Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
Dear Sir, I thank you for sending me the patch file. I tried using the file in my cluster however, when I give the command 'make', I receive the following message: Makefile:9: make.inc: No such file or directory make: *** No rule to make target `make.inc'. Stop. I request you let me know the possible correction. I also wanted to know how can I revert back the patch. Regards Arini Kar M.Sc.-Ph.D. IIT Bombay India ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
I have reproduced a different one, though. It's the usual problem: small differences between different processors, building up for no good reason. It might be related to your problem as well. Solution soon (I hope) Paolo On Thu, Oct 25, 2018 at 10:13 AM Paolo Giannozzi wrote: > From the FAQ: "Mysterious, unpredictable, erratic errors in parallel > execution are almost always coming from bugs in the compiler or/and in the > MPI libraries and sometimes even from flaky hardware." > If the error is not reproducible on a different machine, the above > statement applies. I couldn't reproduce any errors - apart from lack of > convergence - but your job takes too much time for extensive testing > > Paolo > > On Wed, Oct 24, 2018 at 2:56 PM arini kar wrote: > >> Dear Sir, >> >> The error arises in the middle during any scf iteration. In some of the >> calculations, the error arises during the last scf calculation while in >> some other it arises in the middle of the run. >> >> Is it due to some issues with parallelization? If so then what would be >> the appropriate parallelization? I am currently using the default >> parallelization. >> >> Regards >> Arini Kar >> M.Sc.-Ph.D. >> IIT Bombay >> India >> ___ >> users mailing list >> users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
>From the FAQ: "Mysterious, unpredictable, erratic errors in parallel execution are almost always coming from bugs in the compiler or/and in the MPI libraries and sometimes even from flaky hardware." If the error is not reproducible on a different machine, the above statement applies. I couldn't reproduce any errors - apart from lack of convergence - but your job takes too much time for extensive testing Paolo On Wed, Oct 24, 2018 at 2:56 PM arini kar wrote: > Dear Sir, > > The error arises in the middle during any scf iteration. In some of the > calculations, the error arises during the last scf calculation while in > some other it arises in the middle of the run. > > Is it due to some issues with parallelization? If so then what would be > the appropriate parallelization? I am currently using the default > parallelization. > > Regards > Arini Kar > M.Sc.-Ph.D. > IIT Bombay > India > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
Dear Prof. Paolo, I am also having same error on same cluster which Mr. A. Kar using with QE_6.3 and "composer_xe_2015". I am invoking the command "mpirun -np 32 $QE/pw.x -npool 2 *in ... *out for vc-relax. For me it happen in the last scf, after a message "End final coordinates". It went okay till scf cycle 53. It happens in some cases only. Below seems strand for me: (grep scf *out) A final scf calculation at the relaxed structure. estimated scf accuracy< 0.35117344 Ry estimated scf accuracy< 32.50696577 Ry estimated scf accuracy< 0.15737732 Ry estimated scf accuracy< 0.08941433 Ry estimated scf accuracy< 0.04130004 Ry estimated scf accuracy< 0.03367160 Ry estimated scf accuracy< 0.01518230 Ry estimated scf accuracy< 0.01241863 Ry estimated scf accuracy< 0.00237884 Ry estimated scf accuracy< 0.02059544 Ry estimated scf accuracy< 0.01326459 Ry estimated scf accuracy< 0.02823102 Ry estimated scf accuracy< 0.14757734 Ry estimated scf accuracy< 0.05952341 Ry estimated scf accuracy< 0.05929330 Ry estimated scf accuracy< 0.00738492 Ry estimated scf accuracy< 0.00555608 Ry estimated scf accuracy< 0.00535798 Ry estimated scf accuracy< 0.00688829 Ry estimated scf accuracy< 0.00169491 Ry estimated scf accuracy< 0.00067948 Ry estimated scf accuracy< 0.06297539 Ry estimated scf accuracy< 0.05981938 Ry estimated scf accuracy< 0.05814955 Ry estimated scf accuracy< 0.06202781 Ry estimated scf accuracy< 0.06178400 Ry estimated scf accuracy< 0.05837077 Ry estimated scf accuracy< 0.07705482 Ry estimated scf accuracy< 0.03734422 Ry estimated scf accuracy< 0.01355381 Ry estimated scf accuracy< 0.02777065 Ry estimated scf accuracy< 0.02632385 Ry estimated scf accuracy< 0.02607268 Ry estimated scf accuracy< 0.01001318 Ry estimated scf accuracy< 0.00563499 Ry estimated scf accuracy< 0.5798 Ry estimated scf accuracy< 0.00066655 Ry estimated scf accuracy< 0.0103 Ry estimated scf accuracy< 0.0082 Ry estimated scf accuracy< 0.0002 Ry estimated scf accuracy< 0.0001 Ry estimated scf accuracy< 6.0E-11 Ry estimated scf accuracy< 0.7832 Ry estimated scf accuracy< 0.7830 Ry estimated scf accuracy< 0.7712 Ry estimated scf accuracy< 0.7558 Ry estimated scf accuracy< 0.7271 Ry estimated scf accuracy< 0.6239 Ry estimated scf accuracy< 0.4313 Ry estimated scf accuracy< 0.2601 Ry I still have double on my PPs. If this is due to something else, please let me know what additional information I can supply to reproduce the error message. Kind regards Bhamu CSIR-NCL, Pune India On Mon, Oct 22, 2018 at 11:19 AM Paolo Giannozzi wrote: > QE version? > > On Sat, Oct 20, 2018 at 9:01 AM arini kar wrote: > >> Dear Quantum Espresso users, >> >> I have been trying to relax a 2x2x1 supercell of hematite doped with Ge >> and an oxygen vacancy. However, after a few electronic iterations, I >> received the following error: >> >> Fatal error in PMPI_Bcast: Other MPI error, error stack: >> PMPI_Bcast(2112): MPI_Bcast(buf=0x11806c00, count=7500, >> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed >> MPIR_Bcast_impl(1670)...: >> I_MPIR_Bcast_intra(1887): Failure during collective >> MPIR_Bcast_intra(1524)..: Failure during collective >> Fatal error in PMPI_Bcast: Other MPI error, error stack: >> PMPI_Bcast(2112): MPI_Bcast(buf=0x56fced0, count=7500, >> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed >> MPIR_Bcast_impl(1670)...: >> I_MPIR_Bcast_intra(1887): Failure during collective >> MPIR_Bcast_intra(1524)..: Failure during collective >> Fatal error in PMPI_Bcast: Other MPI error, error stack: >> PMPI_Bcast(2112): MPI_Bcast(buf=0x1080d330, count=7500, >> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed >> MPIR_Bcast_impl(1670)...: >> I_MPIR_Bcast_intra(1887): Failure during collective >> MPIR_Bcast_intra(1524)..: Failure during collective >> Fatal error in PMPI_Bcast: Other MPI error, error stack: >> PMPI_Bcast(2112): MPI_Bcast(buf=0x10c025c0, count=7500, >> MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed >> MPIR_Bcast_impl(1670)...: >> I_MPIR_Bcast_intra(1887): Failure during collective >> MPIR_Bcast_intra(1524)..: Failure during collective >> Fatal error in PMPI_Bcast: Other MPI error, error stack:
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
Dear Sir, The error arises in the middle during any scf iteration. In some of the calculations, the error arises during the last scf calculation while in some other it arises in the middle of the run. Is it due to some issues with parallelization? If so then what would be the appropriate parallelization? I am currently using the default parallelization. Regards Arini Kar M.Sc.-Ph.D. IIT Bombay India ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
Does it happen in the last step, after a message like 'A final scf calculation at the relaxed structure' or 'lsda relaxation : a final configuration with zero'? or in the middle of the run? in the latter case, it is impossible to say anything unless the error is reproducible Paolo On Mon, Oct 22, 2018 at 12:13 PM arini kar wrote: > Dear Sir, > > I am using QE v6.3Max for the simulations. > > Regards > Arini Kar > M.Sc.-Ph.D. > IIT Bombay > India > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
Dear Sir, I am using QE v6.3Max for the simulations. Regards Arini Kar M.Sc.-Ph.D. IIT Bombay India ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Problems with DFT + U Calculations: Fatal error in PMPI_Bcast
QE version? On Sat, Oct 20, 2018 at 9:01 AM arini kar wrote: > Dear Quantum Espresso users, > > I have been trying to relax a 2x2x1 supercell of hematite doped with Ge > and an oxygen vacancy. However, after a few electronic iterations, I > received the following error: > > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(2112): MPI_Bcast(buf=0x11806c00, count=7500, > MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed > MPIR_Bcast_impl(1670)...: > I_MPIR_Bcast_intra(1887): Failure during collective > MPIR_Bcast_intra(1524)..: Failure during collective > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(2112): MPI_Bcast(buf=0x56fced0, count=7500, > MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed > MPIR_Bcast_impl(1670)...: > I_MPIR_Bcast_intra(1887): Failure during collective > MPIR_Bcast_intra(1524)..: Failure during collective > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(2112): MPI_Bcast(buf=0x1080d330, count=7500, > MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed > MPIR_Bcast_impl(1670)...: > I_MPIR_Bcast_intra(1887): Failure during collective > MPIR_Bcast_intra(1524)..: Failure during collective > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(2112): MPI_Bcast(buf=0x10c025c0, count=7500, > MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed > MPIR_Bcast_impl(1670)...: > I_MPIR_Bcast_intra(1887): Failure during collective > MPIR_Bcast_intra(1524)..: Failure during collective > Fatal error in PMPI_Bcast: Other MPI error, error stack: > PMPI_Bcast(2112): MPI_Bcast(buf=0x112e96c0, count=7500, > MPI_DOUBLE_PRECISION, root=0, comm=0x8405) failed > MPIR_Bcast_impl(1670)...: > I_MPIR_Bcast_intra(1887): Failure during collective > MPIR_Bcast_intra(1524)..: Failure during collective > [16:ycn213.en.yuva.param] unexpected disconnect completion event from > [7:ycn217.en.yuva.param] > Assertion failed in file ../../dapl_conn_rc.c at line 1128: 0 > internal ABORT - process 16 > > The input file for the same is attached below. Since, I am new to Quantum > Espresso, I am not able to find a solution to the problem. I request you to > help me with possible corrections. > > Regards > Arini Kar > M.Sc.-Ph.D. > IIT Bombay > India > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
