.1.1-xlf/bin
NPROCS=`wc -l < $PBS_NODEFILE`
lamboot -v $PBS_NODEFILE
tping -c1 C
cd /scratch/aritz/MONOLAYERS/C/PHONONS/
# check whether ECHO has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
PSEUDO_LIST="C.pbe-rrkjus.UPF"
TMP_DIR=/scratch/aritz/tmp
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"
E=20.0
ca=6.5
a=4.65
#
for PARAM in `cat qPOINTS2`;
do
QX="`echo $PARAM | awk -F: '{print $1}'`";
QY="`echo $PARAM | awk -F: '{print $2}'`";
QZ="`echo $PARAM | awk -F: '{print $3}'`";
echo "$QX, $QY, $QZ, $a";
# self-consistent calculation
cat > $a.scf.in << EOF
calculation='scf',
restart_mode='from_scratch',
prefix='C'
tstress = .true.
tprnfor = .true.
pseudo_dir = '/lscratch/aritz',
outdir='$TMP_DIR/'
/
ibrav = 4, celldm(1) =$a,celldm(3)=$ca, nat= 2, ntyp= 1,
ecutwfc = $E,occupations='smearing',smearing='m-p',degauss=0.007
/
mixing_beta = 0.5
conv_thr = 1.0d-6
/
ATOMIC_SPECIES
C 12.01 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS
C 0.00 0.0 0.00
C 0.00 0.577350269 0.00
K_POINTS {automatic}
20 20 1 1 1 0
EOF
$ECHO " running the scf calculation...\c"
mpirun C -np $NPROCS /scratch/aritz/pw_root/bin/pw.x < $a.scf.in >>
$a.scf.out
$ECHO " done"
[Pw_forum] execution error
On 01/12/2006 04:17:21 PM, Aritz Leonardo wrote: > I am running for the first time ESPRESSO in a cluster of xserveG5 > with MAC OSX. Are you using the XLF compiler? If I remember correctly, while namelists normally end with a slash, with that compiler there is an environment variable such that, when it's set, namelists end with "" (for backward compatibility, I guess). I don't remember how it's called, sorry. Gerardo
[Pw_forum] problem with ph.x
I tried to patch as you gently suggested, Paolo, but one of the two hungs was rejected: #patch -p0 On Thursday 08 December 2005 16:19, Konzern wrote: > > >>when I tried to run the example in example06, something unexpected >>happened [..] I am running the program with 4 cpus > > > On Saturday 24 December 2005 12:28, Hai-Ping Lan wrote: > >> I have compiled ESPRESSO 2.1.5 package in AMD operon >>workstations. But i cannot perform phonon calculations parallely. > > > On Monday 09 January 2006 11:11, Gabriele Sclauzero wrote: > > >> I tried to run "example06" in the examples that come with the 3.0 >> espresso package: the ph calculation works when using a single cpu, >> but hangs up while calculating alas.dyn3 as soon as I try to use more >> then 1 cpu. > > > there was a subtle bug in the phonon code that could lead to crashes > in parallel execution (and some loss of precision in serial execution). > Save the attached file to the root directory of the 3.0 distribution (the > one containing PH/) and use command "patch -p0 < phonon.diff". This > should produce a patched version of PH/phonon.f90 that fixes the > problem with example06. > > I don't know about the second case, but I think that the 2.1.5 version > has the same problem (but needs a different fix) > > Paolo > > > > > Index: PH/phonon.f90 > === > RCS file: /home/cvs/O-sesame/PH/phonon.f90,v > retrieving revision 1.33 > diff -c -r1.33 phonon.f90 > *** PH/phonon.f90 13 Dec 2005 14:45:35 - 1.33 > --- PH/phonon.f90 11 Jan 2006 17:12:30 - > *** > *** 28,34 > USE lsda_mod,ONLY : nspin > USE gvect, ONLY : nrx1, nrx2, nrx3 > USE parser, ONLY : int_to_char > ! USE control_flags, ONLY : restart, lphonon, tr2, & > mixing_beta, lscf, david, isolve > USE qpoint, ONLY : xq, nksq > USE disp,ONLY : nqs, x_q > --- 28,34 > USE lsda_mod,ONLY : nspin > USE gvect, ONLY : nrx1, nrx2, nrx3 > USE parser, ONLY : int_to_char > ! USE control_flags, ONLY : restart, lphonon, tr2, wg_set, & > mixing_beta, lscf, david, isolve > USE qpoint, ONLY : xq, nksq > USE disp,ONLY : nqs, x_q > *** > *** 222,227 > --- 222,228 > startingconfig = 'input' > startingpot= 'file' > startingwfc= 'atomic' > + wg_set=.false. > ! > ! ... tr2 is set to a default value of 1.D-8 > !
[Pw_forum] execution error
On Thursday 12 January 2006 16:17, Aritz Leonardo wrote: > I am 99% sure that it is an error of the cluster configuration but in > order to fix it I would like to know... > What is the meaning of error#1 ?? it is a game. If you waste your time trying to find out what "error # N" means, you lose. If you disregard the number (which has basically no meaning) and understand what causes the error, you win. You lost :-) > from read_namelists : error # 1 > reading namelist control See here: http://www.pwscf.org/guide/3.0/html-node/node45.html and http://www.pwscf.org/guide/3.0/html-node/node25.html towards the end (option "-inp"). If nothing is wrong in namelist , the only possible explanation is that you are not reading it. P. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale SuperiorePhone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy
[Pw_forum] (no subject)
Dear all, I am trying to perform a temperature rescaling MD with PWscf ion_dynamics = 'verlet' ion_temperature = 'rescaling' tempw = 500.0 nraise = 1 tolp = 1.d-8 wfc_extrapolation = 'first_order' / The starting temperature is correct but it decreases very rapidly 358: Starting temperature = 500.00 K 405: temperature = 496.70493449 K 693: temperature = 0.24166052 K 903: temperature = 0.21332563 K 1113: temperature = 0.18863928 K 1323: temperature = 0.16711531 K 1533: temperature = 0.14835294 K 1743: temperature = 0.13194319 K 1953: temperature = 0.11759977 K 2163: temperature = 0.10503616 K 2373: temperature = 0.09401538 K 2583: temperature = 0.08433571 K 2793: temperature = 0.07582100 K 3003: temperature = 0.06832018 K 3213: temperature = 0.06170251 K 3423: temperature = 0.05585484 K 3633: temperature = 0.05067925 K 3843: temperature = 0.04609150 K 4053: temperature = 0.04201768 K 4263: temperature = 0.03839409 K 4473: temperature = 0.03516576 K 4683: temperature = 0.03228480 K The question is: what is the printed values ? the real scaled temperature, the temperature "before" scaling, the difference between the the calculated and the wanted temperature ? Thanks for your help -- next part -- An HTML attachment was scrubbed... URL: /pipermail/attachments/20060112/d92c67ff/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: Alain.Allouche.vcf Type: text/x-vcard Size: 530 bytes Desc: not available Url : /pipermail/attachments/20060112/d92c67ff/attachment.vcf
[Pw_forum] execution error
Hello all: I am running for the first time ESPRESSO in a cluster of xserveG5 with MAC OSX. The compilation went ok, I am able to run the examples of the package. Then I try to run other very simple 'scf' scripts WHICH I AM COMPLETELY SURE THAT they are correctly typed and I find the following error at execution. I am 99% sure that it is an error of the cluster configuration but in order to fix it I would like to know... What is the meaning of error#1 ?? Parallel version (MPI) Number of processors in use: 1 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 4 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 %%% from read_namelists : error # 1 reading namelist control %% THANKS!!!
[Pw_forum] execution error
On Thu, 12 Jan 2006, Aritz Leonardo wrote: artiz, your input works fine for me, both on a linux machine and on an (older) mac. so there indeed seems to be a AL> 20 20 1 1 1 0 AL> EOF AL> $ECHO " running the scf calculation...\c" AL> mpirun C -np $NPROCS /scratch/aritz/pw_root/bin/pw.x < $a.scf.in >> AL> $a.scf.out please note that using 'C' and '-np $NPROCS' is redundant. with LAM/MPI (which you seem to be using) plain 'C' is sufficient and the preferred way as it will tell mpirun to start just one MPI-thread per allocated processor. however, i still will work as you were using it, with the '-np' taking precedence over 'C'. one thing you may want to check is the carriage-return/ linefeed conventions used on the file. on some machines, the (fortran) parser for the input file will choke on text files that have additional carriage-return characters in them (sometimes visible as ^M or control-M) as they are needed for dos/windows but not for unix-like machines. so if you created the script on a different machine, or converted it somehow to dos/windows text. that may be another explanation. regards, axel. AL> $ECHO " done" AL> AL> AL> AL> ___ AL> Pw_forum mailing list AL> Pw_forum at pwscf.org AL> http://www.democritos.it/mailman/listinfo/pw_forum AL> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] (no subject)
On Thu, 12 Jan 2006, Alain Allouche wrote: AA> Dear all, dear alain, AA> I am trying to perform a temperature rescaling MD with PWscf AA> AA> AA> ion_dynamics = 'verlet' AA> ion_temperature = 'rescaling' AA> tempw = 500.0 AA> nraise = 1 AA> tolp = 1.d-8 AA> wfc_extrapolation = 'first_order' AA> / AA> AA> The starting temperature is correct but it decreases very rapidly AA> AA> 358: Starting temperature = 500.00 K AA> 405: temperature = 496.70493449 K AA> 693: temperature = 0.24166052 K i've seen the same. going from the 3.0 release version to the current CVS seems to 'fix' the rapid decay, however, the rescaling at each nraise still does not occur. my suspicion so far was, that there was a problem distributing the values across all nodes (in my case this was a pretty large system with several k-points run across ~750 processors with one pool per k-point), but i could not find the time to look into this yet. regards, axel. AA> AA> The question is: what is the printed values ? the real scaled AA> temperature, the temperature "before" scaling, the difference between AA> the the calculated and the wanted temperature ? AA> Thanks for your help AA> AA> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] execution error
On Thu, 12 Jan 2006, Aritz Leonardo wrote: AL> Hello all: ... AL> Then I try to run other very simple 'scf' scripts WHICH I AM COMPLETELY AL> SURE THAT they are correctly typed and I find the following error at AL> execution. aritz, a) please do post the input example, so we can all see that it is correct. the error message indicates, that the program could not read the namelist. this can have multiple reasons. b) does your input work with a serial executable? that would give proof that in fact the cluster configuration ist to blame. if the job is too big, you can always - for debugging purposes - set plane wave (and density cutoff) to ridiculously low values just to see whether the input is read correctly. AL> I am 99% sure that it is an error of the cluster configuration but in AL> order to fix it I would like to know... AL> What is the meaning of error#1 ?? c) please describe how you started the job. some MPI implementations do not support reading from STDIN, so that you have to use the -inp flag. see the corresponding section in the manual. regards, axel. AL> AL> AL> AL> Parallel version (MPI) AL> AL> Number of processors in use: 1 AL> AL> Ultrasoft (Vanderbilt) Pseudopotentials AL> AL> Current dimensions of program pwscf are: AL> AL> ntypx = 10 npk = 4 lmax = 3 AL> nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 AL> AL> %%% AL> from read_namelists : error # 1 AL> reading namelist control AL> %% AL> AL> THANKS!!! AL> AL> ___ AL> Pw_forum mailing list AL> Pw_forum at pwscf.org AL> http://www.democritos.it/mailman/listinfo/pw_forum AL> -- === Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 === If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] difference from the output of dynmat.x and Phonon dyn file
On Thursday 12 January 2006 04:59, W. YU wrote:
> I found the difference between the two outputs are not
> connected by a factor of M^{-1/2}). For some modes they
> are almost the same, such as modes 12. But for others
> they differ a lot, such as mode 4. The subtle difference in
> mode 4 may come from the accoustic sum rule.
low-lying modes with low energy tend to have a sizable admixture
of the zero-ferquency translational mode, so it is quite likely that
upon application of the acoustic sum rule they look somewhat
different.
Paolo
--
Paolo Giannozzi e-mail: giannozz at nest.sns.it
Scuola Normale SuperiorePhone: +39/050-509876, Fax:-563513
Piazza dei Cavalieri 7 I-56126 Pisa, Italy
[Pw_forum] phonon branch crossing problem
On Thursday 12 January 2006 04:24, W. YU wrote: > I know there are some rules govening the phonon branch crossing > such as branches belonging to the same irrep will not cross each other. > I don't know how PHONON manages this problem. it doesn't. Once you have the force constants, you can calculate eigenvalues with the correct symmetry at any q-vector. How to connect the points into lines of well-defined symmetry is a different problem. There is a tool that does this for electonic band structures, but not for phonons. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale SuperiorePhone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy
[Pw_forum] temperature control in PWscf
Alain, I've run into this as well. It seems to me that in version 3.0, dynamics.f90 does not save the velocities between MD timesteps. So after the initial velocity scaling they are basically set to zero. Simply adding the vel array to the unit=4 read and write statements in dynamics.f90 seems to fix the problem for me. Is this a known bug? -Eric Schwegler > Dear all, > I am trying to perform a temperature rescaling MD with PWscf > > > ion_dynamics = 'verlet' > ion_temperature = 'rescaling' > tempw = 500.0 > nraise = 1 > tolp = 1.d-8 > wfc_extrapolation = 'first_order' > / > > The starting temperature is correct but it decreases very rapidly > > 358: Starting temperature = 500.00 K > 405: temperature = 496.70493449 K > 693: temperature = 0.24166052 K > 903: temperature = 0.21332563 K > 1113: temperature = 0.18863928 K > 1323: temperature = 0.16711531 K > 1533: temperature = 0.14835294 K > 1743: temperature = 0.13194319 K > 1953: temperature = 0.11759977 K
[Pw_forum] cp with metals
Dear Nicholas, et al - thanks for pointing out some of the inconsistencies in the CG/CP parser - it's being updated, so hopefully with the new release we'll be in good shape. As always, do let us know of any problems you might find. Best, nicola Paolo Umari wrote: > Dear all, > > these are some minor problems due to the double CG/CP > nature of the parser: > In any case they do not affect the results of calculations > > 1- degauss is effectively used in CG+eDFT > the warning was intended only for CP runs > > 2- this is because CP needs them and the parser is the same >However, emass_cutoff is required in CG for setting >the kinetic energy preconditioning > > 3-Yes > > > The parser will be updated with the new verison of the code, > which should be release during the following week. > This version will contain a much faster CG algorithm for > BO simulation with and without eDFT, which is > already available in the CVS. > > > Paolo > - Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
