ABINIT Discussion Forums

Code: Select all

Summary of important options:

  * C compiler      : gnu version 4.6
  * Fortran compiler: gnu version 4.6
  * architecture    :   ( bits)

  * debugging       : basic
  * optimizations   : standard

  * MPI    enabled  : no
  * MPI-IO enabled  : no
  * GPU    enabled  : no (none)

  * TRIO   flavor = netcdf-fallback+etsf_io-fallback
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = netlib (libs: auto-detected)
  * FFT    flavor = none (libs: ignored)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback

Configuration complete.
You may now type "make" to build ABINIT.
(or, on a SMP machine, "make mj4", or "make multi multi_nprocs=<n>")

[b]When I did "make", this was the message I got:[/b]

make  all-recursive
Making all in plugins
Making all in netcdf
make[3]: Nothing to be done for `all'.
Making all in etsf_io
make[3]: Nothing to be done for `all'.
Making all in libxc
make -f ../../plugins/libxc/libxc.mk 
libxc-1.0 has been uncompressed.
touch patches-stamp
libxc-1.0 has been patched.
cd libxc-1.0 && \
    CPP="/usr/local/gfortran/bin/gcc -E" \
    CPPFLAGS="" \
    CC="/usr/local/gfortran/bin/gcc" \
    CFLAGS="-g -O2 -mtune=native -march=native -mfpmath=sse  " \
    FCCPP="cpp " \
    FC="/usr/local/gfortran/bin/gfortran" \
    FCLIBS="" \
    LIBS="" \
    FCFLAGS="-ffree-form -g -ffree-line-length-none  -O2 -mtune=native -march=native -mfpmath=sse" \
    ./configure \
     --prefix="/Users/nikhilsivadas/Downloads/abinit-6.10.3/plugins/libxc/tmp" \
     --enable-fortran --disable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin10.6.0
checking host system type... i386-apple-darwin10.6.0
checking for style of include used by make... GNU
checking for gcc... /usr/local/gfortran/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/local/gfortran/bin/gcc accepts -g... yes
checking for /usr/local/gfortran/bin/gcc option to accept ISO C89... none needed
checking dependency style of /usr/local/gfortran/bin/gcc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by /usr/local/gfortran/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from /usr/local/gfortran/bin/gcc object... rm: conftest.dSYM: is a directory
ok
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking how to run the C preprocessor... /usr/local/gfortran/bin/gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /usr/local/gfortran/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /usr/local/gfortran/bin/gcc option to produce PIC... -fno-common -DPIC
checking if /usr/local/gfortran/bin/gcc PIC flag -fno-common -DPIC works... yes
checking if /usr/local/gfortran/bin/gcc static flag -static works... no
checking if /usr/local/gfortran/bin/gcc supports -c -o file.o... yes
checking if /usr/local/gfortran/bin/gcc supports -c -o file.o... (cached) yes
checking whether the /usr/local/gfortran/bin/gcc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gcc... (cached) /usr/local/gfortran/bin/gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether /usr/local/gfortran/bin/gcc accepts -g... (cached) yes
checking for /usr/local/gfortran/bin/gcc option to accept ISO C89... (cached) none needed
checking dependency style of /usr/local/gfortran/bin/gcc... (cached) gcc3
checking whether /usr/local/gfortran/bin/gcc and cc understand -c and -o together... yes
checking for inline... inline
checking for ANSI C header files... (cached) yes
checking for working alloca.h... yes
checking for alloca... yes
checking size of void*... 4
checking whether we are using the GNU Fortran compiler... yes
checking whether /usr/local/gfortran/bin/gfortran accepts -g... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether /usr/local/gfortran/bin/gfortran accepts -g... (cached) yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for /usr/local/gfortran/bin/gfortran option to produce PIC... -fno-common
checking if /usr/local/gfortran/bin/gfortran PIC flag -fno-common works... yes
checking if /usr/local/gfortran/bin/gfortran static flag -static works... no
checking if /usr/local/gfortran/bin/gfortran supports -c -o file.o... yes
checking if /usr/local/gfortran/bin/gfortran supports -c -o file.o... (cached) yes
checking whether the /usr/local/gfortran/bin/gfortran linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking for Fortran flag to compile .f90 files... none
configure: Using FCFLAGS="-ffree-form -g -ffree-line-length-none  -O2 -mtune=native -march=native -mfpmath=sse"
checking how to get verbose linking output from /usr/local/gfortran/bin/gfortran... -v
checking for Fortran libraries of /usr/local/gfortran/bin/gfortran...  -L/usr/local/gfortran/lib/gcc/i686-apple-darwin10/4.6.1 -L/usr/local/gfortran/lib/gcc/i686-apple-darwin10/4.6.1/../../.. -lgfortran -lquadmath -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether the compiler accepts very long lines... yes
checking whether the compiler accepts "line-number" lines cast by the preprocessor... yes
checking fortran 90 modules extension... mod
checking for the size of a Fortran integer... rm: intsizetest.x.dSYM: is a directory
4 bytes
checking for which C type corresponds to Fortran integer... rm: ccfortranint.x.dSYM: is a directory
int
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating testsuite/Makefile
config.status: creating build/Makefile
config.status: creating build/libxc.pc
config.status: creating build/libxc.spec
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
touch configure-stamp
libxc-1.0 has been configured.
rm -f libxc-1.0/src/libxc.f90
cd libxc-1.0/src && make libxc.f90 \
    AM_CPPFLAGS="-P -std=c99"
cpp   -P -std=c99 ./libxc_master.F90 > ../src/libxc.f90
cd libxc-1.0 && make
make  all-recursive
Making all in build
make[7]: Nothing to be done for `all'.
Making all in src
make  all-am
/bin/sh ../libtool  --tag=FC --tag=F77  --mode=compile /usr/local/gfortran/bin/gfortran  -ffree-form -g -ffree-line-length-none  -O2 -mtune=native -march=native -mfpmath=sse -c -o libxc_la-libxc.lo  `test -f 'libxc.f90' || echo './'`libxc.f90
libtool: ignoring unknown tag F77
libtool: compile:  /usr/local/gfortran/bin/gfortran -ffree-form -g -ffree-line-length-none -O2 -mtune=native -march=native -mfpmath=sse -c libxc.f90 -o libxc_la-libxc.o
libxc.f90:30:

module xc_f90_ ## types_m
1
Error: Unclassifiable statement at (1)
libxc.f90:34.17:

  integer, public, parameter :: xc_f90_kind = selected_real_kind(14)
                 1
Error: PUBLIC attribute at (1) is not allowed outside of the specification part of a module
libxc.f90:37.2:

  type xc_f90_ ## pointer_t
  1
Error: Unclassifiable statement at (1)
libxc.f90:38.11:

    private
           1
Error: PRIVATE statement at (1) is only allowed in the specification part of a module
libxc.f90:40.5:

  end type xc_f90_ ## pointer_t
     1
Error: Expecting END PROGRAM statement at (1)
libxc.f90:42.3:

end module xc_f90_ ## types_m
   1
Error: Expecting END PROGRAM statement at (1)
libxc.f90:46:

module xc_f90_ ## lib_m
1
Error: Unclassifiable statement at (1)
libxc.f90:48.13:

  use xc_f90_ ## types_m
             1
Error: Syntax error in USE statement at (1)
libxc.f90:49.19:

  use libxc_funcs_m
                   1
libxc.f90:39.30:

    integer, pointer :: buffer
                              2
Error: USE statement at (1) cannot follow data declaration statement at (2)
libxc.f90:51.15:

  implicit none
               1
libxc.f90:39.30:

    integer, pointer :: buffer
                              2
Error: IMPLICIT NONE statement at (1) cannot follow data declaration statement at (2)
libxc.f90:53.8:

  public
        1
Error: PUBLIC statement at (1) is only allowed in the specification part of a module
libxc.f90:95.28:

    integer function xc_f90_ ## info_number(info)
                            1
Error: Expected formal argument list in function definition at (1)
libxc.f90:96.17:

      use xc_f90_ ## types_m
                 1
Error: Syntax error in USE statement at (1)
libxc.f90:97.6:

      type(xc_f90_ ## pointer_t), intent(in) :: info
      1
Error: Unclassifiable statement at (1)
libxc.f90:98.7:

    end function xc_f90_ ## info_number
       1
Error: Expecting END INTERFACE statement at (1)
libxc.f90:100.28:

    integer function xc_f90_ ## info_kind(info)
                            1
Internal Error at (1):
insert_bbt(): Duplicate key found!
make[8]: *** [libxc_la-libxc.lo] Error 1
make[7]: *** [all] Error 2
make[6]: *** [all-recursive] Error 1
make[5]: *** [all] Error 2
make[4]: *** [build-stamp] Error 2
make[3]: *** [package-ready] Error 2
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Code: Select all

Basics:
  Prefix:                 /Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports
  Fortran90 compiler:     gfortran
  Fortran90 flags:        -ffree-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -mfpmath=sse -g -O2 -I/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include -I/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include 
  Linker flags:            
  Linked libraries:       -L/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/lib -lnetcdf -L/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/lib -lnetcdf 
  Installed module dir:   /Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include
  Installed lib dir:      /Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/lib
  Installed doc dir:      ${datarootdir}/doc/${PACKAGE_TARNAME}

cd sources/etsf_io-1.0.4 && make -j 4 
Making all in src/low_level
gfortran -I/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include -I. -ffree-form -g -ffree-line-length-none   -O2 -mtune=native -march=native -mfpmath=sse -g -O2 -I/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include -I/Users/michalplucinski/Downloads/abinit-7.0.4/tmp/fallbacks/exports/include  -c -o etsf_io_low_level.o  etsf_io_low_level.f90
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:115:no such instruction: `vmovsd (%rsi), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:129:no such instruction: `vmulsd (%rax), %xmm0,%xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:131:no such instruction: `vmovsd %xmm1, (%rax)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:148:no such instruction: `vmovsd (%rsi), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:174:no such instruction: `vmulsd (%rdx), %xmm0,%xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:176:no such instruction: `vmovsd %xmm1, (%rdx)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:207:no such instruction: `vmovsd (%rsi), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:252:no such instruction: `vmulsd (%rdx), %xmm0,%xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:254:no such instruction: `vmovsd %xmm1, (%rdx)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:294:no such instruction: `vmovsd (%rsi), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:350:no such instruction: `vmulsd (%rdx), %xmm0,%xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:352:no such instruction: `vmovsd %xmm1, (%rdx)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:401:no such instruction: `vmovsd (%rsi), %xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:483:no such instruction: `vmulsd (%rax), %xmm1,%xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:485:no such instruction: `vmovsd %xmm0, (%rax)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:548:no such instruction: `vmovsd (%rsi), %xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:645:no such instruction: `vmulsd (%rax), %xmm1,%xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:647:no such instruction: `vmovsd %xmm0, (%rax)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:699:no such instruction: `vmovsd (%rsi), %xmm1'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:839:no such instruction: `vmulsd (%rax), %xmm1,%xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:841:no such instruction: `vmovsd %xmm0, (%rax)'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:37272:no such instruction: `vmovss 1336(%rsp), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:37277:no such instruction: `vucomiss (%r15), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:37550:no such instruction: `vucomiss LC152(%rip), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:37841:no such instruction: `vmovss LC157(%rip), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:37845:no such instruction: `vucomiss 0(%rbp), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:38288:no such instruction: `vmovss LC157(%rip), %xmm0'
/var/folders/sy/tn179p_x5vz2x4pqpwfx_bg80000gn/T//ccgcglTn.s:38289:no such instruction: `vucomiss 0(%rbp), %xmm0'
make[5]: *** [etsf_io_low_level.o] Error 1
make[4]: *** [all-recursive] Error 1
make[3]: *** [stamps/etsf_io-build-stamp] Error 2
make[2]: [all-local] Error 2 (ignored)
Checking build of etsf_io fallback
test -e stamps/etsf_io-install-stamp
make[2]: *** [all-local] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Code: Select all

otool -L abinit

Code: Select all

configure:33167: checking for the requested FFT support
configure:33169: result: fftw3
configure:33571: /Users/michalplucinski/Downloads/abinit-7.0.4/tmp/config/wrappers/wrap-mpiLFC -o conftest  -g -ffree-line-length-none         conftest.F90 -L/usr/local/Cellar/fftw/3.3.2/lib -lfftw3 -L/usr/local/Cellar/fftw/3.3.2/lib -lfftw3       >&5
Undefined symbols for architecture x86_64:
  "_dfftw_execute_", referenced from:
      _MAIN__ in ccVCae52.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
configure:33571: $? = 1
configure: failed program was:
|       program main
|
|         call dfftw_execute
|
|       end
configure:34275: checking for the actual FFT support
configure:34277: result: broken
configure:34322: error: the specified FFT libraries do not work

Code: Select all

Summary of important options:

  * C compiler      : gnu version 
  * Fortran compiler: gnu version 4.6
  * architecture    :   ( bits)

  * debugging       : basic
  * optimizations   : yes

  * OpenMP enabled  : no (collapse: ignored)
  * MPI    enabled  : yes
  * MPI-IO enabled  : yes
  * GPU    enabled  : no (none)

  * TRIO   flavor = netcdf-fallback+etsf_io-fallback
  * TIMER  flavor = abinit (libs: ignored)
  * LINALG flavor = netlib-fallback (libs: ignored)
  * ALGO   flavor = none (libs: ignored)
  * FFT    flavor = fftw3 (libs: user-defined)
  * MATH   flavor = none (libs: ignored)
  * DFT    flavor = libxc-fallback+atompaw-fallback+bigdft-fallback+wannier90-fallback

LINALG is set to netlib, not openblas as I set it.

Here are my configure options:
../configure FCCPP=/usr/local/gfortran/bin/cpp --enable-mpi="yes" --enable-optim="yes" CFLAGS_OPTIM="-O2" FCFLAGS_OPTIM="-O2" --with-mpi-prefix="/usr/local/Cellar/open-mpi/1.6.3" --with-fft-flavor="fftw3" --with-fft-libs="-L/usr/local/fftw-3.3.3/lib -lfftw3" --with-linalg-flavor="goto" --with-linalg-libs="-L/usr/local/Cellar/openblas/0.2.5/lib -llapack -lcblas -lf77blas -latlas -lopenblas"

What should I do to ensure LINALG is set properly?

Here is the selection of configure output pertaining to linear algebra support:

checking for the requested linear algebra support... goto
checking whether to select a fallback for linear algebra... no
checking for BLAS support in specified libraries... no
checking for AXPBY support in specified BLAS libraries... no
checking for gemm3m in specified libraries... no
checking for mkl_imatcopy in specified libraries... no
checking for mkl_omatcopy in specified libraries... no
checking for mkl_omatadd in specified libraries... no
checking for LAPACK support in specified libraries... no
checking for BLACS support in specified libraries... no
checking for ScaLAPACK support in specified libraries... no
checking for MAGMA (version>=1.1.0) support in specified libraries... checking TEST... no
checking whether we have a serial linear algebra support... no
configure: WARNING: falling back to internal linear algebra libraries
checking whether we have a MPI linear algebra support... no
checking whether we have a GPU linear algebra support... no
checking for the actual linear algebra support... netlib-fallback