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 >>> > >
