Everytime I use configure to creat arch.make, there is a message configure: using DC_LAPACK routines packaged with SIESTA due to bug in library. Linker flag might be needed to avoid duplicate symbols
I wonder whether this is the reason. zhengping -----Original E-mail----- > From: "Marcos Veríssimo Alves" <[email protected]> > Sent time: 2009-10-27 06:02:56 > To: [email protected] > CC: > Subject: Re: Re: [SIESTA-L] VdW XC problem > > Ricardo, > > As I wrote in so many previous emails now, when I tried to compile > ATOM with ifort, I had the errors you mention. When I switched to g95 > or gfortran, I got a working pseudo with the van der Waals functional. > > Marcos > > On Mon, Oct 26, 2009 at 6:06 PM, Ricardo Faccio <[email protected]> wrote: > > Hi Zheng and Marcos > > I tried the pseudo-generation for Ar as it looks at > > siesta-trunk-301/Pseudo/atom/Tutorial/PS_Generation/Ar/Ar.vdw.inp > > I found the same problem as Marcos (first email) and Zheng (last email): > > ############################ > > Stepsize not significant in RKQC. > > Stepsize not significant in RKQC. > > ODEINT - Too many steps. > > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > Image PC Routine Line Source > > atm 0000000000400229 Unknown Unknown Unknown > > ==> Output data in directory Ar.vdw > > ==> Pseudopotential in Ar.vdw.vps and Ar.vdw.psf (and maybe in Ar.vdw.xml) > > ########################################################### > > I tried different rc's, with the same problem. > > Regarding compilation, I tried the same arch.make used for compiling > > siesta-serial, with all the -optimization levels without any important > > change. > > Here is my arch.make > > Regards > > Ricardo > > --------------- > > ifort# > > FFLAGS= -w -O1 -mp1 > > EXTRA_LIBS=-lpthread -lsvml > > FFLAGS_DEBUG= -g > > LDFLAGS= -static > > COMP_LIBS= > > RANLIB=echo > > # > > NETCDF_LIBS= > > NETCDF_INTERFACE= > > DEFS_CDF= > > # > > MPI_INTERFACE= > > MPI_INCLUDE= > > DEFS_MPI= > > # > > GUIDE=/opt/intel/cmkl/10.0.5.025/lib/em64t/libguide.a > > LAPACK=/opt/intel/cmkl/10.0.5.025/lib/em64t/libmkl_lapack.a > > BLAS=/opt/intel/cmkl/10.0.5.025/lib/em64t/libmkl_em64t.a > > LIBS=$(LAPACK) $(BLAS) $(GUIDE) $(EXTRA_LIBS) > > SYS=nag > > FPPFLAGS= $(FPPFLAGS_CDF) $(FPPFLAGS_MPI) > > > > ------------------------------------------------------------------------- > > Dr. Ricardo Faccio > > Prof. Adjunto de Física > > Mail: Cryssmat-Lab., Cátedra de Física, DETEMA > > Facultad de Química, Universidad de la República > > Av. Gral. Flores 2124, C.C. 1157 > > C.P. 11800, Montevideo, Uruguay. > > E-mail: [email protected] > > Phone: 598 2 924 98 59 > > 598 2 929 06 48 > > Fax: 598 2 9241906 > > Web: http://cryssmat.fq.edu.uy/ricardo/ricardo.htm > > --------------------------------------------------------------------------------- > > ----- Original Message ----- From: "Marcos Veríssimo Alves" > > <[email protected]> > > To: <[email protected]> > > Sent: Saturday, October 24, 2009 5:44 PM > > Subject: Re: Re: [SIESTA-L] VdW XC problem > > > > > >> I would, but right now I don't have access to my computer where I have > >> compiled siesta with gfortran. It's very weird that no matter which > >> complier you use, no difference is seen. Instead, please send me: > >> > >> 1) your arch.make, > >> 2) your input file for the pseudo > >> > >> so that I can see and try to check if anything is wrong at all. > >> > >> Cheers, > >> > >> Marcos > >> > >> On Sat, Oct 24, 2009 at 12:46 PM, ZhengPing Fu <[email protected]> wrote: > >>> > >>> Hi, Marcos, > >>> > >>> I compiled serial version of siesta and atom with gfortran -c -g -O2, > >>> it make no difference. The error is > >>> > >>> splint: ERROR: X out of range > >>> Stopping Program from Node: 0 > >>> ../../Utils/pg.sh: line 44: 32613 Aborted $prog > >>> cp: cannot stat `VPSOUT': No such file or directory > >>> cp: cannot stat `VPSFMT': No such file or directory > >>> > >>> no Pseudopotential are created. > >>> > >>> Would you mind to share your atm program with me? > >>> > >>> Thanks > >>> > >>> Zhengping > >>> > >>> > >>> -----Original E-mail----- > >>>> > >>>> From: "Marcos Veríssimo Alves" <[email protected]> > >>>> Sent time: 2009-10-24 01:06:20 > >>>> To: [email protected] > >>>> CC: > >>>> Subject: Re: [SIESTA-L] VdW XC problem > >>>> > >>>> Zhengping, > >>>> > >>>> Some time ago I sent a long email about the use of compilers and maybe > >>>> this issue got diluted in the middle of the whole thing. Use either > >>>> g95 or gfortran to compile it serially, it'll work. > >>>> > >>>> Marcos > >>>> > >>>> On Fri, Oct 23, 2009 at 12:38 PM, ZhengPing Fu <[email protected]> wrote: > >>>> > Hi, Marcos > >>>> > > >>>> > I also try to create vdw pseudopotential of carbon. I use > > >>>> > siesta-trunk-301/Tests/Pseudos/C.vdw.inp > >>>> > as the input file, and I get the error: splint: ERROR: X out of range. > >>>> > It make no difference whether I compile atom program with gcc, ifor, > > >>>> > mpich2, openmpi or serial arch.make. > >>>> > I want to use the XC version because I am try to do some calc on > > >>>> > double layer graphene, while the relaxation results with siesta2.02 > > >>>> > and > >>>> > siesta3.0b give too small layer distance. Maybe it's due to the > > >>>> > incorrect > >>>> > vdw force in > >>>> > siesta2.02 and siesta3.0b. > >>>> > > >>>> > cheers! > >>>> > > >>>> > zhengping > >>>> > > >>>> > -----Original E-mail----- > >>>> >> From: "Marcos Veríssimo Alves" <[email protected]> > >>>> >> Sent time: 2009-10-18 06:49:19 > >>>> >> To: [email protected] > >>>> >> CC: > >>>> >> Subject: [SIESTA-L] VdW XC problem > >>>> >> > >>>> >> Hi SIESTA developers, > >>>> >> > >>>> >> I have compiled the trunk version sucessfully (ifort 10.1.015, mkl > >>>> >> 10.0.1.014, gcc4.3.3-5ubuntu4 for all the libraries) and >> > >>>> >> re-calculated > >>>> >> a relaxation (originally performed with SIESTA 0.12 - !!!!) with it, > >>>> >> with good agreement on the final geometries on GGA. Now I'd like to > >>>> >> perform the same relaxation but using the VdW functional included in > >>>> >> the trunk version. However, I am having trouble generating the >> > >>>> >> pseudos > >>>> >> with the VdW functional, for C, H and O. Using the LDA input file in > >>>> >> the user-contributed pseudo database for SIESTA for H, the >> > >>>> >> calculation > >>>> >> on ATOM starts but after some time (much longer than with the usual > >>>> >> generation times for LDA and GGA) I get the following error: > >>>> >> > >>>> >> ODEINT - Too many steps. > >>>> >> ODEINT - Too many steps. > >>>> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred > >>>> >> Image PC Routine Line > >>>> >> Source > >>>> >> atm 00000000004DC594 Unknown Unknown Unknown > >>>> >> atm 00000000004DB656 Unknown Unknown Unknown > >>>> >> atm 00000000004DF815 Unknown Unknown Unknown > >>>> >> atm 000000000049B787 Unknown Unknown Unknown > >>>> >> atm 000000000043945C Unknown Unknown Unknown > >>>> >> atm 000000000041636A Unknown Unknown Unknown > >>>> >> atm 0000000000409459 Unknown Unknown Unknown > >>>> >> atm 000000000040108B Unknown Unknown Unknown > >>>> >> atm 00000000004002FE Unknown Unknown Unknown > >>>> >> atm 00000000005846E1 Unknown Unknown Unknown > >>>> >> atm 00000000004001E9 Unknown Unknown Unknown > >>>> >> ==> Output data in directory H.vdw > >>>> >> ==> Pseudopotential in H.vdw.vps and H.vdw.psf (and maybe in >> > >>>> >> H.vdw.xml) > >>>> >> > >>>> >> Using a smaller rc (say 0.8 instead of 1.25) for the s channel, I get > >>>> >> a different error: "Stepsize not significant in RKQC". Since the > >>>> >> pseudo files are written nonetheless, I looked at H.vdw.psf and found > >>>> >> that the initial values for the pseudopotential are huge and >> > >>>> >> positive: > >>>> >> > >>>> >> Down Pseudopotential follows (l on next line) > >>>> >> 0 > >>>> >> 0.549103214316E+39 0.117500146714E+40 0.166669234150E+40 >> > >>>> >> 0.237719184583E+40 > >>>> >> 0.285353560992E+40 0.353790433179E+40 0.410640166051E+40 >> > >>>> >> 0.473604557600E+40 > >>>> >> 0.535672527076E+40 0.598766945589E+40 0.662573971183E+40 >> > >>>> >> 0.727126597569E+40 > >>>> >> 0.792432802699E+40 0.858500612833E+40 0.925338124816E+40 >> > >>>> >> 0.992953500075E+40 > >>>> >> 0.106135495208E+41 0.113055080187E+41 0.120054936526E+41 >> > >>>> >> 0.127135908317E+41 > >>>> >> > >>>> >> and that at some point they converge to -2 (?): > >>>> >> > >>>> >> 0.456930826243E+43 0.101859895292E+42 0.314589853862E+41 >> > >>>> >> 0.116397450388E+41 > >>>> >> -0.629471476686E+40 0.760405662914E+39 0.341641877055E+38 >> > >>>> >> 0.196285512413E+35 > >>>> >> -0.101201540265E+31 -0.213016981113E+22 -6742.38640266 -2.00000000052 > >>>> >> -2.00000000025 -2.00000000012 -2.00000000006 -2.00000000003 > >>>> >> -2.00000000001 -2.00000000001 -2.00000000000 -2.00000000000 > >>>> >> > >>>> >> As the compilation of atom is now related to that of siesta itself, I > >>>> >> am including the arch.make of my (serial) siesta-trunk at the end of > >>>> >> this email. In the references to the VdW functional I have not found > >>>> >> anything that could be useful to identify a possible source of error. > >>>> >> I applied the patch for the siesta trunk version before compiling it > >>>> >> as well. Is there a problem with the version of ATOM that comes with > >>>> >> it? > >>>> >> > >>>> >> Cheers, > >>>> >> > >>>> >> Marcos > >>>> >> > >>>> >> # > >>>> >> # This file is part of the SIESTA package. > >>>> >> # > >>>> >> # Copyright (c) Fundacion General Universidad Autonoma de Madrid: > >>>> >> # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, >> > >>>> >> D.Sanchez-Portal > >>>> >> # and J.M.Soler, 1996- . > >>>> >> # > >>>> >> # Use of this software constitutes agreement with the full conditions > >>>> >> # given in the SIESTA license, as signed by all legitimate users. > >>>> >> # > >>>> >> .SUFFIXES: > >>>> >> .SUFFIXES: .f .F .o .a .f90 .F90 > >>>> >> > >>>> >> SIESTA_ARCH=x86_64-unknown-linux-gnu--Intel > >>>> >> > >>>> >> FPP= > >>>> >> FPP_OUTPUT= > >>>> >> FC=ifort > >>>> >> RANLIB=ranlib > >>>> >> > >>>> >> SYS=nag > >>>> >> > >>>> >> SP_KIND=4 > >>>> >> DP_KIND=8 > >>>> >> KINDS=$(SP_KIND) $(DP_KIND) > >>>> >> > >>>> >> #FFLAGS= -w -mp1 -tpp6 -O2 -prec_div -reentrancy none -prefetch > >>>> >> FFLAGS= -g -mp -O2 > >>>> >> FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT > >>>> >> LDFLAGS= -Vaxlib -i-static -static > >>>> >> > >>>> >> ARFLAGS_EXTRA= > >>>> >> > >>>> >> FCFLAGS_fixed_f= > >>>> >> FCFLAGS_free_f90= > >>>> >> FPPFLAGS_fixed_F= > >>>> >> FPPFLAGS_free_F90= > >>>> >> > >>>> >> BLAS_LIBS= -L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_em64t > >>>> >> LAPACK_LIBS=-L/opt/intel/mkl/10.0.1.014/lib/em64t -lmkl_lapack > >>>> >> BLACS_LIBS= > >>>> >> SCALAPACK_LIBS= > >>>> >> > >>>> >> COMP_LIBS= > >>>> >> > >>>> >> NETCDF_LIBS=/usr/lib/libnetcdf.so.4.0.0 > >>>> >> NETCDF_INTERFACE= > >>>> >> > >>>> >> #LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) >> > >>>> >> $(NETCDF_LIBS) > >>>> >> LIBS= -lmkl_lapack -lmkl_em64t -lguide -lpthread -lmkl_core > >>>> >> > >>>> >> #SIESTA needs an F90 interface to MPI > >>>> >> #This will give you SIESTA's own implementation > >>>> >> #If your compiler vendor offers an alternative, you may change > >>>> >> #to it here. > >>>> >> MPI_INTERFACE= > >>>> >> MPI_INCLUDE= > >>>> >> MPI_LIBS= > >>>> >> DEFS_MPI= > >>>> >> > >>>> >> #Dependency rules are created by autoconf according to whether > >>>> >> #discrete preprocessing is necessary or not. > >>>> >> .F.o: > >>>> >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $< > >>>> >> .F90.o: > >>>> >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< > >>>> >> .f.o: > >>>> >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< > >>>> >> .f90.o: > >>>> >> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $< > >>>> > > >>>> > > >>>> > -- > >>>> > > >>>> > 211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104 > >>>> > 215-573-8440 > >>>> > > >>> > >>> > >>> -- > >>> > >>> 211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104 > >>> 215-573-8440 > >>> > > > > -- 211 LRSM, 3231 Walnut Str., Philadelphia, PA 19104 215-573-8440
