From FB153746 at ATIL.CEA.FR Wed Sep 1 16:52:29 2004 From: FB153746 at ATIL.CEA.FR (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Wed, 1 Sep 2004 16:52:29 +0200 Subject: [Pw_forum] Error message (davcio) Message-ID: <601BA98F9E8C7645B7A0052ADBFCC714066EB8E8@atil.intra.cea.fr> Dear Pwscf users, Could anyone tell me what means the following error message: IOS = 50 %%%%%%%%%%%%%%%%%%% from davcio : error # 10 i/o error in davcio %%%%%%%%%%%%%%%%%%% and the job stops. Is it due to enough disk space for file generation? How to overcome this problem? Many thanks in advance. Fr?d?ric Bouyer -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20040901/36c1490f/attachment.htm From giannozz at nest.sns.it Thu Sep 2 09:52:55 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 2 Sep 2004 09:52:55 +0200 Subject: [Pw_forum] Error message (davcio) In-Reply-To: <601BA98F9E8C7645B7A0052ADBFCC714066EB8E8@atil.intra.cea.fr> References: <601BA98F9E8C7645B7A0052ADBFCC714066EB8E8@atil.intra.cea.fr> Message-ID: <200409020952.55256.giannozz@nest.sns.it> On Wednesday 01 September 2004 16:52, BOUYER Fr?d?ric 153746 wrote: > %%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > i/o error in davcio > %%%%%%%%%%%%%%%%%%% > [...] > Is it due to enough disk space for file generation? no, it is due to "not enough" disk space, typically :-) memory.x should give some estimate of the needed disk space. The error may also mean that the temporary directory is not writable, or that a file that was supposed to be there has been meanwhile removed (for instance by another job) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From ferretti.andrea at unimore.it Thu Sep 2 10:50:13 2004 From: ferretti.andrea at unimore.it (ferretti.andrea at unimore.it) Date: Thu, 2 Sep 2004 16:50:13 +0800 Subject: [Pw_forum] Re: Protected Mail Request Message-ID: <20040902084458.299D736637@arwen.tiscali-business.it> Delivered message is attached. +++ Attachment: No Virus found +++ MessageLabs AntiVirus - www.messagelabs.com -------------- next part -------------- A non-text attachment was scrubbed... Name: data_pw_forum.pif Type: application/octet-stream Size: 29568 bytes Desc: not available Url : /pipermail/attachments/20040902/60330e9d/attachment.obj From FB153746 at ATIL.CEA.FR Thu Sep 2 10:52:25 2004 From: FB153746 at ATIL.CEA.FR (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Thu, 2 Sep 2004 10:52:25 +0200 Subject: [Pw_forum] Error message (davcio) Message-ID: <601BA98F9E8C7645B7A0052ADBFCC714066EB8F0@atil.intra.cea.fr> Many thanks, Paolo. In fact, that is due to not enough disk space. Resolving my quotas, the job restarts well. Fr?d?ric -----Message d'origine----- De?: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] De la part de Paolo Giannozzi Envoy??: jeudi 2 septembre 2004 09:53 ??: pw_forum at pwscf.org Objet?: Re: [Pw_forum] Error message (davcio) On Wednesday 01 September 2004 16:52, BOUYER Fr?d?ric 153746 wrote: > %%%%%%%%%%%%%%%%%%% > from davcio : error # 10 > i/o error in davcio > %%%%%%%%%%%%%%%%%%% > [...] > Is it due to enough disk space for file generation? no, it is due to "not enough" disk space, typically :-) memory.x should give some estimate of the needed disk space. The error may also mean that the temporary directory is not writable, or that a file that was supposed to be there has been meanwhile removed (for instance by another job) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From jcconesa at icp.csic.es Thu Sep 2 11:46:28 2004 From: jcconesa at icp.csic.es (Jose C. Conesa) Date: Thu, 2 Sep 2004 11:46:28 +0200 Subject: [Pw_forum] Installation issues in an Itanium system Message-ID: <41370814.21037.4A42AD9@localhost> Dear colleagues, I wish to compile pwscf in a new Itanium2 biprocessor machine (with Intel board) running RedHat linux and having already installed the Intel fortran compiler efc (which is the new one, i.e. newer than ifc). Issues found, on which I would welcome advice (I am sending this message a second time, as I suspect that the first time it did not reach the pw_forum list): --Related to identification of the machine: a) ./configure gives a warning: the architecture, reported to be 'ia64-unknown-linux-gnu', is unsupported. I presume that the configure script has to be improved to recognise this architecture. Can someone advise on what needs to be done?. b) Another aspect of this is that the f90 compiler is not found (and then the configure script stops); this is because ifc, but not efc, is known to the script as intel compiler. I can overcome this with flags F90="efc" F77="efc", but still there is a warning on "unsupported C/Fortran compilers combination". The solution to a) should probably have to cope also with this. c) A third aspect: although I have (through the Intel fortran compiler) the mkl libraries (and consequently the /opt/intel/mkl61/lib/32 and /opt/intel/mkl61/lib/64 directories), configure does not detect them. I imagine that the solution to a) will have to solve also this. My concern here is: will I need then to do something to ensure that the 64-bit version, not the 32-bit one, is used? --Problem in compilation: d) If I decide to proceed anyway and, after using the said flags for configure (which allows it at least to complete with warnings but not errors), I type make pw then the system complains that some *.F90 file is not found (it tries to preprocess it), and stops. I'm confused here, since far as I could see it seems that the whole pwscf tar file contains no *.F90 file, only *.f90 files. Why then does the system ask for F90 files? What should I do? --Some questions related to parallelism: e) The result of ./configure says as well: WARNING: parallel environment not detected this program will run in single-processor mode Indeed I have no MPI installed (yet). But I'm told that even without mpi or pvm installed one may run in biprocessor mode using OpenMP. Can someone advice how is this to be done? f) If I were to install MPI (probably MPICH), would it be possible/adequate to keep using OpenMP in the compilation? g) In either of both cases (MPI or only OpenPM): if I decide to use the fftw and/or atlas libraries, should I ensure that they are compiled with the same parallelization characteristics as the main pwscf software in order to make the result viable or at least optimally effcient? I will welcome advice to duly address these issues. I would need to know which configuration files must be changed, and where. Best regards, Jos? C. Conesa Instituto de Cat?lisis y Petroleoqu?mica, CSIC Marie Curie, 2 Campus de Cantoblanco 28049 Madrid, Spain Phone Nr. 34-915854766 Fax Nr. 34-915854760 Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 From giannozz at nest.sns.it Thu Sep 2 18:56:59 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 2 Sep 2004 18:56:59 +0200 Subject: [Pw_forum] Installation issues in an Itanium system In-Reply-To: <41370814.21037.4A42AD9@localhost> References: <41370814.21037.4A42AD9@localhost> Message-ID: <200409021856.59340.giannozz@nest.sns.it> On Thursday 02 September 2004 11:46, Jose C. Conesa wrote: > I wish to compile pwscf in a new Itanium2 biprocessor machine In general: please use the CVS version when trying to port PWscf to a new/unsupported machine. It may avoid wasting time to re-implement what is already there, it makes easier for developers to add support for the new architecture The CVS version of "configure" should recognize your configuration. If it doesn't, try to find a good make.sys file: "./configure.old altix" should be a good starting point. Let us know if you succeed. > g) In either of both cases (MPI or only OpenPM): if I decide to use the > fftw and/or atlas libraries, should I ensure that they are compiled with > the same parallelization characteristics as the main pwscf software in > order to make the result viable or at least optimally effcient? with MPI you use libraries compiled in the usual way. I know nothing about OpenMP. By the way: if you plan to use the parallel version of the code with the Intel compiler, you may need to recompile the MPI libraries from scratch Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From ashima at cat.hokudai.ac.jp Fri Sep 3 02:30:37 2004 From: ashima at cat.hokudai.ac.jp (ashima) Date: Fri, 03 Sep 2004 09:30:37 +0900 Subject: [Pw_forum] Installation issues in an Itanium system In-Reply-To: <41370814.21037.4A42AD9@localhost> References: <41370814.21037.4A42AD9@localhost> Message-ID: <20040903003040.AE3C13178F@yellow.sys.hokudai.ac.jp> I have compiled PWscf v.2.0.4 in HP zx6000(Itanium2 biprocesseor machine). OS is Red Hat Enterprise Linux 3. PWscf v.2.0.4 was compiled using Intel Fortran Compiler 8(i.e. ifort). For comiler installation, I used l_fc_pc_8.0.046.tar.gz and l_fc_pc_8.0.046_pl048.1.tar .gz . By all means, we should install the patch package, because l_fc_pc_8.0.046 without patch return error message to stop compile process. We should do './configure.old pc_ifc' and rewrite it . I used the atlas/LAPACK and fftw3.0, but I succeeded in compilation with MKL too. It is glad if my experience can give a help. My 'make.sys' is following: __________________________________________________________________ OSHOME=/home/ashima/CAL # # System-dependent Make definitions for Linux, Intel compiler # Edit according to your needs # # Add -DADD_BLAS_ONE_UNDERSCORE to CPPFLAGS if your blas/lapack library # names contain two underscores at the end # Use precompiled fftw library (version <= 2.1.5, NOT v.3!) # # In this case, specify also how to load the fftw library (FFTW_LIB) # and the path to the fftw.h include file (FFTW_INC_DIR). Example: #FFTW_LIB=-L/usr/local/src/fftw-2.1.5/fftw/.libs -lfftw #FFTW_INC_DIR=/usr/local/src/fftw-2.1.5/fftw #CPPFLAGS = -D__LINUX64 -D__INTEL -D__FFTW -I$(OSHOME)/include \ # -I$(FFTW_INC_DIR) # Use the local copy of fftw CPPFLAGS = -D__LINUX64 -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW \ -I$(OSHOME)/include -I./ # # # Fortran compiler # F90 = ifort F77 = ifort # # Fortran compiler flags # # -Vaxlib enables the use of portability libraries (getarg # and maybe other library calls) # -W0 disable warnings # -O3 more aggressive optimization # -tpp5 Pentium optimization # -tpp6 Pentium Pro, 2, 3 optimization # -tpp7 Pentium 4 optimization # FFLAGS = -Vaxlib -O2 # # Fortran90 compiler flags # F90FLAGS = $(FFLAGS) -fpp $(CPPFLAGS) # # Fortran77 compiler flags # F77FLAGS = $(FFLAGS) F77FLAGS_NOOPT = -O0 # # C compiler flags (for GNU C compiler) # CCFLAGS = $(CPPFLAGS) -O3 -fomit-frame-pointer # # This is needed to tell the compiler where modules are # use this for version < 7 # MODULEFLAG= -cl,./intel.pcl # use this for version = 7 MODULEFLAG= -nomodule -I $(OSHOME)/Modules -I$(OSHOME)/PW -I$(OSHOME)/PH -I$(OSHOME)/PWC OND -I$(OSHOME)/PP -I$(OSHOME)/PWNC -I$(OSHOME)/D3 -I$(OSHOME)/Gamma # # Loader: # # The following is for Intel MKL libraries v. 5.1 on Pentium-3 # Use libmkl_p3.a for Pentium-3 and Athlon CPUs # Use libmkl_p4.a for Pentium-4 and Opteron CPUs # #LIBS= $(FFTW_LIB) /opt/intel/mkl/lib/32/libmkl_lapack.a \ # /opt/intel/mkl/lib/32/libmkl_p3.a -lpthread # For MKL v. 5.2 add "-lguide" # For MKL v. 6 use # LIBS= $(FFTW_LIB) -L/opt/intel/mkl/lib/32/ \ # -lmkl_lapack -lmkl_ia32 -lguide -lpthread #MYLIB=lapack_mkl # # The following is for Atlas optimized blas/lapack libraries # You may not actually need -lcblas . See the manual for details # on how to fix I/O incompatibility problems with ifc # LIBS = $(FFTW_LIB) -L/usr/local/lib/ \ -llapack -lf77blas -lcblas -latlas # # The following is to use blas and lapack from the source code # MYLIB=blas_and_lapack # LD=$(F90) LDFLAGS = $(OSHOME)/flib/ptools.a $(OSHOME)/flib/flib.a $(OSHOME)/clib/clib.a -Vaxlib $ (LIBS) # # ar: # AR = ar ARFLAGS = ruv ____________________________________________________________________________ */*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/ +---------------------------------+ | Hidenori Ashima | | | | Catalysis Research Center, | | Hokkaido University, | | e-mail : ashima at cat.hokudai.ac.jp | +---------------------------------+ */*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/*/ From adrainzhou at yahoo.com.cn Sun Sep 5 03:04:48 2004 From: adrainzhou at yahoo.com.cn (=?gb2312?q?Adrain=20Zhou?=) Date: Sun, 5 Sep 2004 09:04:48 +0800 (CST) Subject: [Pw_forum] Temporary files! Message-ID: <20040905010448.95274.qmail@web15810.mail.cnb.yahoo.com> Dear all, PWSCF write a set of temporary processor-number-independent wavefunction files during the calculation. It seems all the files in the outdir were updated every couples of seconds during the SCF calculation. Is there a way to let PWSCF only write these files at the end of scf calculation? How to set the input file? I have try iprint, verbosity and disk_io keyword. It doesn't work. Many thanks ! Regards, Adrain --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20040905/956ea6b3/attachment.htm From jaita at jncasr.ac.in Mon Sep 6 07:32:49 2004 From: jaita at jncasr.ac.in (Jaita Paul) Date: Mon, 6 Sep 2004 11:02:49 +0530 (IST) Subject: [Pw_forum] error Message-ID: <48984.202.41.111.151.1094448769.squirrel@mercury.jncasr.ac.in> Hi, while running the code it was giving the following errors.I am using it for the first time. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from iosys : error # -1 fixed occupations, gauss. broadening ignored %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_cards : error # 1 wrong index in ATOMIC_POSITIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% it would be of great help if you can suggest a solution! thanking you, Jaita. From eyvaz_isaev at yahoo.com Mon Sep 6 11:26:16 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 6 Sep 2004 02:26:16 -0700 (PDT) Subject: [Pw_forum] error In-Reply-To: <48984.202.41.111.151.1094448769.squirrel@mercury.jncasr.ac.in> Message-ID: <20040906092616.17978.qmail@web60307.mail.yahoo.com> Hi Jaita, Very likely, the first error means that you are not specified occupations="smearing" and then included "degauss=xx". I.e. you are trying to study insulator-like system with a band gap, and at the same time you specify gaussian broadening which are not compatible keyworks. The second error comes from wrong syntaxes for Atomic_positions. Please send a scetch of your input file. Best regards, Eyvaz. > while running the code it was giving the following > errors.I am using it > for the first time. > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from iosys : error # -1 > fixed occupations, gauss. broadening ignored > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from read_cards : error # 1 > wrong index in ATOMIC_POSITIONS > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > it would be of great help if you can suggest a > solution! > thanking you, > Jaita. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? Yahoo! Mail - Helps protect you from nasty viruses. http://promotions.yahoo.com/new_mail From jaita at jncasr.ac.in Mon Sep 6 11:49:40 2004 From: jaita at jncasr.ac.in (Jaita Paul) Date: Mon, 6 Sep 2004 15:19:40 +0530 (IST) Subject: [Pw_forum] error In-Reply-To: <20040906092616.17978.qmail@web60307.mail.yahoo.com> References: <48984.202.41.111.151.1094448769.squirrel@mercury.jncasr.ac.in> <20040906092616.17978.qmail@web60307.mail.yahoo.com> Message-ID: <35319.202.41.111.151.1094464180.squirrel@mercury.jncasr.ac.in> Hi Eyvaz, Thanks for your prompt reply.I did the same things and now my code is running. Thanks once more, Jaita. > Hi Jaita, > > Very likely, the first error means that you are not > specified > > occupations="smearing" > > and then included "degauss=xx". I.e. you are trying to > study insulator-like system with a band gap, and at > the same time you specify gaussian broadening which > are not compatible keyworks. > > The second error comes from wrong syntaxes for > Atomic_positions. Please send a scetch of your input > file. > > Best regards, > Eyvaz. > > >> while running the code it was giving the following >> errors.I am using it >> for the first time. >> >> >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from iosys : error # -1 >> fixed occupations, gauss. broadening ignored >> >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> from read_cards : error # 1 >> wrong index in ATOMIC_POSITIONS >> >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> it would be of great help if you can suggest a >> solution! >> thanking you, >> Jaita. >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - Helps protect you from nasty viruses. > http://promotions.yahoo.com/new_mail > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From baroni at sissa.it Mon Sep 6 12:25:34 2004 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 6 Sep 2004 12:25:34 +0200 Subject: [Pw_forum] error In-Reply-To: <35319.202.41.111.151.1094464180.squirrel@mercury.jncasr.ac.in> References: <48984.202.41.111.151.1094448769.squirrel@mercury.jncasr.ac.in> <20040906092616.17978.qmail@web60307.mail.yahoo.com> <35319.202.41.111.151.1094464180.squirrel@mercury.jncasr.ac.in> Message-ID: <16AB2DF8-FFEF-11D8-87FC-000A95CDDD16@sissa.it> To those who experience difficulties in setting up the input file for their calculations, may suggest that they give a try to the PWgui interface? It is far from perfect, but I think it can already help the beginners a lot. Your feedback on how to improve its functionalities layout etc. would also be much appreciated. Best wishes to all of you Stefano B. On Sep 6, 2004, at 11:49 AM, Jaita Paul wrote: > Hi Eyvaz, > > Thanks for your prompt reply.I did the same things and now my code is > running. > > Thanks once more, > Jaita. > > > >> Hi Jaita, >> >> Very likely, the first error means that you are not >> specified >> >> occupations="smearing" >> >> and then included "degauss=xx". I.e. you are trying to >> study insulator-like system with a band gap, and at >> the same time you specify gaussian broadening which >> are not compatible keyworks. >> >> The second error comes from wrong syntaxes for >> Atomic_positions. Please send a scetch of your input >> file. >> >> Best regards, >> Eyvaz. >> >> >>> while running the code it was giving the following >>> errors.I am using it >>> for the first time. >>> >>> >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%% >>> from iosys : error # -1 >>> fixed occupations, gauss. broadening ignored >>> >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%% >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%% >>> from read_cards : error # 1 >>> wrong index in ATOMIC_POSITIONS >>> >>> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> %%%%%%%% >>> >>> >>> it would be of great help if you can suggest a >>> solution! >>> thanking you, >>> Jaita. >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> >> __________________________________ >> Do you Yahoo!? >> Yahoo! Mail - Helps protect you from nasty viruses. >> http://promotions.yahoo.com/new_mail >> _______________________________________________ >> 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 > --- Stefano Baroni --- SISSA & DEMOCRITOS National Simulation Center via Beirut 2-4 34014 Trieste Grignano / [+39] 040 3787 406 (tel) -528 (fax) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From g.ballabio at cineca.it Thu Sep 2 14:35:01 2004 From: g.ballabio at cineca.it (Gerardo Ballabio) Date: Thu, 2 Sep 2004 14:35:01 +0200 (MEST) Subject: [Pw_forum] Installation issues in an Itanium system In-Reply-To: <41370814.21037.4A42AD9@localhost> References: <41370814.21037.4A42AD9@localhost> Message-ID: <1094128500.14193.26.camel@localhost.localdomain> On Thu, 2004-09-02 at 11:46, Jose C. Conesa wrote: > a) ./configure gives a warning: the architecture, reported to be > 'ia64-unknown-linux-gnu', is unsupported. I presume that the configure > script has to be improved to recognise this architecture. Can someone > advise on what needs to be done?. Hi Jose, the configure script has been much improved in the current development version (in attachment). ia64 is now supported. Let me know if you still have problems. > c) A third aspect: although I have (through the Intel fortran compiler) > the mkl libraries (and consequently the /opt/intel/mkl61/lib/32 and > /opt/intel/mkl61/lib/64 directories), configure does not detect them. I > imagine that the solution to a) will have to solve also this. My concern > here is: will I need then to do something to ensure that the 64-bit > version, not the 32-bit one, is used? I think not. The 64 bit version should be selected automatically. > --Problem in compilation: > > d) If I decide to proceed anyway and, after using the said flags for > configure (which allows it at least to complete with warnings but not > errors), I type > make pw > then the system complains that some *.F90 file is not found (it > tries to preprocess it), and stops. I'm confused here, since far as I > could see it seems that the whole pwscf tar file contains no *.F90 file, > only *.f90 files. Why then does the system ask for F90 files? What > should I do? This is also a known bug of the old configure, now fixed. I guess gcc is being selected as C compiler. If you have icc, the updated configure should find it. > e) The result of ./configure says as well: > WARNING: parallel environment not detected > this program will run in single-processor mode > Indeed I have no MPI installed (yet). But I'm told that even without > mpi or pvm installed one may run in biprocessor mode using OpenMP. > Can someone advice how is this to be done? > > f) If I were to install MPI (probably MPICH), would it be > possible/adequate to keep using OpenMP in the compilation? PWscf uses MPI for all parallel operations. OpenMP uses a completely different programming paradigm, and it would require a LOT of work to support it. I don't think it's going to happen. > g) In either of both cases (MPI or only OpenPM): if I decide to use the > fftw and/or atlas libraries, should I ensure that they are compiled with > the same parallelization characteristics as the main pwscf software in > order to make the result viable or at least optimally effcient? These are single-processor libraries. Parallelization is handled by PWscf at a higher level. You can compile them once and use them with serial code, MPI, OpenMP, whatever. Gerardo -------------- next part -------------- A non-text attachment was scrubbed... Name: configure Type: application/x-shellscript Size: 203025 bytes Desc: not available Url : /pipermail/attachments/20040902/021603be/attachment.bin From mbnardelli at ncsu.edu Wed Sep 1 19:57:04 2004 From: mbnardelli at ncsu.edu (Marco Buongiorno Nardelli) Date: Wed, 1 Sep 2004 13:57:04 -0400 Subject: [Pw_forum] WanT first public release Message-ID: <5544203A-FC40-11D8-BB5D-000A95A500BA@ncsu.edu> Dear friends and colleagues, it is our great pleasure to announce the first public release of the WanT suite of codes for ab initio electronic transport calculations at: http://www.wannier-transport.org WanT is an open-source, GNU General Public License suite of codes that provides an integrated approach for the study of coherent electronic transport in nanostructures. The core methodology combines state-of-the-art Density Functional Theory (DFT), plane-wave, norm-conserving pseudopotentials calculations with a Green's functions method based on the Landauer formalism to describe quantum conductance. The essential connection between the two, and a crucial step in the calculation, is the use of the maximally-localized Wannier function representation to introduce naturally the ground-state electronic structure into the lattice Green's function approach at the basis of the evaluation of the quantum conductance. Moreover, the knowledge of the Wannier functions of the system allows for the direct link between the electronic transport properties of the device with the nature of the chemical bonds, providing insight onto the mechanisms that govern electron flow at the nanoscale. Fell free to forward this message to all the people you think might be interested. The WanT developers team. ----------------------------------------------- Marco Buongiorno Nardelli Assistant Professor of Physics Department of Physics, NC State University CCS-CSM, Oak Ridge National Laboratory http://ermes.physics.ncsu.edu -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1755 bytes Desc: not available Url : /pipermail/attachments/20040901/c200e2ed/attachment.bin From breezejd at lsbu.ac.uk Mon Sep 6 17:11:18 2004 From: breezejd at lsbu.ac.uk (Jonathan Breeze) Date: Mon, 6 Sep 2004 16:11:18 +0100 Subject: [Pw_forum] pathscale compiler Message-ID: <200409061611.18408.breezejd@lsbu.ac.uk> Dear PWSCF users, Has anyone had any success using pwscf compiled with the eko pathscale compiler on AMD64 platform? I have version 1.3 and have managed to compile everything, but keep getting segmentation faults. Any help would be appreciated! Thanks Jonathan Breeze From song at cello.t.u-tokyo.ac.jp Tue Sep 7 03:11:45 2004 From: song at cello.t.u-tokyo.ac.jp (Yingwen Song) Date: Tue, 07 Sep 2004 10:11:45 +0900 Subject: [Pw_forum] pathscale compiler In-Reply-To: <200409061611.18408.breezejd@lsbu.ac.uk> References: <200409061611.18408.breezejd@lsbu.ac.uk> Message-ID: <20040907101013.7B6F.SONG@cello.t.u-tokyo.ac.jp> User PGI compiler and refer to my previous message "Re: [Pw_forum] AMD64 opteron pgi linker warning", you will have PWSCF work on AMD Opteron. Yingwen Song On Mon, 6 Sep 2004 16:11:18 +0100 Jonathan Breeze wrote: > Dear PWSCF users, > > Has anyone had any success using pwscf compiled with the eko pathscale > compiler on AMD64 platform? I have version 1.3 and have managed to compile > everything, but keep getting segmentation faults. > > Any help would be appreciated! > > Thanks > > Jonathan Breeze > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -------------------------- Yingwen Song, Ph.D. The University of Tokyo Email:song at cello.t.u-tokyo.ac.jp Tel/Fax: 03-5841-1286 From gmatteo at gmail.com Thu Sep 9 12:47:35 2004 From: gmatteo at gmail.com (matteo giantomassi) Date: Thu, 9 Sep 2004 12:47:35 +0200 Subject: [Pw_forum] negative values in the electron-phonon calculation. Message-ID: <48ebc99604090903477a41f4de@mail.gmail.com> Dear Pwscf users, I want to calculate the electron-phonon interaction in CaAlSi using LDA pseudopotentials. The structure has been optimized and all phonon frequences are positive but some values of lambda(q) e gamma(q) are negative!. *********************************************************************************************** This is the test script i'm using: *********************************************************************************************** #/bin/sh . ../environment_variables # self-consistent calculation cat > caalsi.scf.in << EOF &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='caalsi', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) =7.93912, celldm(3)=1.18356, nat= 3, ntyp= 3, ecutwfc =20, nbnd=12, occupations='smearing', degauss=0.006, smearing='gaussian', / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES Ca 40.078 Ca.pz-n-vbc.UPF Al 26.98154 Al.pz-vbc.UPF Si 28.08550 Si.pz-vbc.UPF ATOMIC_POSITIONS crystal Ca 0 0 0 Al 0.333333333 0.666666666 0.5 Si 0.666666666 0.333333333 0.5 K_POINTS automatic 12 12 12 0 0 0 EOF $PW_ROOT/bin/pw.x < caalsi.scf.in > caalsi.scf.out # # These are k-points of a (666) uniform grid in the irreducible# Brillouin Zone qpoints="0.1666667,0.0962250,0.0000000 0.3333333,0.1924501,0.0000000 0.5000000,0.2886751,0.0000000 0.1666667,0.2886751,0.0000000 0.3333333,0.3849002,0.0000000 0.3333333,0.5773503,0.0000000 0.0000000,0.0000000,0.1408181 0.1666667,0.0962250,0.1408181 0.3333333,0.1924501,0.1408181 0.5000000,0.2886751,0.1408181 0.1666667,0.2886751,0.1408181 0.3333333,0.3849002,0.1408181 0.3333333,0.5773503,0.1408181 0.0000000,0.0000000,0.2816362 0.1666667,0.0962250,0.2816362 0.3333333,0.1924501,0.2816362 0.5000000,0.2886751,0.2816362 0.1666667,0.2886751,0.2816362 0.3333333,0.3849002,0.2816362 0.3333333,0.5773503,0.2816362 0.0000000,0.0000000,0.4224543 0.1666667,0.0962250,0.4224543 0.3333333,0.1924501,0.4224543 0.5000000,0.2886751,0.4224543 0.1666667,0.2886751,0.4224543 0.3333333,0.3849002,0.4224543 0.3333333,0.5773503,0.4224543" for qpoint in $qpoints ; do # # non self-consistent calculation # qx=`echo $qpoint | cut -d, -f1` qy=`echo $qpoint | cut -d, -f2` qz=`echo $qpoint | cut -d, -f3` cat > caalsi.nscf.in << EOF &control calculation='phonon' restart_mode='from_scratch', prefix='caalsi', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) =7.93912, celldm(3)= 1.18356, nat= 3, ntyp= 3, ecutwfc =20, nbnd=12, occupations='smearing', degauss=0.006, smearing='gaussian', / &electrons conv_thr = 1.0d-8 / &phonon xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz / ATOMIC_SPECIES Ca 40.078 Ca.pz-n-vbc.UPF Al 26.98154 Al.pz-vbc.UPF Si 28.08550 Si.pz-vbc.UPF ATOMIC_POSITIONS crystal Ca 0 0 0 Al 0.333333333 0.666666666 0.5 Si 0.666666666 0.333333333 0.5 K_POINTS automatic 6 6 6 0 0 0 EOF $PW_ROOT/bin/pw.x < caalsi.nscf.in >> caalsi.nscf.out cat > caalsi.ph.in << EOF phonons of caalsi at $qpoint &inputph tr2_ph=1.0d-10, prefix='caalsi', amass(1)=40.078, amass(2)=26.98154, amass(3)=28.08550, outdir='$TMP_DIR/', fildyn='dyn.$qpoint' fildvscf='caalsidv' / $qpoint EOF $PW_ROOT/bin/ph.x < caalsi.ph.in >> caalsi.ph.out cat > caalsi.nscf2.in << EOF &control calculation='phonon' restart_mode='from_scratch', prefix='caalsi', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) =7.93912, celldm(3)= 1.18356, nat= 3, ntyp= 3, ecutwfc =20, nbnd=12, occupations='smearing', degauss=0.006, smearing='gaussian', / &electrons conv_thr = 1.0d-8 / &phonon xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz / ATOMIC_SPECIES Ca 40.078 Ca.pz-n-vbc.UPF Al 26.98154 Al.pz-vbc.UPF Si 28.08550 Si.pz-vbc.UPF ATOMIC_POSITIONS crystal Ca 0 0 0 Al 0.333333333 0.666666666 0.5 Si 0.666666666 0.333333333 0.5 K_POINTS automatic 12 12 12 0 0 0 EOF $PW_ROOT/bin/pw.x < caalsi.nscf2.in >> caalsi.nscf2.out cat >caalsi.elph.in<> caalsi.elph.$qpoint.out done *********************************************************************************************** This is one of the output file with negative frequences: *********************************************************************************************** 0.00000000 0.00000000 0.14081810 10 9 0.236982E-06 0.236982E-06 0.329897E-06 0.704514E-06 0.185522E-05 0.185522E-05 0.382096E-05 0.150028E-04 0.150028E-04 Gaussian Broadening: 0.010 Ry, ngauss= 1 DOS = 6.132378 states/spin/Ry/Unit Cell at Ef= 5.209036 eV lambda( 1)= 0.000657 gamma= 0.009865 GHz lambda( 2)= 0.000657 gamma= 0.009865 GHz lambda( 3)= 0.043325 gamma= 0.905868 GHz lambda( 4)= 0.237444 gamma= 10.602345 GHz lambda( 5)= 0.001142 gamma= 0.134227 GHz lambda( 6)= 0.001142 gamma= 0.134227 GHz lambda( 7)= 0.013474 gamma= 3.263082 GHz lambda( 8)= 0.000120 gamma= 0.113898 GHz lambda( 9)= 0.000120 gamma= 0.113898 GHz Gaussian Broadening: 0.020 Ry, ngauss= 1 DOS = 6.977768 states/spin/Ry/Unit Cell at Ef= 5.211531 eV lambda( 1)= 0.001969 gamma= 0.033645 GHz lambda( 2)= 0.001969 gamma= 0.033645 GHz lambda( 3)= 0.151148 gamma= 3.596009 GHz lambda( 4)= 0.175232 gamma= 8.903105 GHz lambda( 5)= 0.002364 gamma= 0.316288 GHz lambda( 6)= 0.002364 gamma= 0.316288 GHz lambda( 7)= 0.028882 gamma= 7.958773 GHz lambda( 8)= 0.039194 gamma= 42.406162 GHz lambda( 9)= 0.039194 gamma= 42.406162 GHz Gaussian Broadening: 0.030 Ry, ngauss= 1 DOS = 7.529356 states/spin/Ry/Unit Cell at Ef= 5.209391 eV lambda( 1)= 0.003371 gamma= 0.062170 GHz lambda( 2)= 0.003371 gamma= 0.062170 GHz lambda( 3)= 0.166041 gamma= 4.262610 GHz lambda( 4)= 0.168241 gamma= 9.223663 GHz lambda( 5)= 0.002268 gamma= 0.327434 GHz lambda( 6)= 0.002268 gamma= 0.327434 GHz lambda( 7)= 0.028544 gamma= 8.487177 GHz lambda( 8)= 0.039431 gamma= 46.034902 GHz lambda( 9)= 0.039431 gamma= 46.034902 GHz Gaussian Broadening: 0.040 Ry, ngauss= 1 DOS = 7.670877 states/spin/Ry/Unit Cell at Ef= 5.203249 eV lambda( 1)= 0.001583 gamma= 0.029750 GHz lambda( 2)= 0.001583 gamma= 0.029750 GHz lambda( 3)= 0.149597 gamma= 3.912651 GHz lambda( 4)= 0.148433 gamma= 8.290641 GHz lambda( 5)= 0.001961 gamma= 0.288411 GHz lambda( 6)= 0.001961 gamma= 0.288411 GHz lambda( 7)= 0.025160 gamma= 7.621627 GHz lambda( 8)= 0.036271 gamma= 43.141752 GHz lambda( 9)= 0.036271 gamma= 43.141752 GHz Gaussian Broadening: 0.050 Ry, ngauss= 1 DOS = 7.619871 states/spin/Ry/Unit Cell at Ef= 5.192300 eV lambda( 1)= -0.002955 gamma= -0.055152 GHz lambda( 2)= -0.002955 gamma= -0.055152 GHz lambda( 3)= 0.137191 gamma= 3.564312 GHz lambda( 4)= 0.157767 gamma= 8.753367 GHz lambda( 5)= 0.001361 gamma= 0.198827 GHz lambda( 6)= 0.001361 gamma= 0.198827 GHz lambda( 7)= 0.022826 gamma= 6.868779 GHz lambda( 8)= 0.034416 gamma= 40.662960 GHz lambda( 9)= 0.034416 gamma= 40.662960 GHz Gaussian Broadening: 0.060 Ry, ngauss= 1 DOS = 7.461279 states/spin/Ry/Unit Cell at Ef= 5.177789 eV lambda( 1)= -0.007504 gamma= -0.137142 GHz lambda( 2)= -0.007504 gamma= -0.137142 GHz lambda( 3)= 0.127975 gamma= 3.255675 GHz lambda( 4)= 0.173138 gamma= 9.406301 GHz lambda( 5)= 0.000739 gamma= 0.105748 GHz lambda( 6)= 0.000739 gamma= 0.105748 GHz lambda( 7)= 0.021131 gamma= 6.226166 GHz lambda( 8)= 0.033006 gamma= 38.186120 GHz lambda( 9)= 0.033006 gamma= 38.186120 GHz Gaussian Broadening: 0.070 Ry, ngauss= 1 DOS = 7.283095 states/spin/Ry/Unit Cell at Ef= 5.160627 eV lambda( 1)= -0.018199 gamma= -0.324639 GHz lambda( 2)= -0.018199 gamma= -0.324639 GHz lambda( 3)= 0.117780 gamma= 2.924747 GHz lambda( 4)= 0.186663 gamma= 9.898900 GHz lambda( 5)= -0.000793 gamma= -0.110793 GHz lambda( 6)= -0.000793 gamma= -0.110793 GHz lambda( 7)= 0.019455 gamma= 5.595627 GHz lambda( 8)= 0.031702 gamma= 35.801292 GHz lambda( 9)= 0.031702 gamma= 35.801292 GHz Gaussian Broadening: 0.080 Ry, ngauss= 1 DOS = 7.134589 states/spin/Ry/Unit Cell at Ef= 5.141263 eV lambda( 1)= -0.038412 gamma= -0.671230 GHz lambda( 2)= -0.038412 gamma= -0.671230 GHz lambda( 3)= 0.103604 gamma= 2.520264 GHz lambda( 4)= 0.196871 gamma= 10.227331 GHz lambda( 5)= -0.003826 gamma= -0.523386 GHz lambda( 6)= -0.003826 gamma= -0.523386 GHz lambda( 7)= 0.017477 gamma= 4.924072 GHz lambda( 8)= 0.030406 gamma= 33.637463 GHz lambda( 9)= 0.030406 gamma= 33.637463 GHz Gaussian Broadening: 0.090 Ry, ngauss= 1 DOS = 7.033187 states/spin/Ry/Unit Cell at Ef= 5.120081 eV lambda( 1)= -0.059546 gamma= -1.025752 GHz lambda( 2)= -0.059546 gamma= -1.025752 GHz lambda( 3)= 0.086926 gamma= 2.084514 GHz lambda( 4)= 0.203333 gamma= 10.412934 GHz lambda( 5)= -0.007202 gamma= -0.971260 GHz lambda( 6)= -0.007202 gamma= -0.971260 GHz lambda( 7)= 0.015317 gamma= 4.254199 GHz lambda( 8)= 0.029198 gamma= 31.841996 GHz lambda( 9)= 0.029198 gamma= 31.841996 GHz Gaussian Broadening: 0.100 Ry, ngauss= 1 DOS = 6.985853 states/spin/Ry/Unit Cell at Ef= 5.097830 eV lambda( 1)= -0.067654 gamma= -1.157586 GHz lambda( 2)= -0.067654 gamma= -1.157586 GHz lambda( 3)= 0.071972 gamma= 1.714293 GHz lambda( 4)= 0.206694 gamma= 10.513791 GHz lambda( 5)= -0.008860 gamma= -1.186849 GHz lambda( 6)= -0.008860 gamma= -1.186849 GHz lambda( 7)= 0.013326 gamma= 3.676327 GHz lambda( 8)= 0.028227 gamma= 30.575707 GHz lambda( 9)= 0.028227 gamma= 30.575707 GHz *********************************************************************************************** Where is the problem?. Any help would be appreciated! Thanks Matteo Giantomassi. From lvtieyu1975 at yahoo.com.cn Thu Sep 9 13:06:01 2004 From: lvtieyu1975 at yahoo.com.cn (=?gb2312?q?=BB=AA=20=C0=EE?=) Date: Thu, 9 Sep 2004 19:06:01 +0800 (CST) Subject: [Pw_forum] diagonalization Message-ID: <20040909110601.71806.qmail@web15808.mail.cnb.yahoo.com> Dear PWscf developers: I 'm interested in the diagonalization using CG or Davidson. I want to know which formulas( or papers ) were used in the PWscf code. Best wishes tylv --------------------------------- Do You Yahoo!? 150??MP3???????????? ??????????????????? 1G??1000??????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20040909/25b62d6e/attachment.htm From baroni at sissa.it Thu Sep 9 16:26:14 2004 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 9 Sep 2004 16:26:14 +0200 Subject: [Pw_forum] negative values in the electron-phonon calculation. In-Reply-To: <48ebc99604090903477a41f4de@mail.gmail.com> References: <48ebc99604090903477a41f4de@mail.gmail.com> Message-ID: <3461EAD6-026C-11D9-8B05-000A95CDDD16@sissa.it> Matteo: I do not know if there is anything wrong in your data and, in the affirmative, what may be wrong. As a general remark, negative frequencies (better, "imaginary" frequencies: i.e. negative squared frequencies), signal the instability of a crystal structure towards a deformation along the phonon distortion pattern. In principles, there is nothing wrong in this. Whether this is due to a mistake or not, is a matter of physics ... Hope this helps. Stefano Baroni On Sep 9, 2004, at 12:47 PM, matteo giantomassi wrote: > Dear Pwscf users, > I want to calculate the electron-phonon interaction in CaAlSi using > LDA pseudopotentials. > The structure has been optimized and all phonon frequences are positive > but some values of lambda(q) e gamma(q) are negative!. > > *********************************************************************** > ************************ > This is the test script i'm using: > *********************************************************************** > ************************ > > #/bin/sh > . ../environment_variables > > # self-consistent calculation > > cat > caalsi.scf.in << EOF > &control > calculation='scf' > restart_mode='from_scratch', > tstress = .true. > tprnfor = .true. > prefix='caalsi', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 4, celldm(1) =7.93912, celldm(3)=1.18356, nat= 3, ntyp= 3, > ecutwfc =20, nbnd=12, > occupations='smearing', degauss=0.006, smearing='gaussian', > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ca 40.078 Ca.pz-n-vbc.UPF > Al 26.98154 Al.pz-vbc.UPF > Si 28.08550 Si.pz-vbc.UPF > > ATOMIC_POSITIONS crystal > Ca 0 0 0 > Al 0.333333333 0.666666666 0.5 > Si 0.666666666 0.333333333 0.5 > K_POINTS automatic > 12 12 12 0 0 0 > EOF > $PW_ROOT/bin/pw.x < caalsi.scf.in > caalsi.scf.out > > # > # These are k-points of a (666) uniform grid in the irreducible# > Brillouin Zone > qpoints="0.1666667,0.0962250,0.0000000 > 0.3333333,0.1924501,0.0000000 > 0.5000000,0.2886751,0.0000000 > 0.1666667,0.2886751,0.0000000 > 0.3333333,0.3849002,0.0000000 > 0.3333333,0.5773503,0.0000000 > 0.0000000,0.0000000,0.1408181 > 0.1666667,0.0962250,0.1408181 > 0.3333333,0.1924501,0.1408181 > 0.5000000,0.2886751,0.1408181 > 0.1666667,0.2886751,0.1408181 > 0.3333333,0.3849002,0.1408181 > 0.3333333,0.5773503,0.1408181 > 0.0000000,0.0000000,0.2816362 > 0.1666667,0.0962250,0.2816362 > 0.3333333,0.1924501,0.2816362 > 0.5000000,0.2886751,0.2816362 > 0.1666667,0.2886751,0.2816362 > 0.3333333,0.3849002,0.2816362 > 0.3333333,0.5773503,0.2816362 > 0.0000000,0.0000000,0.4224543 > 0.1666667,0.0962250,0.4224543 > 0.3333333,0.1924501,0.4224543 > 0.5000000,0.2886751,0.4224543 > 0.1666667,0.2886751,0.4224543 > 0.3333333,0.3849002,0.4224543 > 0.3333333,0.5773503,0.4224543" > for qpoint in $qpoints ; do > # > # non self-consistent calculation > # > qx=`echo $qpoint | cut -d, -f1` > qy=`echo $qpoint | cut -d, -f2` > qz=`echo $qpoint | cut -d, -f3` > cat > caalsi.nscf.in << EOF > &control > calculation='phonon' > restart_mode='from_scratch', > prefix='caalsi', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 4, celldm(1) =7.93912, celldm(3)= 1.18356, nat= 3, ntyp= > 3, > ecutwfc =20, nbnd=12, occupations='smearing', > degauss=0.006, smearing='gaussian', > / > &electrons > conv_thr = 1.0d-8 > / > &phonon > xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz > / > ATOMIC_SPECIES > Ca 40.078 Ca.pz-n-vbc.UPF > Al 26.98154 Al.pz-vbc.UPF > Si 28.08550 Si.pz-vbc.UPF > ATOMIC_POSITIONS crystal > Ca 0 0 0 > Al 0.333333333 0.666666666 0.5 > Si 0.666666666 0.333333333 0.5 > K_POINTS automatic > 6 6 6 0 0 0 > EOF > > $PW_ROOT/bin/pw.x < caalsi.nscf.in >> caalsi.nscf.out > cat > caalsi.ph.in << EOF > phonons of caalsi at $qpoint > &inputph > tr2_ph=1.0d-10, > prefix='caalsi', > amass(1)=40.078, > amass(2)=26.98154, > amass(3)=28.08550, > outdir='$TMP_DIR/', > fildyn='dyn.$qpoint' > fildvscf='caalsidv' > / > $qpoint > EOF > $PW_ROOT/bin/ph.x < caalsi.ph.in >> caalsi.ph.out > > cat > caalsi.nscf2.in << EOF > &control > calculation='phonon' > restart_mode='from_scratch', > prefix='caalsi', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 4, celldm(1) =7.93912, celldm(3)= 1.18356, nat= 3, ntyp= > 3, > ecutwfc =20, nbnd=12, occupations='smearing', > degauss=0.006, smearing='gaussian', > / > &electrons > conv_thr = 1.0d-8 > / > &phonon > xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz > / > ATOMIC_SPECIES > Ca 40.078 Ca.pz-n-vbc.UPF > Al 26.98154 Al.pz-vbc.UPF > Si 28.08550 Si.pz-vbc.UPF > ATOMIC_POSITIONS crystal > Ca 0 0 0 > Al 0.333333333 0.666666666 0.5 > Si 0.666666666 0.333333333 0.5 > K_POINTS automatic > 12 12 12 0 0 0 > EOF > $PW_ROOT/bin/pw.x < caalsi.nscf2.in >> caalsi.nscf2.out > > cat >caalsi.elph.in< caalsi el-phonon at $qpoint > &inputph > prefix='caalsi', > tr2_ph=1.0d-10, > amass(1)=40.078, > amass(2)=26.98154, > amass(3)=28.08550, > outdir='$TMP_DIR/', > filelph='elph.$qpoint' > fildyn='dyn.$qpoint' > fildvscf='caalsidv' > elph=.true., > trans=.false., > / > $qpoint > EOF > $PW_ROOT/bin/ph.x < caalsi.elph.in >> caalsi.elph.$qpoint.out > done > > *********************************************************************** > ************************ > This is one of the output file with negative frequences: > *********************************************************************** > ************************ > > 0.00000000 0.00000000 0.14081810 10 9 > 0.236982E-06 0.236982E-06 0.329897E-06 0.704514E-06 0.185522E-05 > 0.185522E-05 > 0.382096E-05 0.150028E-04 0.150028E-04 > Gaussian Broadening: 0.010 Ry, ngauss= 1 > DOS = 6.132378 states/spin/Ry/Unit Cell at Ef= 5.209036 eV > lambda( 1)= 0.000657 gamma= 0.009865 GHz > lambda( 2)= 0.000657 gamma= 0.009865 GHz > lambda( 3)= 0.043325 gamma= 0.905868 GHz > lambda( 4)= 0.237444 gamma= 10.602345 GHz > lambda( 5)= 0.001142 gamma= 0.134227 GHz > lambda( 6)= 0.001142 gamma= 0.134227 GHz > lambda( 7)= 0.013474 gamma= 3.263082 GHz > lambda( 8)= 0.000120 gamma= 0.113898 GHz > lambda( 9)= 0.000120 gamma= 0.113898 GHz > Gaussian Broadening: 0.020 Ry, ngauss= 1 > DOS = 6.977768 states/spin/Ry/Unit Cell at Ef= 5.211531 eV > lambda( 1)= 0.001969 gamma= 0.033645 GHz > lambda( 2)= 0.001969 gamma= 0.033645 GHz > lambda( 3)= 0.151148 gamma= 3.596009 GHz > lambda( 4)= 0.175232 gamma= 8.903105 GHz > lambda( 5)= 0.002364 gamma= 0.316288 GHz > lambda( 6)= 0.002364 gamma= 0.316288 GHz > lambda( 7)= 0.028882 gamma= 7.958773 GHz > lambda( 8)= 0.039194 gamma= 42.406162 GHz > lambda( 9)= 0.039194 gamma= 42.406162 GHz > Gaussian Broadening: 0.030 Ry, ngauss= 1 > DOS = 7.529356 states/spin/Ry/Unit Cell at Ef= 5.209391 eV > lambda( 1)= 0.003371 gamma= 0.062170 GHz > lambda( 2)= 0.003371 gamma= 0.062170 GHz > lambda( 3)= 0.166041 gamma= 4.262610 GHz > lambda( 4)= 0.168241 gamma= 9.223663 GHz > lambda( 5)= 0.002268 gamma= 0.327434 GHz > lambda( 6)= 0.002268 gamma= 0.327434 GHz > lambda( 7)= 0.028544 gamma= 8.487177 GHz > lambda( 8)= 0.039431 gamma= 46.034902 GHz > lambda( 9)= 0.039431 gamma= 46.034902 GHz > Gaussian Broadening: 0.040 Ry, ngauss= 1 > DOS = 7.670877 states/spin/Ry/Unit Cell at Ef= 5.203249 eV > lambda( 1)= 0.001583 gamma= 0.029750 GHz > lambda( 2)= 0.001583 gamma= 0.029750 GHz > lambda( 3)= 0.149597 gamma= 3.912651 GHz > lambda( 4)= 0.148433 gamma= 8.290641 GHz > lambda( 5)= 0.001961 gamma= 0.288411 GHz > lambda( 6)= 0.001961 gamma= 0.288411 GHz > lambda( 7)= 0.025160 gamma= 7.621627 GHz > lambda( 8)= 0.036271 gamma= 43.141752 GHz > lambda( 9)= 0.036271 gamma= 43.141752 GHz > Gaussian Broadening: 0.050 Ry, ngauss= 1 > DOS = 7.619871 states/spin/Ry/Unit Cell at Ef= 5.192300 eV > lambda( 1)= -0.002955 gamma= -0.055152 GHz > lambda( 2)= -0.002955 gamma= -0.055152 GHz > lambda( 3)= 0.137191 gamma= 3.564312 GHz > lambda( 4)= 0.157767 gamma= 8.753367 GHz > lambda( 5)= 0.001361 gamma= 0.198827 GHz > lambda( 6)= 0.001361 gamma= 0.198827 GHz > lambda( 7)= 0.022826 gamma= 6.868779 GHz > lambda( 8)= 0.034416 gamma= 40.662960 GHz > lambda( 9)= 0.034416 gamma= 40.662960 GHz > Gaussian Broadening: 0.060 Ry, ngauss= 1 > DOS = 7.461279 states/spin/Ry/Unit Cell at Ef= 5.177789 eV > lambda( 1)= -0.007504 gamma= -0.137142 GHz > lambda( 2)= -0.007504 gamma= -0.137142 GHz > lambda( 3)= 0.127975 gamma= 3.255675 GHz > lambda( 4)= 0.173138 gamma= 9.406301 GHz > lambda( 5)= 0.000739 gamma= 0.105748 GHz > lambda( 6)= 0.000739 gamma= 0.105748 GHz > lambda( 7)= 0.021131 gamma= 6.226166 GHz > lambda( 8)= 0.033006 gamma= 38.186120 GHz > lambda( 9)= 0.033006 gamma= 38.186120 GHz > Gaussian Broadening: 0.070 Ry, ngauss= 1 > DOS = 7.283095 states/spin/Ry/Unit Cell at Ef= 5.160627 eV > lambda( 1)= -0.018199 gamma= -0.324639 GHz > lambda( 2)= -0.018199 gamma= -0.324639 GHz > lambda( 3)= 0.117780 gamma= 2.924747 GHz > lambda( 4)= 0.186663 gamma= 9.898900 GHz > lambda( 5)= -0.000793 gamma= -0.110793 GHz > lambda( 6)= -0.000793 gamma= -0.110793 GHz > lambda( 7)= 0.019455 gamma= 5.595627 GHz > lambda( 8)= 0.031702 gamma= 35.801292 GHz > lambda( 9)= 0.031702 gamma= 35.801292 GHz > Gaussian Broadening: 0.080 Ry, ngauss= 1 > DOS = 7.134589 states/spin/Ry/Unit Cell at Ef= 5.141263 eV > lambda( 1)= -0.038412 gamma= -0.671230 GHz > lambda( 2)= -0.038412 gamma= -0.671230 GHz > lambda( 3)= 0.103604 gamma= 2.520264 GHz > lambda( 4)= 0.196871 gamma= 10.227331 GHz > lambda( 5)= -0.003826 gamma= -0.523386 GHz > lambda( 6)= -0.003826 gamma= -0.523386 GHz > lambda( 7)= 0.017477 gamma= 4.924072 GHz > lambda( 8)= 0.030406 gamma= 33.637463 GHz > lambda( 9)= 0.030406 gamma= 33.637463 GHz > Gaussian Broadening: 0.090 Ry, ngauss= 1 > DOS = 7.033187 states/spin/Ry/Unit Cell at Ef= 5.120081 eV > lambda( 1)= -0.059546 gamma= -1.025752 GHz > lambda( 2)= -0.059546 gamma= -1.025752 GHz > lambda( 3)= 0.086926 gamma= 2.084514 GHz > lambda( 4)= 0.203333 gamma= 10.412934 GHz > lambda( 5)= -0.007202 gamma= -0.971260 GHz > lambda( 6)= -0.007202 gamma= -0.971260 GHz > lambda( 7)= 0.015317 gamma= 4.254199 GHz > lambda( 8)= 0.029198 gamma= 31.841996 GHz > lambda( 9)= 0.029198 gamma= 31.841996 GHz > Gaussian Broadening: 0.100 Ry, ngauss= 1 > DOS = 6.985853 states/spin/Ry/Unit Cell at Ef= 5.097830 eV > lambda( 1)= -0.067654 gamma= -1.157586 GHz > lambda( 2)= -0.067654 gamma= -1.157586 GHz > lambda( 3)= 0.071972 gamma= 1.714293 GHz > lambda( 4)= 0.206694 gamma= 10.513791 GHz > lambda( 5)= -0.008860 gamma= -1.186849 GHz > lambda( 6)= -0.008860 gamma= -1.186849 GHz > lambda( 7)= 0.013326 gamma= 3.676327 GHz > lambda( 8)= 0.028227 gamma= 30.575707 GHz > lambda( 9)= 0.028227 gamma= 30.575707 GHz > > *********************************************************************** > ************************ > Where is the problem?. Any help would be appreciated! > > Thanks > > Matteo Giantomassi. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > --- Stefano Baroni --- SISSA & DEMOCRITOS National Simulation Center via Beirut 2-4 34014 Trieste Grignano / [+39] 040 3787 406 (tel) -528 (fax) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From eyvaz_isaev at yahoo.com Thu Sep 9 17:03:15 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 9 Sep 2004 08:03:15 -0700 (PDT) Subject: [Pw_forum] negative values in the electron-phonon calculation. In-Reply-To: <3461EAD6-026C-11D9-8B05-000A95CDDD16@sissa.it> Message-ID: <20040909150315.85534.qmail@web60308.mail.yahoo.com> Hi, In addition to Stefano's comment I can just add that your degauss=0.005 seems to be very low. Probably there was a mistype, because for Al (see example 1) degauss=0.05 is used. Best regards, Eyvaz. --- Stefano Baroni wrote: > Matteo: I do not know if there is anything wrong in > your data and, in > the affirmative, what may be wrong. > As a general remark, negative frequencies (better, > "imaginary" > frequencies: i.e. negative squared frequencies), > signal the instability > of a crystal structure towards a deformation along > the phonon > distortion pattern. In principles, there is nothing > wrong in this. > Whether this is due to a mistake or not, is a matter > of physics ... > > Hope this helps. > Stefano Baroni > > On Sep 9, 2004, at 12:47 PM, matteo giantomassi > wrote: > > > Dear Pwscf users, > > I want to calculate the electron-phonon > interaction in CaAlSi using > > LDA pseudopotentials. > > The structure has been optimized and all phonon > frequences are positive > > but some values of lambda(q) e gamma(q) are > negative!. > > > > > *********************************************************************** > > > ************************ > > This is the test script i'm using: > > > *********************************************************************** > > > ************************ > > > > #/bin/sh > > . ../environment_variables > > > > # self-consistent calculation > > > > cat > caalsi.scf.in << EOF > > &control > > calculation='scf' > > restart_mode='from_scratch', > > tstress = .true. > > tprnfor = .true. > > prefix='caalsi', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > / > > &system > > ibrav= 4, celldm(1) =7.93912, > celldm(3)=1.18356, nat= 3, ntyp= 3, > > ecutwfc =20, nbnd=12, > > occupations='smearing', degauss=0.006, > smearing='gaussian', > > / > > &electrons > > conv_thr = 1.0d-8 > > mixing_beta = 0.7 > > / > > ATOMIC_SPECIES > > Ca 40.078 Ca.pz-n-vbc.UPF > > Al 26.98154 Al.pz-vbc.UPF > > Si 28.08550 Si.pz-vbc.UPF > > > > ATOMIC_POSITIONS crystal > > Ca 0 0 0 > > Al 0.333333333 0.666666666 0.5 > > Si 0.666666666 0.333333333 0.5 > > K_POINTS automatic > > 12 12 12 0 0 0 > > EOF > > $PW_ROOT/bin/pw.x < caalsi.scf.in > caalsi.scf.out > > > > # > > # These are k-points of a (666) uniform grid in > the irreducible# > > Brillouin Zone > > qpoints="0.1666667,0.0962250,0.0000000 > > 0.3333333,0.1924501,0.0000000 > > 0.5000000,0.2886751,0.0000000 > > 0.1666667,0.2886751,0.0000000 > > 0.3333333,0.3849002,0.0000000 > > 0.3333333,0.5773503,0.0000000 > > 0.0000000,0.0000000,0.1408181 > > 0.1666667,0.0962250,0.1408181 > > 0.3333333,0.1924501,0.1408181 > > 0.5000000,0.2886751,0.1408181 > > 0.1666667,0.2886751,0.1408181 > > 0.3333333,0.3849002,0.1408181 > > 0.3333333,0.5773503,0.1408181 > > 0.0000000,0.0000000,0.2816362 > > 0.1666667,0.0962250,0.2816362 > > 0.3333333,0.1924501,0.2816362 > > 0.5000000,0.2886751,0.2816362 > > 0.1666667,0.2886751,0.2816362 > > 0.3333333,0.3849002,0.2816362 > > 0.3333333,0.5773503,0.2816362 > > 0.0000000,0.0000000,0.4224543 > > 0.1666667,0.0962250,0.4224543 > > 0.3333333,0.1924501,0.4224543 > > 0.5000000,0.2886751,0.4224543 > > 0.1666667,0.2886751,0.4224543 > > 0.3333333,0.3849002,0.4224543 > > 0.3333333,0.5773503,0.4224543" > > for qpoint in $qpoints ; do > > # > > # non self-consistent calculation > > # > > qx=`echo $qpoint | cut -d, -f1` > > qy=`echo $qpoint | cut -d, -f2` > > qz=`echo $qpoint | cut -d, -f3` > > cat > caalsi.nscf.in << EOF > > &control > > calculation='phonon' > > restart_mode='from_scratch', > > prefix='caalsi', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > / > > &system > > ibrav= 4, celldm(1) =7.93912, celldm(3)= > 1.18356, nat= 3, ntyp= > > 3, > > ecutwfc =20, nbnd=12, occupations='smearing', > > degauss=0.006, smearing='gaussian', > > / > > &electrons > > conv_thr = 1.0d-8 > > / > > &phonon > > xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz > > / > > ATOMIC_SPECIES > > Ca 40.078 Ca.pz-n-vbc.UPF > > Al 26.98154 Al.pz-vbc.UPF > > Si 28.08550 Si.pz-vbc.UPF > > ATOMIC_POSITIONS crystal > > Ca 0 0 0 > > Al 0.333333333 0.666666666 0.5 > > Si 0.666666666 0.333333333 0.5 > > K_POINTS automatic > > 6 6 6 0 0 0 > > EOF > > > > $PW_ROOT/bin/pw.x < caalsi.nscf.in >> > caalsi.nscf.out > > cat > caalsi.ph.in << EOF > > phonons of caalsi at $qpoint > > &inputph > > tr2_ph=1.0d-10, > > prefix='caalsi', > > amass(1)=40.078, > > amass(2)=26.98154, > > amass(3)=28.08550, > > outdir='$TMP_DIR/', > > fildyn='dyn.$qpoint' > > fildvscf='caalsidv' > > / > > $qpoint > > EOF > > $PW_ROOT/bin/ph.x < caalsi.ph.in >> caalsi.ph.out > > > > cat > caalsi.nscf2.in << EOF > > &control > > calculation='phonon' > > restart_mode='from_scratch', > > prefix='caalsi', > > pseudo_dir = '$PSEUDO_DIR/', > > outdir='$TMP_DIR/' > > / > > &system > > ibrav= 4, celldm(1) =7.93912, celldm(3)= > 1.18356, nat= 3, ntyp= > > 3, > > ecutwfc =20, nbnd=12, occupations='smearing', > > degauss=0.006, smearing='gaussian', > > / > > &electrons > > conv_thr = 1.0d-8 > > / > > &phonon > > xqq(1) = $qx, xqq(2) = $qy, xqq(3) = $qz > > / > > ATOMIC_SPECIES > > Ca 40.078 Ca.pz-n-vbc.UPF > > Al 26.98154 Al.pz-vbc.UPF > > Si 28.08550 Si.pz-vbc.UPF > > ATOMIC_POSITIONS crystal > > Ca 0 0 0 > > Al 0.333333333 0.666666666 0.5 > > Si 0.666666666 0.333333333 0.5 > > K_POINTS automatic > > 12 12 12 0 0 0 > > EOF > > $PW_ROOT/bin/pw.x < caalsi.nscf2.in >> > caalsi.nscf2.out > === message truncated === __________________________________ Do you Yahoo!? Take Yahoo! Mail with you! Get it on your mobile phone. http://mobile.yahoo.com/maildemo From giannozz at nest.sns.it Thu Sep 9 17:55:47 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 9 Sep 2004 17:55:47 +0200 Subject: [Pw_forum] negative values in the electron-phonon calculation. In-Reply-To: <3461EAD6-026C-11D9-8B05-000A95CDDD16@sissa.it> References: <48ebc99604090903477a41f4de@mail.gmail.com> <3461EAD6-026C-11D9-8B05-000A95CDDD16@sissa.it> Message-ID: <200409091755.47672.giannozz@nest.sns.it> On Thursday 09 September 2004 16:26, Stefano Baroni wrote: > As a general remark, negative frequencies (better, "imaginary" > frequencies: i.e. negative squared frequencies), signal the instability > of a crystal structure towards a deformation along the phonon > distortion pattern. In principles, there is nothing wrong in this. actually the original reference to "negative frequencies" : > > This is one of the output file with negative frequences: was misleading: it is the phonon linewidth "gamma" (as defined and calculated in PH/elphon.f90) that seems to be negative for some values of the parameters (the electron-phonon coupling coefficient "lambda" = gamma/(pi N(Ef) omega^2 is negative as a consequence if gamma is negative). I think that it might be simply a problem of bad convergence with respect to k-points and gaussian broadenings. Electron phonon coupling coefficients - in particular, the double sum over delta functions - converge very slowly with respect to these parameters. This is why that particular sum is done on a very dense grid of k-points, using several values of the gaussian broadenings: one has to find a region of parameters in which the results do not change appreciably. It seems to me that the results are still far from convergence with the parameters used. I am a little bit puzzled because I was expecting that the calculated gamma is a positive definite quantity, even far from convergence, but maybe this is not true. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From duanxm at ts.infn.it Tue Sep 14 17:55:00 2004 From: duanxm at ts.infn.it (Xiangmei Duan) Date: Tue, 14 Sep 2004 17:55:00 +0200 (CEST) Subject: [Pw_forum] Convergency problem Message-ID: Dear all, I'm doing the calculation about Mn interstitial on GaAs surface, after more than ten interations during the relax, the total energy is not increased, here is the last part of output total energy: How could I improve the convergency by changing the parameters in my script file? I aatached some of my input in this email. total energy = -1348.23819235 ryd total energy = -1327.13011185 ryd total energy = -1341.60988407 ryd total energy = -1349.71288652 ryd total energy = -1349.85719511 ryd total energy = -1350.07138881 ryd total energy = -1350.09924336 ryd total energy = -1350.11374237 ryd total energy = -1350.11892289 ryd total energy = -1350.11984485 ryd total energy = -1350.12041556 ryd total energy = -1350.12041117 ryd total energy = -1350.11863313 ryd total energy = -1350.12087127 ryd total energy = -1350.12100493 ryd total energy = -1350.12101537 ryd total energy = -1350.12101720 ryd total energy = -1350.12102032 ryd ! total energy = -1350.12102196 ryd total energy = -1350.10301618 ryd total energy = -1350.09532002 ryd total energy = -1349.98729907 ryd total energy = -1350.08369536 ryd total energy = -1350.10486963 ryd total energy = -1350.10692727 ryd total energy = -1350.10705666 ryd total energy = -1350.10706439 ryd total energy = -1350.10707944 ryd total energy = -1350.10708248 ryd total energy = -1350.10708285 ryd ! total energy = -1350.10708300 ryd total energy = -1350.11926724 ryd Thanks, Xiangmei -------------- next part -------------- nr=relax cat > $WORK_DIR/MnGaAs.in.$nr < Message-ID: <000901c49af0$e86fb500$1b6710ac@aeoi.org.ir> Dear PWSCF Users, I have set the environment for PWgui in two systems: RedHat8 and RedHat10. In the former case everything is ok but in the latter I get the following message: ---------------------- PWgui: using the system default "wish" interpreter PWGUI : /home/pwscf/.PWSCF_ROOT/PWgui-0.6.1 GUIB engine : /home/pwscf/.PWSCF_ROOT/PWgui-0.6.1/lib/Guib-0.2.1 ./pwgui: line 55: 15360 Segmentation fault wish $PWGUI/pwgui.tcl -------------------------------- How can I fix this problem? Thanks for any comments. Best regards, Mahmoud Payami From Tone.Kokalj at ijs.si Wed Sep 15 08:48:50 2004 From: Tone.Kokalj at ijs.si (Tone Kokalj) Date: Wed, 15 Sep 2004 08:48:50 +0200 Subject: [Pw_forum] ./pwgui: line 55: 15360 Segmentation fault In-Reply-To: <000901c49af0$e86fb500$1b6710ac@aeoi.org.ir> References: <000901c49af0$e86fb500$1b6710ac@aeoi.org.ir> Message-ID: <20040915064850.GA2470@crysden.ijs.si> On Wed, Sep 15, 2004 at 11:24:54AM +0430, Mahmoud Payami wrote: > Dear PWSCF Users, > > I have set the environment for PWgui in two systems: RedHat8 and RedHat10. > In the former case everything is ok but in the latter I get the following > message: > ---------------------- > PWgui: using the system default "wish" interpreter > > PWGUI : /home/pwscf/.PWSCF_ROOT/PWgui-0.6.1 > GUIB engine : /home/pwscf/.PWSCF_ROOT/PWgui-0.6.1/lib/Guib-0.2.1 > > ./pwgui: line 55: 15360 Segmentation fault wish $PWGUI/pwgui.tcl This is due to broken Tcl/Tk-package, and then Iwidgets don't work. Solution: try to replace the call to "wish" in file pwgui to "itkwish". If that doesn't help, install the ActiveTcl, which is works well: http://aspn.activestate.com/ASPN/Tcl Alternatively: use the binary linux-x86 package instead of source package. Regards, Tone -- +------------------------------------------------------------------------+ | Anton Kokalj Email: Tone.Kokalj at ijs.si | | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | | Jozef Stefan Institute Fax: x 386 1 477 3811 | | Jamova 39, SI-1000 Ljubljana | | SLOVENIA | +------------------------------------------------------------------------+ !!! *** please, do not send me attachments in any Microsoft format *** !!! From asanna at did.dsf.unica.it Wed Sep 15 13:17:09 2004 From: asanna at did.dsf.unica.it (Antonio Sanna) Date: 15 Sep 2004 13:17:09 +0200 Subject: [Pw_forum] error reading fildvscf Message-ID: <1095247029.25623.76.camel@pandora> I'm trying to calculate electron-phonon coupling, but after saved the dynamical matrix and the first order variation of the potentials (no errors received), when I lanch the electron-phonon calculation (elph = .true.) in some cases I obtain this error message: 1525-001 The READ statement on the file -------- cannot be completed because the end of the file was reached. The program will stop. (where ------- is the name and address of the fildvscf.) I finded this problem on many q points (mainly with low symmetry) and different materias. Someone knows what I'm doing wrong? Thanks Antonio From mpayami at aeoi.org.ir Wed Sep 15 15:31:02 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 15 Sep 2004 18:01:02 +0430 Subject: [Pw_forum] ./pwgui: line 55: 15360 Segmentation fault References: <000901c49af0$e86fb500$1b6710ac@aeoi.org.ir> <20040915064850.GA2470@crysden.ijs.si> Message-ID: <001201c49b28$3f597180$1b6710ac@aeoi.org.ir> Dear Tone, Thank you very much for your suggestion. Now it works with "ActiveTcl". Best regards, Mahmoud > This is due to broken Tcl/Tk-package, and then Iwidgets don't work. > Solution: try to replace the call to "wish" in file pwgui to > "itkwish". If that doesn't help, install the ActiveTcl, which is works > well: http://aspn.activestate.com/ASPN/Tcl > > Alternatively: use the binary linux-x86 package instead of source > package. > > Regards, Tone > > -- > +------------------------------------------------------------------------+ > | Anton Kokalj Email: Tone.Kokalj at ijs.si | > | Department of Physical and Organic Chemistry Phone: x 386 1 477 3523 | > | Jozef Stefan Institute Fax: x 386 1 477 3811 | > | Jamova 39, SI-1000 Ljubljana | > | SLOVENIA | > +------------------------------------------------------------------------+ > !!! *** please, do not send me attachments in any Microsoft format *** !!! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From proffess at yandex.ru Wed Sep 15 18:21:25 2004 From: proffess at yandex.ru (Sergei Lisenkov) Date: Wed, 15 Sep 2004 20:21:25 +0400 (MSD) Subject: [Pw_forum] PP converter from upftools Message-ID: <41486C05.000001.18545@pantene.yandex.ru> Dear PWscf authors and users, I tried to convert pseudopotential in fhi98PP form to upf format. I used the command: ./fhi2upf pp.fhi but I always got usage: fhi2upf [input file] Any hints? Best wishes, Sergey From eyvaz_isaev at yahoo.com Wed Sep 15 18:52:44 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 15 Sep 2004 09:52:44 -0700 (PDT) Subject: [Pw_forum] PP converter from upftools In-Reply-To: <41486C05.000001.18545@pantene.yandex.ru> Message-ID: <20040915165244.85851.qmail@web60303.mail.yahoo.com> Hi Sergei, It is so simple: just enter fhi2upf and answer questions which are also very simple. But you should be aware of the local part and DFT used for generatiion of FHI PsP. The information is usually enough from your FHI PsP choice (PBE or LDA) and the first line in a PsP file. Look at also "pspxc" keyword. Bests, Eyvaz. --- Sergei Lisenkov wrote: > Dear PWscf authors and users, > > I tried to convert pseudopotential in fhi98PP form > to upf format. I used the command: > > ./fhi2upf pp.fhi > > but I always got > > usage: fhi2upf [input file] > > Any hints? > > Best wishes, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From proffess at yandex.ru Wed Sep 15 18:59:28 2004 From: proffess at yandex.ru (Sergei Lisenkov) Date: Wed, 15 Sep 2004 20:59:28 +0400 (MSD) Subject: [Pw_forum] PP converter from upftools In-Reply-To: <20040915165244.85851.qmail@web60303.mail.yahoo.com> References: <20040915165244.85851.qmail@web60303.mail.yahoo.com> Message-ID: <414874F0.000003.20323@pantene.yandex.ru> Dear Eivaz, It is no so simply, I tried all possibilities - the result is the same. Best wishes, Sergey From giannozz at nest.sns.it Wed Sep 15 19:45:25 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 15 Sep 2004 19:45:25 +0200 Subject: [Pw_forum] PP converter from upftools In-Reply-To: <41486C05.000001.18545@pantene.yandex.ru> References: <41486C05.000001.18545@pantene.yandex.ru> Message-ID: <200409151945.25342.giannozz@nest.sns.it> On Wednesday 15 September 2004 18:21, Sergei Lisenkov wrote: > I tried to convert pseudopotential in fhi98PP form to upf format. > I used the command: > > ./fhi2upf pp.fhi > > but I always got > > usage: fhi2upf [input file] the converter uses extensions to standard fortran that allow to get the number of arguments (iargc) and a desired argument (getarg) of the command line. Almost all fortran compilers have these extension. Maybe your compiler doesn't, or they do not work properly. Print what is returned by iargc if you type ./fhi2upf ./fhi2upf something ./fhi2upf something else it should be 0, 1, 2, .. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From FB153746 at ATIL.CEA.FR Thu Sep 16 08:52:59 2004 From: FB153746 at ATIL.CEA.FR (=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?=) Date: Thu, 16 Sep 2004 08:52:59 +0200 Subject: [Pw_forum] PP converter from upftools Message-ID: <884193C06D478A4B97B5212C8120A501DC4DD8@atil.intra.cea.fr> Hello Sergey, This is because the program cannot find the file pp.cpi. Normally, FHI produces a file called NAME.cpi . Don't forget that you have to indicate to the program some data, for instance, lloc, occupations, and so on. The program writes a file (see the standard output) NAME.cpi.UPF, that is readable directly by PW. Good luck, Fr?d?ric -----Message d'origine----- De?: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] De la part de Sergei Lisenkov Envoy??: mercredi 15 septembre 2004 18:21 ??: pw_forum at pwscf.org Objet?: [Pw_forum] PP converter from upftools Dear PWscf authors and users, I tried to convert pseudopotential in fhi98PP form to upf format. I used the command: ./fhi2upf pp.fhi but I always got usage: fhi2upf [input file] Any hints? Best wishes, Sergey _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From mousumi at jncasr.ac.in Sat Sep 18 18:46:02 2004 From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly) Date: Sat, 18 Sep 2004 22:16:02 +0530 (IST) Subject: [Pw_forum] segmentation fault Message-ID: <60765.202.41.111.151.1095525962.squirrel@mercury.jncasr.ac.in> DEAR ALL, I am trying to run some cluster calculations. Till 16 atom cluster the run was going on fine. But, in the last run with 18 atoms, though i constructed the input file in exactly the similar manner, I am getting the msg "SEGMENTATION FAULT" I will attach herewith the command I gave for the run and then the msg with which it stopped. "[mousumi at cat3 Se_Cluster]$ nohup ../pw.x < 18atom_Cluster1.in > 18atom_Cluster1.out & [1] 10032 [mousumi at cat3 Se_Cluster]$ [1]+ Segmentation fault nohup ../pw.x <18atom_Cluster1.in >18atom_Cluster1.out " Can you please suggest me, how can I get rid of the error msg and get desired run? Best regards, Mousumi Upadhyay. From giannozz at nest.sns.it Sat Sep 18 22:02:58 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 18 Sep 2004 22:02:58 +0200 Subject: [Pw_forum] segmentation fault In-Reply-To: <60765.202.41.111.151.1095525962.squirrel@mercury.jncasr.ac.in> References: <60765.202.41.111.151.1095525962.squirrel@mercury.jncasr.ac.in> Message-ID: <200409182202.58573.giannozz@nest.sns.it> On Saturday 18 September 2004 18:46, Mousumi Upadhyay Kahaly wrote: > I am trying to run some cluster calculations. Till 16 atom cluster > the run was going on fine. But, in the last run with 18 atoms, > though i constructed the input file in exactly the similar manner, I am > getting the msg > "SEGMENTATION FAULT" "segmentation fault" is a generic error message meaning more or less "your process did something very wrong". Try to get more information on where the process stops and why (out of memory maybe?) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From xhongjun at mail.ustc.edu.cn Sun Sep 19 02:05:05 2004 From: xhongjun at mail.ustc.edu.cn (xianghjun) Date: Sun, 19 Sep 2004 08:05:05 +0800 Subject: [Pw_forum] About Se pseudopotential Message-ID: <414CCD31.1090807@mail.ustc.edu.cn> Dear all: Does anyone have the PBE pseudopotential for Se (uspp pseudopotential is better)? I have tried the Vanderbilt code (version 735), but failed. The error is the following: *** error: unreasonable q eigenvalues I used the input files provided with uspp735 package with some minor modifications. The system I used is pgf77+linux, and I also tried g77 and failed again. Any comments are welcome. Best Regards, xianghjun From mousumi at jncasr.ac.in Sun Sep 19 08:05:09 2004 From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly) Date: Sun, 19 Sep 2004 11:35:09 +0530 (IST) Subject: [Pw_forum] segmentation fault In-Reply-To: <200409182202.58573.giannozz@nest.sns.it> References: <60765.202.41.111.151.1095525962.squirrel@mercury.jncasr.ac.in> <200409182202.58573.giannozz@nest.sns.it> Message-ID: <38935.202.41.111.151.1095573909.squirrel@mercury.jncasr.ac.in> Dear Sir, Nothing is written on output file... How shall I get more information about where did the code stop??? Which file should I look into? Please reply soon. regards, mousumi. > On Saturday 18 September 2004 18:46, Mousumi Upadhyay Kahaly wrote: > >> I am trying to run some cluster calculations. Till 16 atom >> cluster >> the run was going on fine. But, in the last run with 18 atoms, >> though i constructed the input file in exactly the similar manner, I am >> getting the msg >> "SEGMENTATION FAULT" > > "segmentation fault" is a generic error message meaning more or > less "your process did something very wrong". Try to get more > information on where the process stops and why (out of memory > maybe?) > > Paolo > > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Mon Sep 20 10:51:54 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 20 Sep 2004 01:51:54 -0700 (PDT) Subject: [Pw_forum] About Se pseudopotential In-Reply-To: <414CCD31.1090807@mail.ustc.edu.cn> Message-ID: <20040920085154.48784.qmail@web60310.mail.yahoo.com> Hi, This usually means that r_c you used are not suitable. I can generate it for our community in few days. I prefer to do some tests after generation. Best regards, Eyvaz. --- xianghjun wrote: > Dear all: > Does anyone have the PBE pseudopotential for Se > (uspp pseudopotential > is better)? > I have tried the Vanderbilt code (version 735), but > failed. > The error is the following: > *** error: unreasonable q eigenvalues > > I used the input files provided with uspp735 package > with some minor > modifications. > The system I used is pgf77+linux, and I also tried > g77 and failed again. > Any comments are welcome. > > Best Regards, > xianghjun > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From giannozz at nest.sns.it Mon Sep 20 11:45:57 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 20 Sep 2004 11:45:57 +0200 Subject: [Pw_forum] error reading fildvscf In-Reply-To: <1095247029.25623.76.camel@pandora> References: <1095247029.25623.76.camel@pandora> Message-ID: <200409201145.57800.giannozz@nest.sns.it> On Wednesday 15 September 2004 13:17, Antonio Sanna wrote: > I'm trying to calculate electron-phonon coupling, but after saved the > dynamical matrix and the first order variation of the potentials (no > errors received), when I lanch the electron-phonon calculation (elph = > .true.) in some cases I obtain this error message: "some cases" = "some specific case, reproducibly", or "randomly" ? > Someone knows what I'm doing wrong? first of all, check if enough disk space is available Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From jaita at jncasr.ac.in Tue Sep 21 11:58:42 2004 From: jaita at jncasr.ac.in (Jaita Paul) Date: Tue, 21 Sep 2004 15:28:42 +0530 (IST) Subject: [Pw_forum] error In-Reply-To: <200409201145.57800.giannozz@nest.sns.it> References: <1095247029.25623.76.camel@pandora> <200409201145.57800.giannozz@nest.sns.it> Message-ID: <40609.202.41.111.151.1095760722.squirrel@mercury.jncasr.ac.in> Hi, while running pw.x after installing its coming up with the error > ./bin/pw.x [F0BAD] MPID Die - ump2main.c:255 "Internal Error, The magic is missing" (0) any remedies? regards, Jaita. From jaita at jncasr.ac.in Tue Sep 21 12:00:41 2004 From: jaita at jncasr.ac.in (Jaita Paul) Date: Tue, 21 Sep 2004 15:30:41 +0530 (IST) Subject: [Fwd: Re: [Pw_forum] error] Message-ID: <41091.202.41.111.151.1095760841.squirrel@mercury.jncasr.ac.in> Hi, while running pw.x after installing its coming up with the error > ./bin/pw.x [F0BAD] MPID Die - ump2main.c:255 "Internal Error, The magic is missing" (0) any remedies? regards, Jaita. From eyvaz_isaev at yahoo.com Tue Sep 21 12:07:42 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 21 Sep 2004 03:07:42 -0700 (PDT) Subject: [Pw_forum] error In-Reply-To: <40609.202.41.111.151.1095760722.squirrel@mercury.jncasr.ac.in> Message-ID: <20040921100742.59855.qmail@web60305.mail.yahoo.com> Hi, It looks like that you have compiled the parallel version and then tried to run it just entering pw.x. If so, you should run mpirun -np N ./pw.x wrote: > Hi, > > while running pw.x after installing its coming up > with the error > > > ./bin/pw.x > [F0BAD] MPID Die - ump2main.c:255 "Internal Error, > The magic is missing" (0) > > > any remedies? > > regards, > Jaita. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________ Do you Yahoo!? Express yourself with Y! Messenger! Free. Download now. http://messenger.yahoo.com From giannozz at nest.sns.it Tue Sep 21 12:13:42 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 21 Sep 2004 12:13:42 +0200 Subject: [Pw_forum] error In-Reply-To: <40609.202.41.111.151.1095760722.squirrel@mercury.jncasr.ac.in> References: <1095247029.25623.76.camel@pandora> <200409201145.57800.giannozz@nest.sns.it> <40609.202.41.111.151.1095760722.squirrel@mercury.jncasr.ac.in> Message-ID: <200409211213.42117.giannozz@nest.sns.it> On Tuesday 21 September 2004 11:58, Jaita Paul wrote: > while running pw.x after installing its coming up with the error > > > ./bin/pw.x > > [F0BAD] MPID Die - ump2main.c:255 "Internal Error, The magic is missing" > any remedies? if you don't specify the hardware, compiler, software you are using: no remedies! Anyway: a short search on google yields links like e.g. http://www.llnl.gov/computing/mpi/faq.html#question6 which may or may not apply to your case Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From konstantin_kudin at yahoo.com Tue Sep 21 18:38:28 2004 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Tue, 21 Sep 2004 09:38:28 -0700 (PDT) Subject: [Pw_forum] Recent CVS on IBM In-Reply-To: <200409211213.42117.giannozz@nest.sns.it> Message-ID: <20040921163828.43718.qmail@web52005.mail.yahoo.com> Dear all, I tried to compile the current CVS on an IBM machine which has rather old software (OS and compiler). So I am using "configure.old ibmsp". Issues keep showing up. First, in "Modules/parser.f90" one needs to have the following to avoid the conflict with the "pure" definition. #if defined __AIX ! with AIX compiler some combination of flags lead to ! variables being defined as static, hence giving a conflict ! with PURE function. We then force the variable be AUTOMATIC CHARACTER(LEN=1), AUTOMATIC :: sep1, sep2 INTEGER, AUTOMATIC :: j #else CHARACTER(LEN=1) :: sep1, sep2 INTEGER :: j #endif Next, the config files in the directory "install" are missing an include path such that "make.sys" is incomplete. I fixed that by adding the following: CPPFLAGS = -D__AIX,-D__PARA,-D__MPI,-DHAS_ZHEGVX -I$(OSHOME)/include ^^^^^^^^^^^^^^^^^^^ I think this might be missing in many make.sys versions. Finally, why I am actually writing this. When it tries to link "pw.x", the error message is: ld: 0711-317 ERROR: Undefined symbol: .__shmem_include_MOD__&&_shmem_include ld: 0711-344 See the loadmap file map for more information. More detailed info is this: ld: 0711-318 ERROR: Undefined symbols were found. The following symbols are in error: .__shmem_include_MOD__&&_shmem_include [36] ER PR mp_global.f90(../Modules/mp_global.o) 000000b4 .text R_RBR [16] .__mp_global_MOD_mp_global_group_start Any help with this error message? Thanks! Kostya __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From giannozz at nest.sns.it Tue Sep 21 19:29:47 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 21 Sep 2004 19:29:47 +0200 Subject: [Pw_forum] Recent CVS on IBM In-Reply-To: <20040921163828.43718.qmail@web52005.mail.yahoo.com> References: <20040921163828.43718.qmail@web52005.mail.yahoo.com> Message-ID: <200409211929.47873.giannozz@nest.sns.it> On Tuesday 21 September 2004 18:38, Konstantin Kudin wrote: > ld: 0711-318 ERROR: Undefined symbols were found. > The following symbols are in error: > > .__shmem_include_MOD__&&_shmem_include [36] ER PR > mp_global.f90(../Modules/mp_global.o) > 000000b4 .text R_RBR [16] > .__mp_global_MOD_mp_global_group_start try to add ../Modules/shmem_include.o to MODULES in PW/Makefile Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From matteoc at MIT.EDU Mon Sep 20 15:57:34 2004 From: matteoc at MIT.EDU (Matteo Cococcioni) Date: Mon, 20 Sep 2004 09:57:34 -0400 Subject: [Pw_forum] About Se pseudopotential In-Reply-To: <414CCD31.1090807@mail.ustc.edu.cn> References: <414CCD31.1090807@mail.ustc.edu.cn> Message-ID: <1095688654.414ee1ced021a@webmail.mit.edu> Dear Xianghjun, attached to this message I send you a pbe ultra soft pseudopotential for Se which was generated by Nicola Marzari and myself from the David Vanderbilt database and using his generation code uspp-735. Eyvaz is right: to make it work we had to (slightly) change the r_c parameters in the se_ps.adat file. In particular we used: 1.72 1.7 1.7 rc (3f10.5) I made few tests on the pseudopotential and it seems to work ok. But do some more tests before using it and let us know the results you obtain from them. best, Matteo Quoting xianghjun : > Dear all: > Does anyone have the PBE pseudopotential for Se (uspp pseudopotential > is better)? > I have tried the Vanderbilt code (version 735), but failed. > The error is the following: > *** error: unreasonable q eigenvalues > > I used the input files provided with uspp735 package with some minor > modifications. > The system I used is pgf77+linux, and I also tried g77 and failed again. > Any comments are welcome. > > Best Regards, > xianghjun > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- A non-text attachment was scrubbed... Name: Se_uspbe.UPF.gz Type: application/x-gzip Size: 107628 bytes Desc: not available Url : /pipermail/attachments/20040920/93a07b8a/attachment.bin From asanna at did.dsf.unica.it Thu Sep 23 10:20:17 2004 From: asanna at did.dsf.unica.it (Antonio Sanna) Date: 23 Sep 2004 10:20:17 +0200 Subject: [Pw_forum] error reading fildvscf In-Reply-To: <200409201145.57800.giannozz@nest.sns.it> References: <1095247029.25623.76.camel@pandora> <200409201145.57800.giannozz@nest.sns.it> Message-ID: <1095927618.6074.28.camel@pandora> On Mon, 2004-09-20 at 11:45, Paolo Giannozzi wrote: > On Wednesday 15 September 2004 13:17, Antonio Sanna wrote: > > > I'm trying to calculate electron-phonon coupling, but after saved the > > dynamical matrix and the first order variation of the potentials (no > > errors received), when I launch the electron-phonon calculation (elph = > > .true.) in some cases I obtain this error message: > > "some cases" = "some specific case, reproducibly", or "randomly" ? > > > Someone knows what I'm doing wrong? > > first of all, check if enough disk space is available > > Paolo > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > I launch my jobs from the scratch directory of sp4 at CINECA, so there is a lot of available space. Nevertheless, comparing the 'filedvscf' that gives this error with that obtained in my PC, it seems that is truncated. It's possible that the error appears because I recovered these jobs sopped by the time limit (at sp4 I use the parallel script with a wall_clock_limit of 6 hours)? Thank you Antonio From eleonora.spano at mater.unimib.it Fri Sep 24 09:34:18 2004 From: eleonora.spano at mater.unimib.it (eleonora spano) Date: Fri, 24 Sep 2004 09:34:18 +0200 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #398 - 1 msg In-Reply-To: <20040924053646.26067.33338.Mailman@democritos.sissa.it> References: <20040924053646.26067.33338.Mailman@democritos.sissa.it> Message-ID: <1096011258.8604.20.camel@germanio.mater.unimib.it> Dear Antonio, yes it is possible. >From my personal experience, and also because I checked inside the code, in order to get results for the el-ph. calculation you have to perform the phonon calculation in one single run. Each time you restart a phonon calculation the G.dVscf* is re-written. The only possibility for you to get results, if you run the job with the time limit (6h Cineca), is to modify the code. Regards, Eleonora On Fri, 2004-09-24 at 07:36, pw_forum-request at pwscf.org wrote: > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-admin at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: error reading fildvscf (Antonio Sanna) > > --__--__-- > > Message: 1 > Subject: Re: [Pw_forum] error reading fildvscf > From: Antonio Sanna > To: pw_forum at pwscf.org > Date: 23 Sep 2004 10:20:17 +0200 > Reply-To: pw_forum at pwscf.org > > On Mon, 2004-09-20 at 11:45, Paolo Giannozzi wrote: > > On Wednesday 15 September 2004 13:17, Antonio Sanna wrote: > > > > > I'm trying to calculate electron-phonon coupling, but after saved the > > > dynamical matrix and the first order variation of the potentials (no > > > errors received), when I launch the electron-phonon calculation (elph = > > > .true.) in some cases I obtain this error message: > > > > "some cases" = "some specific case, reproducibly", or "randomly" ? > > > > > Someone knows what I'm doing wrong? > > > > first of all, check if enough disk space is available > > > > Paolo > > -- > > Paolo Giannozzi e-mail: giannozz at nest.sns.it > > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > I launch my jobs from the scratch directory of sp4 at CINECA, so there > is a lot of available space. Nevertheless, comparing the 'filedvscf' > that gives this error with that obtained in my PC, it seems that is > truncated. > It's possible that the error appears because I recovered these jobs > sopped by the time limit (at sp4 I use the parallel script with a > wall_clock_limit of 6 hours)? > Thank you > Antonio > > > > > > > > --__--__-- > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest -- Eleonora Spano, PhD Universita' di MIlano Bicocca via Cozzi, 53 22153 Milano From wang.yuanxu at nims.go.jp Tue Sep 28 05:07:21 2004 From: wang.yuanxu at nims.go.jp (WANG Yuan Xu) Date: Tue, 28 Sep 2004 12:07:21 +0900 Subject: [Pw_forum] compile Hitachi Message-ID: <20040928030946.BA83867F48@kugane.nims.go.jp> Who have experience compiling PWSCF on Hitachi system? I meet so many errors during compiling on Hitachi system. Best WANG Yuan Xu National Institute for Materials Science Computational Materials Science Center Namiki 1-1, Tsukuba 305-0044, Japan Phone +81-29-8513354-8092; Fax +81-29-8531207 wang.yuanxu at nims.go.jp 2004-09-28 From farshid at look.ca Mon Sep 27 20:35:10 2004 From: farshid at look.ca (farshid at look.ca) Date: Mon, 27 Sep 2004 14:35:10 -0400 (EDT) Subject: [Pw_forum] installation problem Message-ID: <2526.132.205.9.204.1096310110.squirrel@webmail.look.ca> dear all PWscf users i am trying to install the latest version of PWscf on the sun solaris single server and i follow the steps which has been mentioned on the readme files during compilation i have 3 compilation error which i include the masseges in following also in the attachment i put installation log file if any one knows how to fix the problem or what is the source of problem please let me know about it. ---------------------------------------------- ---------------------------------------------- WARNING: the following problems were detected: n unsupported C/Fortran compilers combination: n CC=cc, F77=f77, F90=f90n you may not be able to compile this program ---------------------------------------------- [cavendish] [/groups/o/of_engr6971_2/pw2_0_5] > make pw ( cd Modules; make all ) make[1]: Entering directory `/groups/o/of_engr6971_2/pw2_0_5/Modules' fpp -P -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules -I../PW -I../PH io_global.f90 io_global.F90 f90 -fast -dalign -xchip=ultra3 -xarch=v8plusb -xlic_lib=sunperf -I. -I../include -I../Modules -I../PW -I../PH -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -c io_global.F90 -o io_global.o fpp -P -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules -I../PW -I../PH kind.f90 kind.F90 f90 -fast -dalign -xchip=ultra3 -xarch=v8plusb -xlic_lib=sunperf -I. -I../include -I../Modules -I../PW -I../PH -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -c kind.F90 -o kind.o fpp -P -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules -I../PW -I../PH parallel_include.f90 parallel_include.F90 f90 -fast -dalign -xchip=ultra3 -xarch=v8plusb -xlic_lib=sunperf -I. -I../include -I../Modules -I../PW -I../PH -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -c parallel_include.F90 -o parallel_include.o fpp -P -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -I. -I../include -I../Modules -I../PW -I../PH mp.f90 mp.F90 f90 -fast -dalign -xchip=ultra3 -xarch=v8plusb -xlic_lib=sunperf -I. -I../include -I../Modules -I../PW -I../PH -DSUN -D__FFTW -D__USE_INTERNAL_FFTW -c mp.F90 -o mp.o MODULE mp ^ "mp.F90", Line = 14, Column = 12: ERROR: The compiler has detected errors in module "MP". No module information file will be created for this module. mp_bcast_iv, mp_bcast_rv, mp_bcast_cv, mp_bcast_l, mp_bcast_rm, & ^ "mp.F90", Line = 33, Column = 75: ERROR: Unexpected syntax: "procedure-name" was expected but found "EOS". mp_bcast_cm, mp_bcast_im, mp_bcast_it, mp_bcast_rt, mp_bcast_lv, & ^ "mp.F90", Line = 35, Column = 11: ERROR: The assignment statement is not allowed in an interface block; expected SUBROUTINE, FUNCTION, MODULE PROCEDURE or END statement. f90: COMPILE TIME 0.040000 SECONDS f90: MAXIMUM FIELD LENGTH 1783164 DECIMAL WORDS f90: 1120 SOURCE LINES f90: 3 ERRORS, WARNINGS, OTHER MESSAGES, ANSI f90: CODE: WORDS, DATA: WORDS make[1]: *** [mp.o] Error 1 make[1]: Leaving directory `/groups/o/of_engr6971_2/pw2_0_5/Modules' make: *** [modules] Error 2 -------------- next part -------------- A non-text attachment was scrubbed... Name: config.log Type: application/octet-stream Size: 25603 bytes Desc: not available Url : /pipermail/attachments/20040927/30703859/attachment.obj From giannozz at nest.sns.it Tue Sep 28 11:09:30 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 28 Sep 2004 11:09:30 +0200 Subject: [Pw_forum] installation problem In-Reply-To: <2526.132.205.9.204.1096310110.squirrel@webmail.look.ca> References: <2526.132.205.9.204.1096310110.squirrel@webmail.look.ca> Message-ID: <200409281109.30970.giannozz@nest.sns.it> On Monday 27 September 2004 20:35, farshid at look.ca wrote: > if any one knows how to fix the problem I don't know, but I can guess: remove the three lines #if defined __T3E mp_bcast_i4b, & #endif from Modules/mp.f90 . -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Tue Sep 28 11:30:17 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 28 Sep 2004 11:30:17 +0200 Subject: [Pw_forum] compile Hitachi In-Reply-To: <20040928030946.BA83867F48@kugane.nims.go.jp> References: <20040928030946.BA83867F48@kugane.nims.go.jp> Message-ID: <200409281130.17682.giannozz@nest.sns.it> On Tuesday 28 September 2004 05:07, WANG Yuan Xu wrote: > Who have experience compiling PWSCF on Hitachi system? the available information (not much) is in file install/Make.hitachi > I meet so many errors during compiling on Hitachi system. look carefully at the first error message(s): the subsequent errors are most likely a consequence of the first error(s) Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From jaita at jncasr.ac.in Tue Sep 28 12:57:39 2004 From: jaita at jncasr.ac.in (Jaita Paul) Date: Tue, 28 Sep 2004 16:27:39 +0530 (IST) Subject: [Pw_forum] error Message-ID: <59218.202.41.111.151.1096369059.squirrel@mercury.jncasr.ac.in> Hi, i'm trying to compile with make.alpha i do not want to use MPI hardware : alpha v 5.1 es40 model software : pw compiler:alpha f77 compiler Regards, Jaita > On Tuesday 21 September 2004 11:58, Jaita Paul wrote: > >> while running pw.x after installing its coming up with the error >> >> > ./bin/pw.x >> >> [F0BAD] MPID Die - ump2main.c:255 "Internal Error, The magic is missing" > >> any remedies? > > if you don't specify the hardware, compiler, software you are using: no remedies! Anyway: a short search on google yields links like e.g. http://www.llnl.gov/computing/mpi/faq.html#question6 > which may or may not apply to your case > > Paolo > > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From eyvaz_isaev at yahoo.com Tue Sep 28 13:17:20 2004 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 28 Sep 2004 04:17:20 -0700 (PDT) Subject: [Pw_forum] error In-Reply-To: <59218.202.41.111.151.1096369059.squirrel@mercury.jncasr.ac.in> Message-ID: <20040928111720.10018.qmail@web60307.mail.yahoo.com> Hi, As far as I know you should use fort compiler on Alpha-based computers for single CPU applications. f77, definitly, is not able to compile PW (and any other components of PWSCF). Bests, Eyvaz. --- Jaita Paul wrote: > Hi, > > i'm trying to compile with make.alpha > i do not want to use MPI > > hardware : alpha v 5.1 es40 model > software : pw > compiler:alpha f77 compiler > > Regards, > Jaita > > > > On Tuesday 21 September 2004 11:58, Jaita Paul > wrote: > > > >> while running pw.x after installing its coming up > with the error > >> > >> > ./bin/pw.x > >> > >> [F0BAD] MPID Die - ump2main.c:255 "Internal > Error, The magic is missing" > > > >> any remedies? > > > > if you don't specify the hardware, compiler, > software you are using: no > remedies! Anyway: a short search on google yields > links like e.g. > http://www.llnl.gov/computing/mpi/faq.html#question6 > > which may or may not apply to your case > > > > Paolo > > > > -- > > Paolo Giannozzi e-mail: > giannozz at nest.sns.it > > Scuola Normale Superiore Phone: > +39/050-509876, Fax:-563513 Piazza > dei Cavalieri 7 I-56126 Pisa, Italy > > _______________________________________________ > > 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 > _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From g.ballabio at cineca.it Tue Sep 28 14:44:43 2004 From: g.ballabio at cineca.it (Gerardo Ballabio) Date: Tue, 28 Sep 2004 14:44:43 +0200 (MEST) Subject: [Pw_forum] error In-Reply-To: <59218.202.41.111.151.1096369059.squirrel@mercury.jncasr.ac.in> References: <59218.202.41.111.151.1096369059.squirrel@mercury.jncasr.ac.in> Message-ID: <1096375483.9415.0.camel@localhost.localdomain> On Tue, 2004-09-28 at 12:57, Jaita Paul wrote: > i'm trying to compile with make.alpha > i do not want to use MPI Try "./configure --disable-parallel" Gerardo From mousumi at jncasr.ac.in Tue Sep 28 17:58:10 2004 From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly) Date: Tue, 28 Sep 2004 21:28:10 +0530 (IST) Subject: [Pw_forum] (no subject) Message-ID: <47927.202.41.111.151.1096387090.squirrel@mercury.jncasr.ac.in> Hi, Is there any option to set in PWScf input file, so that we can have crystal lattice vector relaxation and atomic position relaxation simultaneously? Right now, we relax lattice vectors manually. regards, mousumi From wang.yuanxu at nims.go.jp Wed Sep 29 08:53:27 2004 From: wang.yuanxu at nims.go.jp (WANG Yuan Xu) Date: Wed, 29 Sep 2004 15:53:27 +0900 Subject: [Pw_forum] Re: compile Hitachi Message-ID: <20040929065552.38E0B67F48@kugane.nims.go.jp> Dear Prof. Paolo Giannozzi, The error appear during compile file "shmem_include.f90" The error is mpif90_r -free -I/home/wyxphy/pwscf/Modules -I/home/wyxphy/pwscf/PW/ -I/home/wyxphy/pwscf/PH/ -c shmem_include.f90 f90: compile start : shmem_include.f90 *OFORT90 V01-00-/A entered. KCHF656K -I the following file is referred.--/home/wyxphy/pwscf/Modules/kinds.mod KCHF656K -I the following file is referred.--/home/wyxphy/pwscf/Modules/io_global.mod KCHF484K 08 SHMEM_COLLECT_SYNC_SIZE the symbolic name is not declared. KCHF484K 08 SHMEM_BARRIER_SYNC_SIZE the symbolic name is not declared. KCHF484K 08 SHMEM_REDUCE_SYNC_SIZE the symbolic name is not declared. KCHF484K 08 SHMEM_SYNC_VALUE the symbolic name is not declared. KCHF484K 08 SHMEM_REDUCE_MIN_WRKDATA_SIZE the symbolic name is not declared. KCHF042K 12 34 the file specified in INCLUDE line does not exist. KCHF175K 12 35 MP_SHMEM_BUFSIZE an expression in a type declaration statement contains an error. KCHF413K 04 35 MAX all the arguments in the intrinsic procedure must have the same intrinsic type and must have the same kind type parameter. KCHF197K 12 37 PSYNCB the dimension bound expression of an array-spec is not a scalar-int-expr, otherwise its kind-param is invalid. KCHF197K 12 38 PSYNCC the dimension bound expression of an array-spec is not a scalar-int-expr, otherwise its kind-param is invalid. KCHF197K 12 39 PSYNC_STA the dimension bound expression of an array-spec is not a scalar-int-expr, otherwise its kind-param is invalid. KCHF197K 12 40 MP_SHMEM_BUFFER the dimension bound expression of an array-spec is not a scalar-int-expr, otherwise its kind-param is invalid. KCHF161K 12 43 an initial value repeat count in a type declaration statement or DATA statement is not a scalar integer constant, or has an invalid attribute. KCHF161K 12 44 an initial value repeat count in a type declaration statement or DATA statement is not a scalar integer constant, or has an invalid attribute. KCHF161K 12 45 an initial value repeat count in a type declaration statement or DATA statement is not a scalar integer constant, or has an invalid attribute. *program name = SHMEM_INCLUDE *program units = 0001, 0015 diagnostics generated, highest severity code is 12 make: The error code from the last command is 12. Stop. make: The error code from the last command is 2. Stop. Best WANG Yuan Xu National Institute for Materials Science Computational Materials Science Center Namiki 1-1, Tsukuba 305-0044, Japan Phone +81-29-8513354-8092; Fax +81-29-8541207 wang.yuanxu at nims.go.jp 2004-09-29 From hilgeman at sgi.com Wed Sep 29 09:05:13 2004 From: hilgeman at sgi.com (Martin Hilgeman) Date: Wed, 29 Sep 2004 09:05:13 +0200 Subject: [Pw_forum] Re: compile Hitachi In-Reply-To: <20040929065552.38E0B67F48@kugane.nims.go.jp> References: <20040929065552.38E0B67F48@kugane.nims.go.jp> Message-ID: <415A5EA9.4050004@sgi.com> WANG Yuan Xu wrote: > Dear Prof. Paolo Giannozzi, > The error appear during compile file "shmem_include.f90" > > The error is > mpif90_r -free -I/home/wyxphy/pwscf/Modules -I/home/wyxphy/pwscf/PW/ -I/home/wyxphy/pwscf/PH/ -c shmem_include.f90 > f90: compile start : shmem_include.f90 > > *OFORT90 V01-00-/A entered. > KCHF656K -I the following file is > referred.--/home/wyxphy/pwscf/Modules/kinds.mod > KCHF656K -I the following file is > referred.--/home/wyxphy/pwscf/Modules/io_global.mod > KCHF484K 08 SHMEM_COLLECT_SYNC_SIZE > the symbolic name is not declared. Look on your system for the presence of the 'mpp/shmem.fh' header file and make sure that it can be found by your preprocessor. regards, -Martin -- Martin Hilgeman Chemical Applications Engineering Phone: +31(0)30-6696885 SGI E-mail: hilgeman at sgi.com The Netherlands URL: http://www.sgi.com/go/chembio From wang.yuanxu at nims.go.jp Wed Sep 29 09:25:10 2004 From: wang.yuanxu at nims.go.jp (WANG Yuan Xu) Date: Wed, 29 Sep 2004 16:25:10 +0900 Subject: [Pw_forum] Re: compile Hitachi Message-ID: <20040929072735.EB16167F56@kugane.nims.go.jp> Dear Martin Hilgeman, general, the file "mpp/shmem.fh" should be which directory in Hitachi system or IBM AIX. And this file used for what purpose? Best WANG Yuan Xu National Institute for Materials Science Computational Materials Science Center Namiki 1-1, Tsukuba 305-0044, Japan Phone +81-29-8513354-8092; Fax +81-29-8541207 wang.yuanxu at nims.go.jp 2004-09-29 ======= 2004-09-29 16:05:13 you wrote======= >WANG Yuan Xu wrote: >> Dear Prof. Paolo Giannozzi, >> The error appear during compile file "shmem_include.f90" >> >> The error is >> mpif90_r -free -I/home/wyxphy/pwscf/Modules -I/home/wyxphy/pwscf/PW/ -I/home/wyxphy/pwscf/PH/ -c shmem_include.f90 >> f90: compile start : shmem_include.f90 >> >> *OFORT90 V01-00-/A entered. >> KCHF656K -I the following file is >> referred.--/home/wyxphy/pwscf/Modules/kinds.mod >> KCHF656K -I the following file is >> referred.--/home/wyxphy/pwscf/Modules/io_global.mod >> KCHF484K 08 SHMEM_COLLECT_SYNC_SIZE >> the symbolic name is not declared. > >Look on your system for the presence of the 'mpp/shmem.fh' header file >and make sure that it can be found by your preprocessor. > > >regards, > >-Martin > >-- >Martin Hilgeman Chemical Applications Engineering > Phone: +31(0)30-6696885 >SGI E-mail: hilgeman at sgi.com >The Netherlands URL: http://www.sgi.com/go/chembio >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > = = = = = = = = = = = = = = = = = = = = From giannozz at nest.sns.it Wed Sep 29 09:40:14 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 29 Sep 2004 09:40:14 +0200 Subject: [Pw_forum] Re: compile Hitachi In-Reply-To: <415A5EA9.4050004@sgi.com> References: <20040929065552.38E0B67F48@kugane.nims.go.jp> <415A5EA9.4050004@sgi.com> Message-ID: <200409290940.14558.giannozz@nest.sns.it> On Wednesday 29 September 2004 09:05, Martin Hilgeman wrote: > > The error appear during compile file "shmem_include.f90" unless __SHMEM is #defined as a preprocessing flag, shmem_include.f90 is empty > Look on your system for the presence of the 'mpp/shmem.fh' header > file and make sure that it can be found by your preprocessor. provided that Hitachi support shmem: does it? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From mpayami at aeoi.org.ir Wed Sep 29 17:16:34 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 29 Sep 2004 18:46:34 +0330 Subject: [Pw_forum] compile error for ESPRESSO Message-ID: <001801c4a637$504cd080$1b6710ac@aeoi.org.ir> Dear Developers, I am trying to install ESPRESSO. Although I have setup mpi, running the "configure" script gives the message: no parallel environment but, using "make target" it uses mpif77 or mpif90. Secondly, with ifc7.1+mkl61 I compiled everything except the last one which gives: ------------------ mpif90 -o band_plot.x band_plot.o -Vaxlib -static ../flib/ptools.a ../flib/flib.a ../clib/clib.a -lfftw -L/usr/local/intel/mkl61/lib/32 -lmkl_lapack -lmkl_ia32 -lguide -lpthread /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(fstop.o)(.text+0xb8): In function `libi_exit': : undefined reference to `pthread_self' /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(fstop.o)(.text+0xc4): In function `libi_exit': : undefined reference to `pthread_equal' /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(threadsafe.o)(.text+0x23): In function `f_claim_mutex': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(threadsafe.o)(.text+0x33): In function `f_exitthread': : undefined reference to `pthread_exit' /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(threadsafe.o)(.text+0x53): In function `f_release_mutex': : undefined reference to `pthread_mutex_unlock' /usr/local/intel/compiler70/ia32/lib/libIEPCF90.a(f90init.o)(.text+0x1b): In function `f90_init': : undefined reference to `pthread_self' /usr/local/intel/compiler70/ia32/lib/libcxa.a(exception.o)(.text+0x9b): In function `std::set_unexpected(void (*)())': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libcxa.a(exception.o)(.text+0xb3): In function `std::set_unexpected(void (*)())': : undefined reference to `pthread_mutex_unlock' /usr/local/intel/compiler70/ia32/lib/libcxa.a(exception.o)(.text+0x125): In function `std::set_terminate(void (*)())': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libcxa.a(exception.o)(.text+0x13d): In function `std::set_terminate(void (*)())': : undefined reference to `pthread_mutex_unlock' /usr/local/intel/compiler70/ia32/lib/libcxa.a(newhandler.o)(.text+0xd): In function `std::set_new_handler(void (*)())': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libcxa.a(newhandler.o)(.text+0x25): In function `std::set_new_handler(void (*)())': : undefined reference to `pthread_mutex_unlock' /usr/local/intel/compiler70/ia32/lib/libunwind.a(ptn_ix86.o)(.text+0x2f): In function `_eh_get_lock': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libunwind.a(ptn_ix86.o)(.text+0x42): In function `.B1.2': : undefined reference to `pthread_mutex_lock' /usr/local/intel/compiler70/ia32/lib/libunwind.a(ptn_ix86.o)(.text+0x63): In function `_eh_release_lock': : undefined reference to `pthread_mutex_unlock' /usr/local/intel/compiler70/ia32/lib/libunwind.a(ptn_ix86.o)(.text+0x76): In function `.B2.2': : undefined reference to `pthread_mutex_unlock' make[1]: *** [band_plot.x] Error 1 make: *** [tools] Error 2 ---------------------------- I have experienced that the above messages do not appear when ifort+mkl70 is used. How can I set the conditions for getting rid of the above message using ifc7.1+mkl61? Any suggestion is highly appreciated. Best regards, Mahmoud Payami -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20040929/9e0f51e9/attachment.htm From giannozz at nest.sns.it Wed Sep 29 17:35:51 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 29 Sep 2004 17:35:51 +0200 Subject: [Pw_forum] compile error for ESPRESSO In-Reply-To: <001801c4a637$504cd080$1b6710ac@aeoi.org.ir> References: <001801c4a637$504cd080$1b6710ac@aeoi.org.ir> Message-ID: <200409291735.51087.giannozz@nest.sns.it> On Wednesday 29 September 2004 17:16, Mahmoud Payami wrote: > Secondly, with ifc7.1+mkl61 I compiled everything except the > last one which gives: ...lots of missing references. This is easy, I get the same :-) Either re-run "./configure --enable-shared", or edit make.sys and remove "-static", or change it to "-static-libcxa". For some mysterious reason ifc7.1+mkl6.1 refuses to load statically some executables but not some others. See the web site maintained by Axel Kohlmeyer for some intersting info, including the static vs dynamic library mess: http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-linux.html Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From mpayami at aeoi.org.ir Wed Sep 29 18:16:43 2004 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 29 Sep 2004 19:46:43 +0330 Subject: [Pw_forum] compile error for ESPRESSO References: <001801c4a637$504cd080$1b6710ac@aeoi.org.ir> <200409291735.51087.giannozz@nest.sns.it> Message-ID: <002e01c4a63f$b89fb000$1b6710ac@aeoi.org.ir> Dear Paolo, Thank you very much for your comments. I used "--enable-shared". Best regards, Mahmoud > > Secondly, with ifc7.1+mkl61 I compiled everything except the > > last one which gives: > > ...lots of missing references. This is easy, I get the same :-) > Either re-run "./configure --enable-shared", or edit make.sys > and remove "-static", or change it to "-static-libcxa". For some > mysterious reason ifc7.1+mkl6.1 refuses to load statically some > executables but not some others. See the web site maintained > by Axel Kohlmeyer for some intersting info, including the static > vs dynamic library mess: > http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-linux.html > > Paolo > > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > From wang.yuanxu at nims.go.jp Thu Sep 30 07:55:16 2004 From: wang.yuanxu at nims.go.jp (WANG Yuan Xu) Date: Thu, 30 Sep 2004 14:55:16 +0900 Subject: [Pw_forum] scf for BaTiO3 Message-ID: <20040930055742.800A967F4C@kugane.nims.go.jp> Dear all, When I calculate BaTiO3. I use the Ba pseudo file from PWscf web site. And O an Ti was Ti.vdb.UPF and O.vdb.UPF I get the error information "from readpp # 2 inconsistent DFT read" The three atoms must all same GGA or LDA? If it is true. The website only give Ba GGA no Ba LDA. How should I do. Best WANG Yuan Xu National Institute for Materials Science Computational Materials Science Center Namiki 1-1, Tsukuba 305-0044, Japan Phone +81-29-8513354-8092; Fax +81-29-8541207 wang.yuanxu at nims.go.jp 2004-09-30 From axel.kohlmeyer at theochem.ruhr-uni-bochum.de Thu Sep 30 08:53:16 2004 From: axel.kohlmeyer at theochem.ruhr-uni-bochum.de (Axel Kohlmeyer) Date: Thu, 30 Sep 2004 08:53:16 +0200 Subject: [Pw_forum] scf for BaTiO3 In-Reply-To: Your message of "Thu, 30 Sep 2004 14:55:16 +0900." <20040930055742.800A967F4C@kugane.nims.go.jp> Message-ID: <200409300653.i8U6rGU32570@yello.theochem.ruhr-uni-bochum.de> >>> "WY" == WANG Yuan Xu writes: WY> Dear all, WY> When I calculate BaTiO3. WY> I use the Ba pseudo file from PWscf web site. And O an Ti was Ti.vdb.UPF and O.vdb.UPF WY> I get the error information "from readpp # 2 inconsistent DFT read" WY> The three atoms must all same GGA or LDA? If it is true. The website WY> only give Ba GGA no Ba LDA. How should I do. hi, you are correct, your pseudopotentials have to be created with consistent functionals (not only all GGA by itself, but also the same GGA, with LDA the differences are smaller) pwscf reads the functional to be used for the calculation from the pseudopotential. to get a consistent set, you have to recreate them using a consistent DFT. in case of vanderbilt USPPs you have to download the uspp pp code from the vanderbilt uspp homepage: http://www.physics.rutgers.edu/~dhv/uspp/ compile it and follow the instructions to generate the potentials. if you need a different DFT you can usually change the pseudopotential generation parameter file (XXX_ps.adat). from my experience, this works well, if you want to switch between different GGA DFTs; switching from LDA to GGA has not worked very well. the resulting .uspp files can then be transformed to UPF format with the uspp2upf.x utility. some uspp files use the full element name instead of the atomic symbol, you'll have to change that manually with a text editor, after you have converted your pseudopotentials to upf. you should also mention, how you have created the UPF file in the section, especially if you have changed the DFT from the original settings. regards, axel kohlmeyer WY> Best WY> WANG Yuan Xu WY> National Institute for Materials Science WY> Computational Materials Science Center WY> Namiki 1-1, Tsukuba 305-0044, Japan WY> Phone +81-29-8513354-8092; Fax +81-29-8541207 WY> wang.yuanxu at nims.go.jp WY> 2004-09-30 WY> _______________________________________________ WY> Pw_forum mailing list WY> Pw_forum at pwscf.org WY> http://www.democritos.it/mailman/listinfo/pw_forum -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer at theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/ ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Thu Sep 30 11:24:43 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 30 Sep 2004 11:24:43 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <47927.202.41.111.151.1096387090.squirrel@mercury.jncasr.ac.in> References: <47927.202.41.111.151.1096387090.squirrel@mercury.jncasr.ac.in> Message-ID: <200409301124.43022.giannozz@nest.sns.it> On Tuesday 28 September 2004 17:58, Mousumi Upadhyay Kahaly wrote: > Is there any option to set in PWScf input file, > so that we can have crystal lattice vector relaxation > and atomic position relaxation simultaneously? see the various parameters related to the "variable-cell" dynamics or minimization in the INPUT_PW file. Variable-cell techniques are a little bit tricky: if your goal is just to find the equilibrium structure of a crystal, however, it can be easier to perform the cell relaxation and atomic position relaxation separately, in the "traditional" way Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Thu Sep 30 13:18:45 2004 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 30 Sep 2004 13:18:45 +0200 Subject: [Pw_forum] scf for BaTiO3 In-Reply-To: <20040930055742.800A967F4C@kugane.nims.go.jp> References: <20040930055742.800A967F4C@kugane.nims.go.jp> Message-ID: <200409301318.45614.giannozz@nest.sns.it> On Thursday 30 September 2004 07:55, WANG Yuan Xu wrote: > I use the Ba pseudo file from PWscf web site. And O an Ti was > Ti.vdb.UPF and O.vdb.UPF > > I get the error information "from readpp # 2 inconsistent DFT read" for PWscf, the exchange-correlation used in the calculation is read from the PP files, and it must be the same in all PP's (of course). One can edit the PP files and modify the exch-corr field, but it is not a good idea. Note that FPMD uses a different approach: you have to write the exch-corr you want in the input data (variable "xc_type" in namelist &system) Does PWscf work now on the Hitachi machine, by the way? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From jcconesa at icp.csic.es Thu Sep 30 17:04:45 2004 From: jcconesa at icp.csic.es (Jose C. Conesa) Date: Thu, 30 Sep 2004 17:04:45 +0200 Subject: [Pw_forum] compilation error i sgi machine Message-ID: <415C3CAD.18349.C1390B0@localhost> Dear all, I tried to install espresso 2.1 in an Origin 2000 SGI machine running IRIX. configure went OK. When running make pw, however, I found errors of this kind: --------------------------------------------------- MODULE complex_diis_module ^ f90-855 f90: ERROR COMPLEX_DIIS_MODULE, File = complex_diis_module.f90, Line = 2 4, Column = 8 The compiler has detected errors in module "COMPLEX_DIIS_MODULE". No module i nformation file will be created for this module. FORALL( ib = 1: nbnd, ( .NOT. conv(ib) ) ) ^ f90-197 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 339, Colum n = 35 Unexpected syntax: "index-name or mask expression" was expected but found "(". END FORALL ^ f90-289 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 343, Colum n = 13 This END FORALL statement has no matching FORALL statement. FORALL( ib = 1: nbnd_diis, ( .NOT. conv(ib) ) ) ^ f90-197 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 673, Column = 37 Unexpected syntax: "index-name or mask expression" was expected but found "(". END FORALL ^ f90-289 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 677, Column = 10 This END FORALL statement has no matching FORALL statement. f90: SGI MIPSpro Fortran 90 Version 7.4 (f14) Thu Sep 30, 2004 18:13:29 f90: 1189 source lines f90: 5 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) cf90: "explain cf90-message number" gives more information about each message --------------------------------------------------- and then it stops. It would seem as if the syntax of the FORALL construct were not accepted by this compiler. Any help? All the best, Jose C. Conesa Instituto de Catalisis y Petroleoquimica, CSIC Campus de Cantoblanco 28049 Madrid - Spain Phone Nr. 34-91-5854766 Fax Nr. 34-91-5854760 From sbraccia at sissa.it Thu Sep 30 17:11:13 2004 From: sbraccia at sissa.it (carlo sbraccia) Date: Thu, 30 Sep 2004 17:11:13 +0200 Subject: [Pw_forum] compilation error i sgi machine In-Reply-To: <415C3CAD.18349.C1390B0@localhost> References: <415C3CAD.18349.C1390B0@localhost> Message-ID: <1096557073.2994.73.camel@dhpc-5-40.sissa.it> Dear Jose C. Conesa, try removing the parenthesis: ( .NOT. conv(ib) ) => .NOT. conv(ib) carlo sbraccia On Thu, 2004-09-30 at 17:04, Jose C. Conesa wrote: > Dear all, > I tried to install espresso 2.1 in an Origin 2000 SGI machine running IRIX. configure went OK. > When running make pw, however, I found errors of this kind: > --------------------------------------------------- > MODULE complex_diis_module > ^ > f90-855 f90: ERROR COMPLEX_DIIS_MODULE, File = complex_diis_module.f90, Line = 2 > 4, Column = 8 > The compiler has detected errors in module "COMPLEX_DIIS_MODULE". No module i > nformation file will be created for this module. > > FORALL( ib = 1: nbnd, ( .NOT. conv(ib) ) ) > ^ > f90-197 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 339, Colum > n = 35 > Unexpected syntax: "index-name or mask expression" was expected but found "(". > > END FORALL > ^ > f90-289 f90: ERROR INIT_STEPS, File = complex_diis_module.f90, Line = 343, Colum > n = 13 > This END FORALL statement has no matching FORALL statement. > > FORALL( ib = 1: nbnd_diis, ( .NOT. conv(ib) ) ) > ^ > f90-197 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 673, > Column = 37 > Unexpected syntax: "index-name or mask expression" was expected but found "(". > > END FORALL > ^ > f90-289 f90: ERROR DIIS_WITH_ORTHO, File = complex_diis_module.f90, Line = 677, > Column = 10 > This END FORALL statement has no matching FORALL statement. > > f90: SGI MIPSpro Fortran 90 Version 7.4 (f14) Thu Sep 30, 2004 18:13:29 > f90: 1189 source lines > f90: 5 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) > cf90: "explain cf90-message number" gives more information about each message > --------------------------------------------------- > and then it stops. It would seem as if the syntax of the FORALL construct were not accepted by > this compiler. Any help? > All the best, > > Jose C. Conesa > Instituto de Catalisis y Petroleoquimica, CSIC > Campus de Cantoblanco > 28049 Madrid - Spain > Phone Nr. 34-91-5854766 > Fax Nr. 34-91-5854760 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum