Code: Select all
CC=$MPIC_COMP FC=$MPIF_COMP CXX=$MPIF_COMP LDFLAGS="-L$ROOT_DIR/MPICH/libs" FCFLAGS="-I$ROOT_DIR/BIGDFT/include" LIBS="-lfmpich -lmpi -lmpichcxx -lmpichf90 -lmpich -lmpicxx -lmpifort -lmpifort -lmpl -lopa" CPPFLAGS="-I$ROOT_DIR/lapack-3.5.0/lapacke/include" ./configure --prefix=$ROOT_DIR/ABINIT --enable-mpi --enable-mpi-io --with-mpi-incs="-I$ROOT_DIR/MPICH/include" --with-mpi-libs="-L$ROOT_DIR/MPICH/libs -lfmpich -lmpi -lmpichcxx -lmpichf90 -lmpich -lmpicxx -lmpifort -lmpifort -lmpl -lopa" --with-netcdf-libs="-L$ROOT_DIR/NETCDF_FORTRAN/lib -lnetcdff -lnetcdf" --with-fft-flavor="fftw3" --with-fft-incs="-I$ROOT_DIR/FFTW/include/" --with-fft-libs="-L$ROOT_DIR/FFTW/lib -lfftw3_mpi -lfftw3" --with-linalg-libs="-L$ROOT_DIR/magma -lmagma -L$ROOT_DIR/scalapack-2.0.2/lib -lscalapack -L$ROOT_DIR/lapack-3.5.0/ -llapack -ltmglib -L$ROOT_DIR/CBLAS/lib -lcblas -L$ROOT_DIR/ATLAS/lib/ -ltstatlas -latlas -L$ROOT_DIR/BLAS -lblas" --with-dft-flavor="atompaw+bigdft+libxc+wannier90" --enable-gpu --with-gpu-flavor="cuda-double" --with-gpu-prefix="/usr/local/cuda-7.0" --enable-gw-dpc --with-atompaw-bins="$ROOT_DIR/ATOMPAW/bin" --with-atompaw-incs="-I$ROOT_DIR/ATOMPAW/include" --with-atompaw-libs="-L$ROOT_DIR/ATOMPAW/lib -latompaw" --with-bigdft-incs="-I$ROOT_DIR/BIGDFT/include" --with-bigdft-libs="-L$ROOT_DIR/BIGDFT/lib -labinit -lbigdft -lbigdft-1" --with-wannier90-bins="$ROOT_DIR/wannier90-2.0.0/bin" --with-wannier90-libs="-L$ROOT_DIR/wannier90-2.0.0/libs -lwannier" --with-yaml-incs="-I$ROOT_DIR/BIGDFT/include" --with-yaml-libs="-L$ROOT_DIR/BIGDFT/lib -lyaml" --with-libxc-incs="-I$ROOT_DIR/BIGDFT/include" --with-libxc-libs="-L$ROOT_DIR/BIGDFT/lib -lxcf90 -lxc" --enable-openmpthe error i got :
configure: error: external bigdft support does not work
attached: configlog_1.log
now from config.log file the following line caught my attention:
call init_restart_objects(iproc,inputs,atoms,rst,routine)
1
Error: Symbol 'rst' at (1) has no IMPLICIT type
configure:48763: $? = 1
i did grep -r "restart_objects" & saw bigdft_run.mod defines the restart_objects!
so i manually etited configure file & changed :
Code: Select all
use bigdft_api
implicit none
integer iprocto
Code: Select all
use bigdft_api
[b] + use bigdft_run[/b]
implicit none
integer iproc.Again i ran configure script , again i got error but error was diffrent this time & Now i am unable to fix the problem further. The error log is attached: configlog_2.log
since problem is related to BigDFT , the commands used for BigDFT configuration is:
CC=$C_COMP CXX=$CXX_COMP FC=$F_COMP F77=$F_COMP FFLAGS="-fPIC" ./configure --prefix=$ROOT_DIR/BIGDFT/ --with-cuda-path=/usr/local/cuda-7.0 --with-mpi-include="-I$ROOT_DIR/MPICH/include" --with-mpi-ldflags="-L$ROOT_DIR/MPICH/lib" --with-mpi-libs="-lfmpich -lmpi -lmpichcxx -lmpichf90 -lmpich -lmpicxx -lmpifort -lopa" --with-openmp --with-etsf-io --with-etsf-io-path="$ROOT_DIR/ETSF_IO" --with-netcdf-path="$ROOT_DIR/NETCDF_C" --with-netcdf-libs="-lnetcdff -lnetcdf" --with-blas --with-blas-path="$ROOT_DIR/BLAS" --with-lapack --with-lapack-path="$ROOT_DIR/lapack-3.5.0" --with-scalapack --with-scalapack-path="$ROOT_DIR/scalapack-2.0.2"
top_builddir=$ROOT_DIR/bigdft-1.7.6 make
Any hint/help will be very fruitful.
Eagerly awaiting your reply
Regards,
Puneet Singh
The terminal log is :
########################################
#########################################
Code: Select all
==============================================================================
=== Overall startup ===
==============================================================================
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking how to create a ustar tar archive... gnutar
checking whether make sets $(MAKE)... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether ln -s works... yes
checking for a sed that does not truncate output... /bin/sed
checking for gawk... (cached) gawk
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for realpath,readlink... no
configure: not loading options (no config file available)
==============================================================================
=== Build-system information ===
==============================================================================
configure: ABINIT version 7.10.4
configure: M4 010413 - Autoconf 026300 - Automake 011101 - Libtool 020206
configure: reporting user interface changes:
==============================================================================
=== Option consistency checking ===
==============================================================================
configure: checking consistency of library-related options
configure: |---> all OK
configure:
configure: checking consistency of experimental options
configure: |---> all OK
configure:
configure: checking consistency of maintainer options
configure: |---> all OK
configure:
configure: parsing command-line options
==============================================================================
=== Multicore architecture startup ===
==============================================================================
configure: Initializing MPI support
configure: compiler checks deferred
configure: Initializing GPU support
checking which kind of GPU we want... cuda-double
configure: looking for GPU support in /usr/local/cuda-7.0
checking for the nVidia C compiler... /usr/local/cuda-7.0/bin/nvcc
checking for Cuda headers... run-time fft blas
checking for Cuda libraries... common run-time fft blas
checking for Cuda link flags... -Wl,-rpath=/usr/local/cuda-7.0/lib64
configure: Cuda incs: -I/usr/local/cuda-7.0/include
configure: Cuda libs: -L/usr/local/cuda-7.0/lib64 -lcublas -lcufft -lcudart -lcuda
==============================================================================
=== Utilities ===
==============================================================================
checking for sh... /bin/sh
checking for mv... /bin/mv
checking for perl... /usr/bin/perl
checking for rm... /bin/rm
checking for patch... patch
checking for tar... tar
==============================================================================
=== C support ===
==============================================================================
checking for mpicc... /home/puneet/ABINIT/MPICH/bin/mpicc
checking for gcc... mpicc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of mpicc... gcc3
checking how to run the C preprocessor... mpicc -E
checking which type of compiler we have... gnu 4.4
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 whether byte ordering is bigendian... no
==============================================================================
=== C++ support ===
==============================================================================
checking for mpifort... /home/puneet/ABINIT/MPICH/bin/mpifort
checking whether we are using the GNU C++ compiler... yes
checking whether mpifort accepts -g... yes
checking dependency style of mpifort... gcc3
checking which type of C++ compiler we have... gnu 4.4
==============================================================================
=== Fortran support ===
==============================================================================
checking for mpifort... /home/puneet/ABINIT/MPICH/bin/mpifort
checking whether we are using the GNU Fortran compiler... yes
checking whether mpifort accepts -g... yes
checking which type of Fortran compiler we have... gnu 4.4
checking fortran 90 modules extension... mod
checking for Fortran flag to compile .F90 files... none
configure: determining Fortran module case
checking whether Fortran modules are upper-case... no
checking how to get verbose linking output from mpifort... -v
checking for Fortran libraries of mpifort... -L/home/puneet/ABINIT/MPICH/libs -L/home/puneet/ABINIT/MPICH/lib -L/usr/local/cuda-7.0/lib64/../lib64 -L/usr/local/cuda-7.0/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/home/puneet/ABINIT/ETSF_IO/lib -L/home/puneet/ABINIT/ATOMPAW/lib -L/home/puneet/ABINIT/BIGDFT/lib -L/home/puneet/ABINIT/wannier90-2.0.0 -L/home/puneet/ABINIT/HDF5/lib -L/home/puneet/ABINIT/NETCDF_C/lib -L/home/puneet/ABINIT/NETCDF_FORTRAN/lib -L/home/puneet/ABINIT/NETCDF/lib -L/home/puneet/ABINIT/SZIP/lib -L/home/puneet/ABINIT/ZLIB/lib -L/home/puneet/ABINIT/JPEG/lib -L/home/puneet/ABINIT/magma/lib -L/home/puneet/ABINIT/FFTW/lib -L/home/puneet/ABINIT/lapack-3.5.0 -L/home/puneet/ABINIT/CBLAS/lib -L/home/puneet/ABINIT/BLAS -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib -L/opt/intel/composer_xe_2015.0.090/compiler/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/ipp/lib/intel64 -L/opt/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lfmpich -lmpi -lmpichcxx -lmpichf90 -lmpich -lmpicxx -lmpifort -lmpl -lopa -lgfortranbegin -lgfortran -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
==============================================================================
=== Python support ===
==============================================================================
checking for python... python
checking for Python CPPFLAGS... -I/usr/include/python2.6 -I/usr/lib64/python2.6/site-packages/numpy/core/include
checking for bzr... no
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking for numpy/arrayobject.h... yes
==============================================================================
=== Libraries and linking ===
==============================================================================
checking for ar... ar
checking for ranlib... ranlib
==============================================================================
=== Hints ===
==============================================================================
checking for cpp... cpp
checking for a true C preprocessor... cpp
checking which cpp hints to apply... default/default/default
checking which cc hints to apply... gnu/default/default
checking which xpp hints to apply... none/none/none
checking which cxx hints to apply... gnu/default/default
checking which fpp hints to apply... default/default/default
checking which fc hints to apply... gnu/default/default
checking which ar hints to apply... none/none/none
checking which Fortran preprocessor to use...
checking which Fortran preprocessor flags to apply...
checking whether to wrap Fortran compiler calls... no
==============================================================================
=== Debugging ===
==============================================================================
checking debugging status... enabled (profile mode: basic)
configure: setting C debug flags to '-g'
configure: setting C++ debug flags to '-g'
configure: setting Fortran debug flags to '-g'
checking whether to activate debug mode in source files... no
checking whether to activate debug verbosity in source files... no
checking which cc debug flags to apply... gnu/default/default
checking which cxx debug flags to apply... none/none/none
checking which fc debug flags to apply... gnu/default/default
checking whether to activate design-by-contract debugging... no
==============================================================================
=== Optimizations ===
==============================================================================
checking optimization status... enabled (profile mode: standard)
checking which cc optimizations to apply... gnu/default/default
checking which cxx optimizations to apply... gnu/default/default
checking which fc optimizations to apply... gnu/default/default
checking whether to apply per-directory optimizations... yes
==============================================================================
=== 64-bit support ===
==============================================================================
checking for a 64-bit architecture... yes
checking whether to use 64-bit flags... no
checking for user-defined 64-bit flags...
==============================================================================
=== Build flags ===
==============================================================================
configure: static builds may be performed
==============================================================================
=== Advanced compiler features ===
==============================================================================
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking sys/malloc.h usability... no
checking sys/malloc.h presence... no
checking for sys/malloc.h... no
checking mcheck.h usability... yes
checking mcheck.h presence... yes
checking for mcheck.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking for abort... yes
checking for mallinfo... yes
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of unsigned int... 4
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of size_t... 8
checking size of ptrdiff_t... 8
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether the Fortran compiler accepts the ASYNCHRONOUS attribute... no
checking whether the Gfortran compiler supports BACKTRACE... no
checking whether the Fortran compiler supports GET_COMMAND_ARGUMENT... yes
checking whether the Fortran compiler supports EXECUTE_COMMAND_LINE... no
checking whether the Fortran compiler supports SYSTEM... yes
checking whether the Fortran compiler accepts the CONTIGUOUS attribute... no
checking whether the Fortran compiler supports allocatable arrays in datatypes... yes
checking whether the Fortran compiler supports IEEE_EXCEPTIONS... no
checking whether the Fortran compiler supports IOMSG... yes
checking whether the Fortran compiler provides the iso_c_binding module... yes
checking whether the Fortran compiler accepts exit()... yes
checking whether the Fortran compiler accepts flush()... yes
checking whether the Fortran compiler accepts flush_()... no
checking whether the Fortran compiler accepts gamma()... yes
checking whether the Fortran compiler accepts getenv()... yes
checking whether the Fortran compiler accepts getpid()... no
checking whether the Fortran compiler accepts quadruple integers... yes
checking whether the Fortran compiler accepts long lines... yes
checking whether the Fortran compiler supports \newline in CPP macros... no
checking whether the Fortran compiler supports MOVE_ALLOC (F2003)... yes
checking whether the Fortran compiler accepts the PRIVATE attribute... yes
checking whether the Fortran compiler accepts the PROTECTED attribute... yes
checking whether the Fortran compiler supports stream IO... yes
checking whether the Fortran compiler accepts cpu_time()... yes
checking whether the Fortran compiler accepts etime()... no
checking whether to use C clock for timings... no
==============================================================================
=== Multicore architecture support ===
==============================================================================
checking whether to enable OpenMP support... yes
checking Fortran flags for OpenMP... -fopenmp
checking whether OpenMP's COLLAPSE works... yes
configure: OpenMP support is enabled in Fortran source code only
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... yes
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... yes
checking whether MPI is usable... yes
checking whether to build MPI I/O code... yes
checking which level of MPI is supported by the Fortran compiler... 2
checking whether the MPI library supports MPI_CREATE_TYPE_STRUCT... yes
checking whether the MPI library supports MPI_IALLTOALL (MPI3)... yes
checking whether the MPI library supports MPI_IALLTOALLV (MPI3)... yes
checking whether the MPI library supports MPI_IALLREDUCE (MPI3)... yes
checking whether to activate GPU support... yes
checking for the requested GPU support... cuda-double
configure: Cuda incs: -I/usr/local/cuda-7.0/include
configure: Cuda libs: -L/usr/local/cuda-7.0/lib64 -lcublas -lcufft -lcudart -lcuda
checking cuda_runtime_api.h usability... yes
checking cuda_runtime_api.h presence... yes
checking for cuda_runtime_api.h... yes
checking cufft.h usability... yes
checking cufft.h presence... yes
checking for cufft.h... yes
checking cublas.h usability... yes
checking cublas.h presence... yes
checking for cublas.h... yes
checking whether Cuda programs can be compiled... yes
checking whether we have Cuda < 4... no
checking for the actual GPU support... cuda-double
==============================================================================
=== Feature triggers ===
==============================================================================
configure: using tarball repository /home/puneet/.abinit/tarballs
checking for the requested linear algebra support... netlib
checking whether to select a fallback for linear algebra... no
checking for BLAS support in specified libraries... yes
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... yes
checking for LAPACKE C API support in specified libraries... yes
checking for BLACS support in specified libraries... yes
checking for ScaLAPACK support in specified libraries... yes
checking for ELPA support in specified libraries... no
checking for PLASMA support in specified libraries... no
checking for MAGMA (version>=1.1.0) support in specified libraries... yes
checking whether we have a serial linear algebra support... yes
checking whether we have a MPI linear algebra support... yes
checking whether we have a GPU linear algebra support... yes
checking for the actual linear algebra support... netlib
checking for the requested FFT support... fftw3
checking for the actual FFT support... fftw3
==============================================================================
=== Connectors / Fallbacks ===
==============================================================================
checking for the requested transferable I/O support... none
checking for the actual transferable I/O support... none
checking for the requested timer support... abinit
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for clock_gettime in -lrt... yes
checking for clock_gettime... yes
checking for the actual timer support... abinit
checking for the requested algorithmic support... none
checking for the actual algorithmic support... none
checking for the requested math support... none
checking for the actual math support... none
checking for the requested DFT support... atompaw+bigdft+libxc+wannier90
checking whether to select a fallback for libxc... no
checking xc.h usability... yes
checking xc.h presence... yes
checking for xc.h... yes
checking xc_funcs.h usability... yes
checking xc_funcs.h presence... yes
checking for xc_funcs.h... yes
checking for Fortran module includes... none required
checking whether LibXC has Fortran support... yes
checking whether this is LibXC version 2.0... yes
checking whether LibXC has xc_f90_functional_get_number()... yes
checking whether to select a fallback for atompaw... no
checking whether to select a fallback for bigdft... no
checking for Fortran module includes... none required (cached)
checking whether BigDFT libraries work... no
+--------------------------------------------------------------+
| Connector detection failure |
+--------------------------------------------------------------+
| The build system of Abinit has not been able to detect |
| one or more requested external packages, probably because |
| you did not provide sufficient information. This means |
| that the build cannot proceed, and the configure script |
| will thus abort now with an error. |
| |
| To address this issue, you may: |
| |
| * make sure that the prerequisites of the external |
| packages are available and enabled, e.g. |
| --with-dft-flavor="libxc+bigdft" or |
| --with-trio-flavor="netcdf+etsf_io" |
| |
| * use the --with-*-bins, --with-*-incs, and |
| --with-*-libs options of configure to provide |
| additional information; please see the section related |
| to connectors in |
| ~abinit/doc/build/config-template.ac for available |
| options and details; |
| |
| * disable the corresponding extensions, by using the |
| associated --with-*-flavor="none" options of |
| configure; please see the section associated to |
| connectors in ~abinit/doc/build/config-template.ac for |
| details. |
| |
+--------------------------------------------------------------+
configure: error: external bigdft support does not work/ 
