Dear Nick, many thanks for your kind reply. Everything worked following your suggestion (MKL)
Have a nice weekend Giacomo Il giorno gio 5 mar 2020 alle ore 22:01 Nick Papior <[email protected]> ha scritto: > Sorry for the delay. > > I have now runned your big system, and I am not able to reproduce the > problem. > I would suggest you try with other linear algebra packages. > The standard shipped BLAS+LAPACK packages are also *extremely* slow. > > Den ons. 4. mar. 2020 kl. 22.12 skrev Giacomo Giorgi <[email protected] > >: > >> Dear all, >> following a previous unanswered message I would like to ask you your >> opinion about this weird behavior of my calculations with siesta. >> >> I am working with TiO2 anatase. >> Bulk worked perfectly. Also the (101) surface unit cell worked perfectly. >> >> Now I need a (5x3) supercell. (attached the fdf). >> Running it as a replica of the initial unit cell I get the following >> error: >> >> .... >> .... >> cdiag: Error in Cholesky factorisation >> Stopping Program from Node: 4 >> 160 >> cdiag: Error in Cholesky factorisation >> Stopping Program from Node: 5 >> 160 >> cdiag: Error in Cholesky factorisation >> Stopping Program from Node: 0 >> -------------------------------------------------------------------------- >> MPI_ABORT was invoked on rank 6 in communicator MPI COMMUNICATOR 3 CREATE >> FROM 0 >> with errorcode 1. >> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> You may or may not see output from other processes, depending on >> exactly when Open MPI kills them. >> -------------------------------------------------------------------------- >> [node03:300332] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at >> line 2079 >> [node03:300332] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at >> line 2079 >> [node03:300332] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at >> line 2079 >> [node03:300332] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at >> line 2079 >> [node03:300332] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at >> line 2079 >> [node03:300332] 23 more processes have sent help message help-mpi-api.txt >> / mpi-abort >> [node03:300332] Set MCA parameter "orte_base_help_aggregate" to 0 to see >> all help / error messages >> >> >> Maybe the structure is too large (strange...), thus I decided to run a >> calculation on a smaller (1x3) supercell (still fdf atteched along with psf >> used). >> Then this time I get this new error: >> ... >> ... >> Stopping Program from Node: 19 >> Bad DM normalization: Qtot, Tr[D*S] = 576.00000000 >> 638080922.01711190 >> Stopping Program from Node: 21 >> Bad DM normalization: Qtot, Tr[D*S] = 576.00000000 >> 638080922.01711190 >> Stopping Program from Node: 22 >> -------------------------------------------------------------------------- >> MPI_ABORT was invoked on rank 15 in communicator MPI COMMUNICATOR 3 >> CREATE FROM 0 >> with errorcode 1. >> >> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> You may or may not see output from other processes, depending on >> exactly when Open MPI kills them. >> -------------------------------------------------------------------------- >> [node03:306841] 23 more processes have sent help message help-mpi-api.txt >> / mpi-abort >> [node03:306841] Set MCA parameter "orte_base_help_aggregate" to 0 to see >> all help / error messages >> >> Since I do not find anyone able to fix this issue, which actually seems >> to be system-independent ( I have had similar behaviour with other slabs), >> I wonder if there is any of you able to help me. >> >> Thanks a lot- >> Regards, >> Giacomo >> >> >> Siesta Version : v4.1-b4 >> Architecture : unknown >> Compiler version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36) >> Compiler flags : mpif90 -O2 -fPIC -ftree-vectorize >> PP flags : -DFC_HAVE_ABORT -DMPI -DSIESTA__DIAG_2STAGE >> Libraries : libsiestaLAPACK.a libsiestaBLAS.a >> /opt/share/scalapack_gnu/libscalapack.a >> PARALLEL version >> >> * Running on 24 nodes in parallel >> >> Start of run: 3-MAR-2020 10:41:40 >> >> >> >> >> -- >> G >> >> >> "Oltre le illusioni di Timbuctù e le gambe lunghe di Babalù c'era questa >> strada...Questa strada zitta che vola via come una farfalla, una nostalgia, >> nostalgia al gusto di curaçao...Forse un giorno meglio mi spiegherò" >> >> (Paolo Conte, "Hemingway") >> >> -- >> SIESTA is supported by the Spanish Research Agency (AEI) and by the >> European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) >> > > > -- > Kind regards Nick > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- G "Oltre le illusioni di Timbuctù e le gambe lunghe di Babalù c'era questa strada...Questa strada zitta che vola via come una farfalla, una nostalgia, nostalgia al gusto di curaçao...Forse un giorno meglio mi spiegherò" (Paolo Conte, "Hemingway")
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
