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Parallel-NetCDF / PnetCDF

Source code repository of PnetCDF library and utilities
https://parallel-netcdf.github.io
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Unable to compile 1.11.1 #45

Closed ArchangeGabriel closed 5 years ago

ArchangeGabriel commented 5 years ago

Build log:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for mpicc... /usr/bin/mpicc
checking for gcc... /usr/bin/mpicc
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/bin/mpicc accepts -g... yes
checking for /usr/bin/mpicc option to accept ISO C89... none needed
checking whether /usr/bin/mpicc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of /usr/bin/mpicc... gcc3
checking how to run the C preprocessor... /usr/bin/mpicc -E
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking if C compiler is IBM XLC... no
checking if C compiler is pgcc... no
checking if C compiler is Fujitsu fccpx... no
checking for MPI_Comm_rank... yes
checking for MPI_File_open... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for ar... ar
checking the archiver (ar) interface... ar
checking how to print strings... printf
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/bin/mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from /usr/bin/mpicc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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/bin/mpicc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/mpicc option to produce PIC... -fPIC -DPIC
checking if /usr/bin/mpicc PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/mpicc static flag -static works... no
checking if /usr/bin/mpicc supports -c -o file.o... yes
checking if /usr/bin/mpicc supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
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... yes
checking whether to build static libraries... yes
checking for mpicxx... /usr/bin/mpicxx
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/mpicxx accepts -g... yes
checking dependency style of /usr/bin/mpicxx... gcc3
checking how to run the C++ preprocessor... /usr/bin/mpicxx -E
checking for ld used by /usr/bin/mpicxx... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the /usr/bin/mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for /usr/bin/mpicxx option to produce PIC... -fPIC -DPIC
checking if /usr/bin/mpicxx PIC flag -fPIC -DPIC works... yes
checking if /usr/bin/mpicxx static flag -static works... no
checking if /usr/bin/mpicxx supports -c -o file.o... yes
checking if /usr/bin/mpicxx supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpicxx linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for MPI_File_close... yes
checking whether MPI C++ compiler redefines SEEK_SET ... no
checking for mpif77... /usr/bin/mpif77
checking for mpif90... /usr/bin/mpif90
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /usr/bin/mpif77 accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for /usr/bin/mpif77 option to produce PIC... -fPIC
checking if /usr/bin/mpif77 PIC flag -fPIC works... yes
checking if /usr/bin/mpif77 static flag -static works... no
checking if /usr/bin/mpif77 supports -c -o file.o... yes
checking if /usr/bin/mpif77 supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpif77 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to get verbose linking output from /usr/bin/mpif77... -v
checking for Fortran 77 libraries of /usr/bin/mpif77...  -L/usr/lib/openmpi -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/../../.. -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread
checking whether /usr/bin/mpif77 is a valid MPI compiler... yes
checking whether we are using the GNU Fortran compiler... yes
checking whether /usr/bin/mpif90 accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for /usr/bin/mpif90 option to produce PIC... -fPIC
checking if /usr/bin/mpif90 PIC flag -fPIC works... yes
checking if /usr/bin/mpif90 static flag -static works... no
checking if /usr/bin/mpif90 supports -c -o file.o... yes
checking if /usr/bin/mpif90 supports -c -o file.o... (cached) yes
checking whether the /usr/bin/mpif90 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to get verbose linking output from /usr/bin/mpif90... -v
checking for Fortran libraries of /usr/bin/mpif90...  -L/usr/lib/openmpi -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.1/../../.. -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread
checking whether mpi.mod is available... yes
checking whether /usr/bin/mpif90 is a valid MPI compiler... yes
checking for Fortran flag needed to accept free-form source... -ffree-form
checking for Fortran flag to compile preprocessed .F files... none
checking for Fortran flag to compile preprocessed .F90 files... none
checking for Fortran flag to compile preprocessed .F files... (cached) none
checking how to define symbols for preprocessed Fortran... -D
checking for Fortran flag to compile .f files... none
checking for Fortran flag to compile .F files... none
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .F90 files... none
checking for Fortran flag needed to accept fixed-form source... -ffixed-form
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for C-equivalent to Fortran routine "SUB_A"... sub_a_
checking if Fortran compiler is NAG... no
checking Fortran compiler treating constant modifier... 8
checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
checking Fortran 90 module extension... (cached) mod
checking whether Fortran 90 compiler capitalizes .mod filenames... no
configure: creating ./config.lt
config.lt: creating libtool
checking whether MPI library is built with shared library support... yes
checking for egrep... (cached) /usr/bin/grep -E
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for sed handling option -i ... /usr/bin/sed -i''
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for m4... m4
checking m4 additional flags... none needed
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for IEEE floating point format... yes
checking for strerror... yes
checking for access... yes
checking for unlink... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... yes
checking for tsearch... yes
checking for tdelete... yes
checking for MPI_Offset... yes
checking size of MPI_Offset... 8
checking size of MPI_Aint... 8
checking for MPI_Get_address... yes
checking for MPI_Type_create_subarray... yes
checking for MPI_Type_create_hvector... yes
checking for MPI_Type_create_hindexed... yes
checking for MPI_Type_create_struct... yes
checking for MPI_Type_create_resized... yes
checking for MPI_Type_get_extent... yes
checking whether MPI_COMBINER_DUP is declared... yes
checking whether MPI_COMBINER_HVECTOR_INTEGER is declared... yes
checking whether MPI_COMBINER_HINDEXED_INTEGER is declared... yes
checking whether MPI_COMBINER_SUBARRAY is declared... yes
checking whether MPI_COMBINER_DARRAY is declared... yes
checking whether MPI_COMBINER_RESIZED is declared... yes
checking whether MPI_COMBINER_STRUCT_INTEGER is declared... yes
checking whether MPI_COMBINER_INDEXED_BLOCK is declared... yes
checking whether MPI_COMBINER_F90_REAL is declared... yes
checking whether MPI_COMBINER_F90_INTEGER is declared... yes
checking whether MPI_COMBINER_F90_COMPLEX is declared... yes
checking whether MPI_ERR_FILE_EXISTS is declared... yes
checking whether MPI_ERR_NO_SUCH_FILE is declared... yes
checking whether MPI_ERR_AMODE is declared... yes
checking whether MPI_ERR_NOT_SAME is declared... yes
checking whether MPI_ERR_BAD_FILE is declared... yes
checking whether MPI_ERR_READ_ONLY is declared... yes
checking whether MPI_ERR_ACCESS is declared... yes
checking whether MPI_ERR_NO_SPACE is declared... yes
checking whether MPI_ERR_QUOTA is declared... yes
checking whether MPI datatype MPI_OFFSET is defined ... yes
checking whether MPI datatype MPI_INTEGER8 is defined ... yes
checking whether MPI datatype MPI_CHARACTER is defined ... yes
checking whether MPI datatype MPI_REAL is defined ... yes
checking whether MPI datatype MPI_INTEGER is defined ... yes
checking whether MPI datatype MPI_DOUBLE_PRECISION is defined ... yes
checking whether MPI datatype MPI_INTEGER1 is defined ... yes
checking whether MPI datatype MPI_INTEGER2 is defined ... yes
checking whether MPI datatype MPI_INTEGER4 is defined ... yes
checking whether MPI datatype MPI_REAL2 is defined ... no
checking whether MPI datatype MPI_REAL4 is defined ... yes
checking whether MPI datatype MPI_REAL8 is defined ... yes
checking whether char is unsigned... no
checking whether byte ordering is bigendian... no
checking for size_t... yes
checking for off_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking for schar... no
checking for uchar... no
checking for ushort... yes
checking for uint... yes
checking for longlong... no
checking for ulonglong... no
checking for int64... no
checking for uint64... no
checking size of size_t... 8
checking size of off_t... 8
checking size of char... 1
checking size of signed char... 1
checking size of unsigned char... 1
checking size of short... 2
checking size of unsigned short int... 2
checking size of unsigned short... 2
checking size of int... 4
checking size of unsigned int... 4
checking size of long... 8
checking size of float... 4
checking size of double... 8
checking size of long long... 8
checking size of unsigned long long... 8
checking size of ptrdiff_t... 8
checking size of ushort... 2
checking size of uint... 4
checking size of MPI_Fint... 4
checking for /usr/bin/nm... /usr/bin/nm -B
checking nm flags... 
checking for C-equivalent to Fortran routine "SUB"... sub_
checking for Fortran "integer*1"... yes
checking for Fortran "integer*2"... yes
checking for Fortran "integer*8"... yes
checking if Fortran "integer*1" is ... "signed char" in C
checking if Fortran "integer*2" is ... "short" in C
checking if Fortran "integer*8" is ... "int" in C
checking if Fortran "integer" is ... "int" in C
checking if Fortran "real" is ... "float" in C
checking if Fortran "doubleprecision" is ... "double" in C
checking for Fortran-equivalent to netCDF "byte"... byte
checking for Fortran-equivalent to netCDF "short"... integer*2
checking for Fortran 77 GNU intrinsic INT... yes
checking for Fortran 77 intrinsic INT1... no
checking for Fortran 77 intrinsic INT2... yes
checking for Fortran 77 intrinsic INT8... yes
checking for gcov... gcov
checking if C++ macro __func__ or __FUNCTION__ is defined... yes
checking for nc-config... /usr/bin/nc-config
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking netcdf_par.h usability... yes
checking netcdf_par.h presence... yes
checking for netcdf_par.h... yes
checking netcdf_meta.h usability... yes
checking netcdf_meta.h presence... yes
checking for netcdf_meta.h... yes
checking whether NetCDF version is 4.6.2 or later... yes
checking whether NetCDF library is built with parallel I/O enabled... yes
checking whether relax-coord-bound is enabled in NetCDF-4... yes
checking for library containing nc_open... -lnetcdf
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking whether HDF5 version is 1.10.4 or later... yes
checking for latex... no
checking for dvipdf... no
checking for mpiexec... /usr/bin/mpiexec
checking for gcc... /usr/bin/gcc
date: invalid date '1555416712'
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/dispatchers/Makefile
config.status: creating src/libs/Makefile
config.status: creating src/include/Makefile
config.status: creating src/include/pnetcdf.h
config.status: creating src/drivers/Makefile
config.status: creating src/drivers/common/Makefile
config.status: creating src/drivers/include/Makefile
config.status: creating src/drivers/ncmpio/Makefile
config.status: creating src/drivers/nc4io/Makefile
config.status: creating src/drivers/ncbbio/Makefile
config.status: creating src/drivers/ncfoo/Makefile
config.status: creating src/binding/Makefile
config.status: creating src/binding/cxx/Makefile
config.status: creating src/binding/f77/Makefile
config.status: creating src/binding/f77/pnetcdf.inc
config.status: creating src/binding/f90/Makefile
config.status: creating src/binding/f90/pnetcdf.f90
config.status: creating src/binding/f90/api.fh
config.status: creating src/binding/f90/nfmpi_constants.fh
config.status: creating src/utils/Makefile
config.status: creating src/utils/ncoffsets/Makefile
config.status: creating src/utils/pnetcdf_version/Makefile
config.status: creating src/utils/ncvalidator/Makefile
config.status: creating src/utils/ncmpidiff/Makefile
config.status: creating src/utils/ncmpidump/Makefile
config.status: creating src/utils/ncmpigen/Makefile
config.status: creating src/utils/ncmpilogdump/Makefile
config.status: creating src/utils/pnetcdf-config
config.status: creating src/packaging/Makefile
config.status: creating src/packaging/pnetcdf.pc
config.status: creating examples/Makefile
config.status: creating examples/C/Makefile
config.status: creating examples/tutorial/Makefile
config.status: creating examples/CXX/Makefile
config.status: creating examples/F77/Makefile
config.status: creating examples/F90/Makefile
config.status: creating examples/burst_buffer/Makefile
config.status: creating benchmarks/Makefile
config.status: creating benchmarks/C/Makefile
config.status: creating benchmarks/FLASH-IO/Makefile
config.status: creating doc/Makefile
config.status: creating doc/pnetcdf-api/Makefile
config.status: creating man/Makefile
config.status: creating test/Makefile
config.status: creating test/common/Makefile
config.status: creating test/C/Makefile
config.status: creating test/fandc/Makefile
config.status: creating test/nc_test/Makefile
config.status: creating test/cdf_format/Makefile
config.status: creating test/nc4/Makefile
config.status: creating test/header/Makefile
config.status: creating test/testcases/Makefile
config.status: creating test/nonblocking/Makefile
config.status: creating test/largefile/Makefile
config.status: creating test/CXX/Makefile
config.status: creating test/subfile/Makefile
config.status: creating test/nf_test/Makefile
config.status: creating test/nf_test/tests.inc
config.status: creating test/nf90_test/Makefile
config.status: creating test/nf90_test/tests.inc
config.status: creating test/F90/Makefile
config.status: creating test/burst_buffer/Makefile
config.status: creating src/include/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
------------------------------------------------------------------------------

   PnetCDF Version 1.11.1

   Features:  Build static libraries                      - yes
              Build shared libraries                      - yes
              Build Fortran APIs                          - yes
              Build C++ APIs                              - yes
              NetCDF-4 support                            - enabled

   Compilers: MPICC    = /usr/bin/mpicc
              MPICXX   = /usr/bin/mpicxx
              MPIF77   = /usr/bin/mpif77
              MPIF90   = /usr/bin/mpif90
              CPPFLAGS = -D_FORTIFY_SOURCE=2 -fPIC
              CFLAGS   = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt
              CXXFLAGS = -march=x86-64 -mtune=generic -O2 -pipe -fno-plt
              FFLAGS   = -g -O2
              FCFLAGS  = -g -O2
              LDFLAGS  = -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now

   NetCDF-4 library:
              NETCDF4_INC     = -I/usr/include
              NETCDF4_LDFLAGS = -L/usr/lib
              NETCDF4_LIBS    = -lnetcdf

   Now run 'make' to build the library and utility tools.
   Then run 'make [<target>]' for testing and installation, where the
   optional <target> can be:
              tests    - build all test programs (build only, no run)
              check    - run sequential test programs
              ptest    - run parallel test programs on 4 MPI processes
              ptests   - run parallel test programs on 3,4,6,8 MPI processes
              install  - install PnetCDF library in /usr

------------------------------------------------------------------------------
Making all in src
make[1]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src'
Making all in include
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/include'
make  all-am
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/include'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/include'
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/include'
Making all in dispatchers
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/dispatchers'
m4  -DPNETCDF -I../../m4 attr_getput.m4 >attr_getput.c
m4  -DPNETCDF -I../../m4 var_getput.m4 >var_getput.c
make  all-am
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/dispatchers'
  CC       lib_version.lo
  CC       file.lo
  CC       dimension.lo
  CC       variable.lo
  CC       attribute.lo
  CC       error_codes.lo
  CC       attr_getput.lo
  CC       var_getput.lo
  CCLD     libdispatchers.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/dispatchers'
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/dispatchers'
Making all in drivers
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers'
Making all in include
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/include'
m4  -DPNETCDF -I../../../m4 ncx_h.m4 >ncx.h
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/include'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/include'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/include'
Making all in common
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/common'
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncx.m4 >ncx.c
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL convert_swap.m4 >convert_swap.c
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/common'
  CC       mem_alloc.lo
  CC       utf8proc.lo
  CC       dtype_decode.lo
  CC       create_imaptype.lo
  CC       error_mpi2nc.lo
  CC       check_name.lo
  CC       pack_unpack.lo
  CC       utils.lo
  CC       error_posix2nc.lo
  CC       hash_map.lo
  CC       ncx.lo
  CC       convert_swap.lo
  CCLD     libcommon.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/common'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/common'
Making all in ncmpio
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/ncmpio'
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncmpio_getput.m4 >ncmpio_getput.c
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncmpio_i_getput.m4 >ncmpio_i_getput.c
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncmpio_varn.m4 >ncmpio_varn.c
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncmpio_i_varn.m4 >ncmpio_i_varn.c
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL ncmpio_attr.m4 >ncmpio_attr.c
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/ncmpio'
  CC       ncmpio_create.lo
  CC       ncmpio_driver.lo
  CC       ncmpio_close.lo
  CC       ncmpio_open.lo
  CC       ncmpio_enddef.lo
  CC       ncmpio_sync.lo
  CC       ncmpio_file_misc.lo
  CC       ncmpio_header_get.lo
  CC       ncmpio_header_put.lo
  CC       ncmpio_dim.lo
  CC       ncmpio_var.lo
  CC       ncmpio_bput.lo
  CC       ncmpio_filetype.lo
  CC       ncmpio_wait.lo
  CC       ncmpio_vard.lo
  CC       ncmpio_fill.lo
  CC       ncmpio_util.lo
  CC       ncmpio_hash_func.lo
  CC       ncmpio_file_io.lo
  CC       ncmpio_getput.lo
  CC       ncmpio_i_getput.lo
  CC       ncmpio_varn.lo
  CC       ncmpio_i_varn.lo
  CC       ncmpio_attr.lo
  CCLD     libncmpio.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/ncmpio'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/ncmpio'
Making all in nc4io
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/nc4io'
m4  -DPNETCDF -I../../../m4 -DERANGE_FILL nc4io_get_put.m4 >nc4io_get_put.c
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/nc4io'
  CC       nc4io_file.lo
  CC       nc4io_attr.lo
  CC       nc4io_dim.lo
  CC       nc4io_var.lo
  CC       nc4io_driver.lo
  CC       nc4io_get_put.lo
  CCLD     libnc4io.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/nc4io'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers/nc4io'
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers'
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/drivers'
Making all in binding
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding'
Making all in cxx
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/cxx'
cat ./pnetcdf.in >pnetcdf
set -e; for i in ncmpi_notyet.h ncmpiCheck.h ncmpiType.h ncmpiAtt.h ncmpiEnumType.h ncmpiGroupAtt.h ncmpiGroup.h ncmpiByte.h ncmpiChar.h ncmpiCompoundType.h ncmpiDouble.h ncmpiFloat.h ncmpiInt.h ncmpiInt64.h ncmpiOpaqueType.h ncmpiShort.h ncmpiUbyte.h ncmpiUint.h ncmpiUint64.h ncmpiUshort.h ncmpiException.h ncmpiDim.h ncmpiFile.h ncmpiVarAtt.h ncmpiVar.h ncmpiVlenType.h; do ( \
/usr/bin/sed -e '/#ifndef/d' -e '/#define/d' -e '/#endif/d' -e '/#include/d' ./$i >> pnetcdf ; \
) ; done
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/cxx'
  CXX      ncmpiAtt.lo
  CXX      ncmpi_notyet.lo
  CXX      ncmpiCheck.lo
  CXX      ncmpiType.lo
  CXX      ncmpiEnumType.lo
  CXX      ncmpiGroupAtt.lo
  CXX      ncmpiGroup.lo
  CXX      ncmpiByte.lo
  CXX      ncmpiChar.lo
  CXX      ncmpiCompoundType.lo
  CXX      ncmpiDouble.lo
  CXX      ncmpiFloat.lo
  CXX      ncmpiInt.lo
  CXX      ncmpiInt64.lo
  CXX      ncmpiOpaqueType.lo
  CXX      ncmpiShort.lo
  CXX      ncmpiUbyte.lo
  CXX      ncmpiUint.lo
  CXX      ncmpiUint64.lo
  CXX      ncmpiUshort.lo
  CXX      ncmpiException.lo
  CXX      ncmpiDim.lo
  CXX      ncmpiFile.lo
  CXX      ncmpiVarAtt.lo
  CXX      ncmpiVar.lo
  CXX      ncmpiVlenType.lo
  CXXLD    libcxx.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/cxx'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/cxx'
Making all in f77
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f77'
rm -f mpifnetcdf.h issyserrf.c xstrerrorf.c xstrerrnof.c xinq_libversf.c allf.c
./buildiface -infile=../../../src/include/pnetcdf.h -deffile=./defs > allf.c
  F77      strerrnof.lo
  F77      inq_libversf.lo
  F77      strerrorf.lo
  CC       issyserrf.lo
  CC       xstrerrorf.lo
  CC       xstrerrnof.lo
  CC       xinq_libversf.lo
  CC       allf.lo
  F77LD    libf77.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f77'
Making all in f90
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f90'
m4  -DPNETCDF -DINTENTV=INOUT getput_text.m4 >getput_text.fh
m4  -DPNETCDF -DINTENTV=INOUT getput_var.m4 >getput_var.fh
m4  -DPNETCDF -DINTENTV=INOUT getput_varn.m4 >getput_varn.fh
m4  -DPNETCDF -DINTENTV=INOUT getput_vard.m4 >getput_vard.fh
make  all-am
make[4]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f90'
  FC       pnetcdf.lo
  FCLD     libf90.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f90'
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding/f90'
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding'
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/binding'
Making all in packaging
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/packaging'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/packaging'
Making all in .
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src'
Making all in libs
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/libs'
  GEN      libpnetcdf.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/libs'
Making all in utils
make[2]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/utils'
Making all in ncmpigen
make[3]: Entering directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/utils/ncmpigen'
  CC       main.o
  CC       load.o
  CC       escapes.o
  CC       getfill.o
  CC       init.o
  CC       genlib.o
  CC       ncmpigentab.o
  CCLD     ncmpigen
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_unlimdim'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_def_var_fill'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_def_dim'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_abort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc__enddef'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_dim'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_redef'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_dimid'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_open'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_del_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_vardimid'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_dimlen'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_attid'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_rename_var'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_copy_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_create_par'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_attname'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_close'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_enddef'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_format'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_varndims'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_open_par'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_var_fill'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_sync'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_set_fill'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_var_par_access'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_rename_dim'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_var'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_def_var'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_rename_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var_long'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_att_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_varid'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_int'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_ushort'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_double'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_att'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_vartype'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_var1_longlong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vara_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_short'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_schar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vara_uint'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_att_ulonglong'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_varm_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var1_uchar'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_varm_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_vars_float'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_inq_varids'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_put_vars_text'
/usr/bin/ld: ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `nc_get_var_ulonglong'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:540: ncmpigen] Error 1
make[3]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/utils/ncmpigen'
make[2]: *** [Makefile:530: all-recursive] Error 1
make[2]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src/utils'
make[1]: *** [Makefile:461: all-recursive] Error 1
make[1]: Leaving directory '/build/pnetcdf-openmpi/src/pnetcdf-1.11.1/src'
make: *** [Makefile:518: all-recursive] Error 1
wkliao commented 5 years ago

Similar errors were also discovered yesterday. A fix has been created in a branch name nc4_build_bug. Could you please give it a try to see if it solves the problem for you. FYI. Commands to download and build.

git clone https://github.com/Parallel-NetCDF/PnetCDF.git
cd PnetCDF
git checkout nc4_build_bug
autoreconf
./configure --enable-shared ...

Note adding -fPIC to CPPFLAGS is not necessary. If you would like to build shared libraries, adding --enable-shared to the configure command line is sufficient. I am not sure other flags you used are necessary. In my case, I only use -g or -O2.

ArchangeGabriel commented 5 years ago

This branch indeed solves the issue. Regarding -fPIC, IIRC it was necessary to get suitable static libs (we ship both shared and static libs). All flags are distro (Arch Linux) defaults by the way.

wkliao commented 5 years ago

Thanks for testing. I am glad it works for Arch Linux and will soon make another release, 1.11.2.

From your configure output on screen, iI can see option --enable-shared was used. Because PnetCDF configure script makes use of GNU libtool, this option automatically adds -fPIC -DPIC. To show the compile and link command lines during make, use below.

make LIBTOOLFLAGS=--verbose

But there is no harm either to add -fPIC to CPPFLAGS .

ArchangeGabriel commented 5 years ago

Oh, you’re right. I guess this is a leftover from when PnetCDF could not be built shared at all. Thanks for the remark. I’ll wait for the 1.11.2 release to push then.

wkliao commented 5 years ago

Hi @ArchangeGabriel I am trying to find the real cause of the problem you encountered. My current understanding is this problem happens only when NetCDF4 is built with static libraries only. But in my test, this case always fails at the configure time, not make time like your case. Could you check if your NetCDF4 library under /usr/lib is built with static libraries only? In addition, could you provide config.log from your earlier build of 1.11.1? thanks

ArchangeGabriel commented 5 years ago

Hi @wkliao, I’ll do this but when I find a bit of time for it, which unfortunately might not be before this week-end.

ArchangeGabriel commented 5 years ago

Sorry for the delay, as discussed over email I’ve uploaded the config.log here: https://paste.xinu.at/muAKho/

Also, I always have static+shared libs for NetCDF4.