[SIESTA-L] Pseudopotential for Fe and Bi
Hi all Could someone share pseudopotentials (LDA flavor) for Bi(Bismuth) and Fe. Thanks Swaroop -- M.Sairam Swaroop Theoretical Sciences Unit JNCASR,Jakkur Bangalore-64 INDIA
[SIESTA-L] failed to get XV file
Dear siesta users, Maybe a bit stupid question, but how to obtain Systemlabel.XV file needed by grid2cube utility? I set LongOutput, WriteCoorInitial and WriteCoorStep options to "true" but after calculation was finished, there was no XV file in the working directory. After searching through mailing list archives, I found I'm not the one who has faced this problem: there were reports, that SIESTA 2.0 doesn't produce XV for large systems. Can this issue somehow be solved? -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] siesta-output Description: Binary data
Re: [SIESTA-L] More on Cholesky in parallel siesta
Dear Sergey, We don't have installed it on our cluster but it might be a good idea to get it. I will think about it. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown On Sat, 2 Jun 2007, Sergey Lisenkov wrote: Mariusz, Did you ever try to use scalapack/blacs from CMKL? I never get such error on our clusters, including itanium and other (non)intel platforms. sergey 02.06.07, 14:56, Mariusz Krawiec <[EMAIL PROTECTED]>: Dear Vasilii, Thanks for your message. Unfortunately nothing is working in my case. Indeed, it would be nice if the developers have a look at this. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown On Sat, 2 Jun 2007, Vasilii Artyukhov wrote: That's strange, since as far as I could figure out, Cholesky factorization in cdiag.o seems to be called only in parallel diagonalizations - it's related to the decomposition of matrices over processors. You can trace the error from cdiag to a ScaLAPACK routine, can't recall its name, and take a look yourself. At the same time, when you parallelize over K-points, the matrices are diagonalized sequentially for each k-point by the corresponding CPUs. Still, I remember having this problem with k-point parallelization, as well. It was solved (I think) by explicitly setting the BlockSize in the input file. Could be some sort of a bug, since BlockSize refers to parallelization over states, not k-points. Another flag that seem to help from time to time is Diag.Use2D .false., it calls a different ScaLAPACK routine. Of course, it would be very nice if the developers could look into this... 2007/6/2, Mariusz Krawiec <[EMAIL PROTECTED]>: Hi there, Has anybody solved the problem of Cholesky factorisation in parallel siesta ? I got the same error on IA-64 when using Diag.ParallelOverK. When I run it on a single processor (even with mpirun command) everything works fine. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown
Re: [SIESTA-L] More on Cholesky in parallel siesta
Mariusz, Did you ever try to use scalapack/blacs from CMKL? I never get such error on our clusters, including itanium and other (non)intel platforms. sergey 02.06.07, 14:56, Mariusz Krawiec <[EMAIL PROTECTED]>: > Dear Vasilii, > Thanks for your message. > Unfortunately nothing is working in my case. > Indeed, it would be nice if the developers have a look at this. > All the best, > Mariusz. > -- > Dr Mariusz Krawiec > Institute of PhysicsPhone: +48 81 537 6146 > M Curie-Sklodowska University Fax: +48 81 537 6191 > pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] > 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl > > If you think of MS-DOS as mono, and Windows as stereo, then Linux is > Dolby Pro-Logic Surround Sound with Bass Boost and all the music is > free. - unknown > > On Sat, 2 Jun 2007, Vasilii Artyukhov wrote: > > That's strange, since as far as I could figure out, Cholesky factorization > > in cdiag.o seems to be called only in parallel diagonalizations - it's > > related to the decomposition of matrices over processors. You can trace the > > error from cdiag to a ScaLAPACK routine, can't recall its name, and take a > > look yourself. At the same time, when you parallelize over K-points, the > > matrices are diagonalized sequentially for each k-point by the corresponding > > CPUs. > > > > Still, I remember having this problem with k-point parallelization, as well. > > It was solved (I think) by explicitly setting the BlockSize in the input > > file. Could be some sort of a bug, since BlockSize refers to parallelization > > over states, not k-points. > > > > Another flag that seem to help from time to time is Diag.Use2D .false., it > > calls a different ScaLAPACK routine. Of course, it would be very nice if the > > developers could look into this... > > > > 2007/6/2, Mariusz Krawiec <[EMAIL PROTECTED]>: > >> > >> Hi there, > >> > >> Has anybody solved the problem of Cholesky factorisation in parallel > >> siesta ? > >> I got the same error on IA-64 when using Diag.ParallelOverK. > >> When I run it on a single processor (even with mpirun command) everything > >> works fine. > >> > >> All the best, > >> Mariusz. > >> > >> -- > >> Dr Mariusz Krawiec > >> Institute of PhysicsPhone: +48 81 537 6146 > >> M Curie-Sklodowska University Fax: +48 81 537 6191 > >> pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] > >> 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl > >> > >> > >> If you think of MS-DOS as mono, and Windows as stereo, then Linux is > >> Dolby Pro-Logic Surround Sound with Bass Boost and all the music is > >> free. - unknown > >> > >> > >
Re: [SIESTA-L] More on Cholesky in parallel siesta
Dear Vasilii, Thanks for your message. Unfortunately nothing is working in my case. Indeed, it would be nice if the developers have a look at this. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown On Sat, 2 Jun 2007, Vasilii Artyukhov wrote: That's strange, since as far as I could figure out, Cholesky factorization in cdiag.o seems to be called only in parallel diagonalizations - it's related to the decomposition of matrices over processors. You can trace the error from cdiag to a ScaLAPACK routine, can't recall its name, and take a look yourself. At the same time, when you parallelize over K-points, the matrices are diagonalized sequentially for each k-point by the corresponding CPUs. Still, I remember having this problem with k-point parallelization, as well. It was solved (I think) by explicitly setting the BlockSize in the input file. Could be some sort of a bug, since BlockSize refers to parallelization over states, not k-points. Another flag that seem to help from time to time is Diag.Use2D .false., it calls a different ScaLAPACK routine. Of course, it would be very nice if the developers could look into this... 2007/6/2, Mariusz Krawiec <[EMAIL PROTECTED]>: Hi there, Has anybody solved the problem of Cholesky factorisation in parallel siesta ? I got the same error on IA-64 when using Diag.ParallelOverK. When I run it on a single processor (even with mpirun command) everything works fine. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown
Re: [SIESTA-L] LAM SCALAPACK
Try removing -Bstatic flag, it causes such errors on many compilers On 02/06/07, Cherry Y. Yates <[EMAIL PROTECTED]> wrote: DEAR Developer, Do you have any suggestions for compiling a parallel version of SIESTA using LAM-MPI? I always got the following error messages: rdiag.o(.text+0x2a77): In function `rdiag_': : undefined reference to `blacs_gridinit__' libscalapack.a(descinit.o)(.text+0x54): In function `descinit_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pxerbla.o)(.text+0x41): In function `pxerbla_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pdpotrf.o)(.text+0x60): In function `pdpotrf_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pbdtrnv.o)(.text+0xa1): In function `pbdtrnv_': : undefined reference to `blacs_gridinfo__' ... I compiled BLACS, SCALAPACK, and SIESTA using lam mpif77 -O3 -Bstatic. It looks like the names are not compatible. Anyone have a successful story with LAM? By the way, did anyone test the scaling of SIESTA for Gamma point only SCF calculations? Many thanks! Cherry Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/ -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
Re: [SIESTA-L] More on Cholesky in parallel siesta
That's strange, since as far as I could figure out, Cholesky factorization in cdiag.o seems to be called only in parallel diagonalizations - it's related to the decomposition of matrices over processors. You can trace the error from cdiag to a ScaLAPACK routine, can't recall its name, and take a look yourself. At the same time, when you parallelize over K-points, the matrices are diagonalized sequentially for each k-point by the corresponding CPUs. Still, I remember having this problem with k-point parallelization, as well. It was solved (I think) by explicitly setting the BlockSize in the input file. Could be some sort of a bug, since BlockSize refers to parallelization over states, not k-points. Another flag that seem to help from time to time is Diag.Use2D .false., it calls a different ScaLAPACK routine. Of course, it would be very nice if the developers could look into this... 2007/6/2, Mariusz Krawiec <[EMAIL PROTECTED]>: Hi there, Has anybody solved the problem of Cholesky factorisation in parallel siesta ? I got the same error on IA-64 when using Diag.ParallelOverK. When I run it on a single processor (even with mpirun command) everything works fine. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown
[SIESTA-L] More on Cholesky in parallel siesta
Hi there, Has anybody solved the problem of Cholesky factorisation in parallel siesta ? I got the same error on IA-64 when using Diag.ParallelOverK. When I run it on a single processor (even with mpirun command) everything works fine. All the best, Mariusz. -- Dr Mariusz Krawiec Institute of PhysicsPhone: +48 81 537 6146 M Curie-Sklodowska University Fax: +48 81 537 6191 pl. M. Curie-Sklodowskiej 1 E-mail: [EMAIL PROTECTED] 20-031 Lublin, Poland http://www.fnano.umcs.lublin.pl If you think of MS-DOS as mono, and Windows as stereo, then Linux is Dolby Pro-Logic Surround Sound with Bass Boost and all the music is free. - unknown
[SIESTA-L] parallel calculation with GGA method
Dear Siesta users, I compiled the parallel version of siesta code sucessfully, but it seems that it can't run normally with GGA method. For the pseudopotential was generated by means of GGA-PBE method, I defined XC.functional GGA and XC.authors PBE in the .fdf file. But it can't work and the following is the error information in the output file: InitMesh: MESH =30 x24 x24 = 17280 InitMesh: Mesh cutoff (required, used) =10.00012.406 Ry rank 1 in job 51 mitp4.emsl.pnl.gov_58106 caused collective abort of all ranks exit status of rank 1: killed by signal 9 However, if I delete the above definitions, then the job can run normally. It seems that there is something wrong with the parallel calculation with GGA method. I wonder if someone has ever met such problem and can give me some suggestions on how to solve such problem. Thank you very much. Helean
[SIESTA-L] LAM SCALAPACK
DEAR Developer, Do you have any suggestions for compiling a parallel version of SIESTA using LAM-MPI? I always got the following error messages: rdiag.o(.text+0x2a77): In function `rdiag_': : undefined reference to `blacs_gridinit__' libscalapack.a(descinit.o)(.text+0x54): In function `descinit_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pxerbla.o)(.text+0x41): In function `pxerbla_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pdpotrf.o)(.text+0x60): In function `pdpotrf_': : undefined reference to `blacs_gridinfo__' libscalapack.a(pbdtrnv.o)(.text+0xa1): In function `pbdtrnv_': : undefined reference to `blacs_gridinfo__' ... I compiled BLACS, SCALAPACK, and SIESTA using lam mpif77 -O3 -Bstatic. It looks like the names are not compatible. Anyone have a successful story with LAM? By the way, did anyone test the scaling of SIESTA for Gamma point only SCF calculations? Many thanks! Cherry Moody friends. Drama queens. Your life? Nope! - their life, your story. Play Sims Stories at Yahoo! Games. http://sims.yahoo.com/
