paralell-netcdf-1.1.1 installation problem
Shawn Kim
shawn.subscribe at gmail.com
Wed Feb 3 10:40:37 CST 2010
Hi,
I did autoreconf before "configure". I attached the output from configure
and macros.make.
Thank you.
- Shawn
$ ./configure
--prefix=/home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1/install
--with-mpi=/home/mdl/yuazhang/IOTracing/mpich2-1.0.8 --enable-fortran | &
tee c.txt
checking for top-level source-directory...
/home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1
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 how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for bison... bison -y
checking for flex... flex
checking for yywrap in -lfl... yes
checking lex output file root... lex.yy
checking whether yytext is a pointer... yes
configure: checking for m4 preprocessor...
checking for m4... m4
checking m4 flags... -B10000
checking for gcc... (cached) mpicc
checking whether we are using the GNU C compiler... (cached) yes
checking whether mpicc accepts -g... (cached) yes
checking for mpicc option to accept ISO C89... (cached) none needed
checking user-defined Fortran-77 compiler "mpif77"... works
checking for Fortran .F compiler...
checking if Fortran-77 compiler handles *.F files... yes
checking how to make dependencies... false
configure: checking for nm utility...
checking for nm... nm
checking nm flags...
checking for C-equivalent to Fortran routine "SUB"... sub_
configure: checking for math library...
checking for tanh in -lc... no
checking for tanh in -lm... yes
configure: checking for ar utility...
checking for ar... ar
checking ar flags... cru
configure: checking for nm utility...
checking for nm... (cached) nm
checking nm flags...
checking for ranlib... ranlib
checking for C-equivalent to Fortran routine "SUB_A"... sub_a__
checking mpi C compiler ... configure: WARNING: mpicc either does not exist
or is not executable: falling back to mpicc
using mpicc
checking mpi C++ compiler ... using
/home/mdl/yuazhang/IOTracing/mpich2-1.0.8/bin/mpicxx
checking mpi Fortran 77 compiler ... configure: WARNING: mpif77 either does
not exist or is not executable: falling back to mpif77
using mpif77
checking mpi Fortran 90 compiler ... configure: WARNING: mpif90 either does
not exist or is not executable: falling back to mpif77
using mpif77
checking MPI-IO support in MPI implementation... 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 stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for strerror... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for struct stat.st_blksize... yes
checking for IEEE floating point format... yes
checking for size_t... yes
checking if MPI_Offset is size 8... yes
checking for MPI_Request_get_status... yes
checking for MPI_Type_dup... yes
checking for MPI_Info_dup... yes
checking if MPI includes MPI_COMBINER_DUP... yes
checking if MPI includes MPI_COMBINER_HVECTOR_INTEGER... yes
checking if MPI includes MPI_COMBINER_HINDEXED_INTEGER... yes
checking if MPI includes MPI_COMBINER_SUBARRAY... yes
checking if MPI includes MPI_COMBINER_DARRAY... yes
checking if MPI includes MPI_COMBINER_RESIZED... yes
checking if MPI includes MPI_COMBINER_STRUCT_INTEGER... yes
checking if MPI includes MPI_COMBINER_INDEXED_BLOCK... yes
checking if MPI includes MPI_COMBINER_F90_REAL... yes
checking if MPI includes MPI_COMBINER_F90_INTEGER... yes
checking if MPI includes MPI_COMBINER_F90_COMPLEX... yes
checking if MPI includes MPI_CHARACTER... yes
checking if MPI includes MPI_REAL... yes
checking if MPI includes MPI_INTEGER... yes
checking if MPI includes MPI_DOUBLE_PRECISION... yes
checking if MPI includes MPI_INTEGER1... yes
checking if MPI includes MPI_INTEGER2... yes
checking if MPI includes MPI_INTEGER4... yes
checking if MPI includes MPI_INTEGER8... yes
checking if MPI includes MPI_INTEGER16... yes
checking if MPI includes MPI_REAL4... yes
checking if MPI includes MPI_REAL8... yes
checking if MPI includes MPI_REAL16... yes
checking if MPI includes MPI_COMPLEX8... yes
checking if MPI includes MPI_COMPLEX16... yes
checking if MPI includes MPI_COMPLEX32... yes
checking if MPI includes MPI_UB... yes
checking if MPI includes MPI_LB... yes
checking for off_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking for uchar... no
checking whether char is unsigned... no
checking whether byte ordering is bigendian... no
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 4
checking for float... yes
checking size of float... 4
checking for double... yes
checking size of double... 8
checking for size_t... (cached) yes
checking size of size_t... 4
checking sizeof MPI_Offset... (cached) 8
checking for Fortran "byte"... yes
checking for Fortran "integer*2"... yes
checking if Fortran "byte" is C "signed char"... yes
checking if Fortran "byte" is C "short"... no
checking if Fortran "byte" is C "int"... no
checking if Fortran "byte" is C "long"... no
checking if Fortran "integer*2" is C "short"... yes
checking if Fortran "integer*2" is C "int"... no
checking if Fortran "integer*2" is C "long"... no
checking if Fortran "integer" is C "int"... yes
checking if Fortran "real" is C "float"... yes
checking if Fortran "doubleprecision" is C "double"... yes
checking for Fortran-equivalent to netCDF "byte"... byte
checking for Fortran-equivalent to netCDF "short"... integer*2
checking for Fortran "integer*8"... yes
checking for manual-page index command...
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for _LARGE_FILES value needed for large files... no
checking for library containing MPI_File_sync... none required
checking for off_t... (cached) yes
checking size of off_t... 8
configure: creating ./config.status
config.status: creating macros.make
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating src/lib/Makefile
config.status: creating src/lib/pnetcdf.h
config.status: creating src/libf/Makefile
config.status: creating test/common/Makefile
config.status: creating test/test_double/Makefile
config.status: creating test/test_double_int/Makefile
config.status: creating test/test_float/Makefile
config.status: creating test/test_int/Makefile
config.status: creating test/test_dtype/Makefile
config.status: creating test/nc_test/Makefile
config.status: creating test/nf_test/Makefile
config.status: creating test/fandc/Makefile
config.status: creating src/utils/Makefile
config.status: creating src/utils/ncdump/Makefile
config.status: creating src/utils/ncgen/Makefile
config.status: creating test/testcases/Makefile
config.status: creating test/C/Makefile
config.status: creating test/mcoll_perf/Makefile
config.status: creating test/test_check_header/Makefile
config.status: creating test/largefile/Makefile
config.status: creating test/mcoll_fortran/Makefile
config.status: creating src/lib/ncconfig.h
config.status: src/lib/ncconfig.h is unchanged
config.status: creating src/libf/pnetcdf.inc
config.status: creating src/libf/nfconfig.inc
parallel-netCDF version 1.1.1pre1 features:
. parallel-netcdf configured WITH support for large files
. parallel-netcdf configured WITH fortran bindings
. parallel-netcdf configured WITH nonblocking routines
. parallel-netcdf configured WITH giant variable support
macros.make
# $Id: macros.make.in 771 2010-01-22 21:00:23Z robl $
# The purpose of this file is to contain common make(1) macros.
# It should be processed by every execution of that utility.
# POSIX shell. Shouldn't be necessary -- but is under IRIX 5.3.
SHELL = /bin/sh
# Installation Directories:
SRCDIR =
/home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1
prefix =
/home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1/install
exec_prefix = $(prefix)
INCDIR = $(exec_prefix)/include
LIBDIR = $(exec_prefix)/lib
BINDIR = $(exec_prefix)/bin
MANDIR = $(prefix)/man
# Preprocessing:
M4 = m4
M4FLAGS = -B10000
CPP = mpicc -E
CPPFLAGS = $(INCLUDES) $(DEFINES)
FPP =
FPPFLAGS = $(CPPFLAGS)
CXXCPPFLAGS = $(CPPFLAGS)
# Compilation:
CC = mpicc
CXX = /home/mdl/yuazhang/IOTracing/mpich2-1.0.8/bin/mpicxx
FC = mpif77
F90 = mpif77
CFLAGS = -g -O2
CXXFLAGS = -g -O2
FFLAGS =
F90FLAGS =
NETCDF.MOD = @NETCDF_MOD@
CC_MAKEDEPEND = false
COMPILE.c = $(CC) -c $(CFLAGS) $(CPPFLAGS)
COMPILE.cxx = $(CXX) -c $(CXXFLAGS) $(CXXCPPFLAGS)
COMPILE.f = $(FC) -c $(FFLAGS)
COMPILE.F90 = $(F90) -c $(F90FLAGS)
# The following command isn't available on some systems; therefore, the
# `.F.o' rule is relatively complicated.
COMPILE.F = $(COMPILE.f) $(FPPFLAGS)
# Linking:
MATHLIB = -lm
FLIBS =
F90LIBS = @F90LIBS@
LIBS =
F90LDFLAGS = $(LDFLAGS)
LINK.c = $(CC) -o $@ $(CFLAGS) $(LDFLAGS)
LINK.cxx = $(CXX) -o $@ $(CXXFLAGS) $(LDFLAGS)
LINK.F = $(FC) -o $@ $(FFLAGS) $(FLDFLAGS)
LINK.f = $(FC) -o $@ $(FFLAGS) $(FLDFLAGS)
LINK.F90 = $(F90) -o $@ $(F90FLAGS) $(F90LDFLAGS)
# Manual pages:
WHATIS = whatis
# The following macro should be empty on systems that don't
# allow users to create their own manual-page indexes.
MAKEWHATIS_CMD =
# Misc. Utilities:
AR = ar
ARFLAGS = cru
RANLIB = ranlib
TARFLAGS = -chf
# Dummy macros: used only as placeholders to silence GNU make. They are
# redefined, as necessary, in subdirectory makefiles.
HEADER = dummy_header
HEADER1 = dummy_header1
HEADER2 = dummy_header2
HEADER3 = dummy_header3
LIBRARY = dummy_library.a
MANUAL = dummy_manual
PROGRAM = dummy_program
# Distribution macros:
FTPDIR = /home/ftp/pub/$(PACKAGE)
FTPBINDIR = @FTPBINDIR@
VERSION = dummy_version
On Wed, Feb 3, 2010 at 2:09 AM, Wei-keng Liao
<wkliao at ece.northwestern.edu>wrote:
> Hi, Shawn
>
> Did you run "autoreconf" before "configure"?
>
> Can you send us the standard output from you configure run
> and the file macros.make?
>
> Wei-keng
>
>
>
> On Feb 2, 2010, at 11:30 PM, Shawn Kim wrote:
>
> Hi, all
>>
>> I recently installed the newest parallel-netcdf-1.1.1 on two different
>> machines with different (MPICH2 + PVFS2)'s.
>> I succeeded it on one machine but I failed it on the other machine. (I
>> slighly modified MPI_IO function calls but I believed it didn't affect the
>> compilation.)
>> Both are in the same clusters. Error occurred while compiling libf.
>>
>> /bin/rm -f pnetcdf.F90
>> echo "module pnetcdf" > pnetcdf.F90
>> /bin/cat pnetcdf.inc >> pnetcdf.F90
>> echo "end module pnetcdf" >> pnetcdf.F90
>> mpif77 -c -c pnetcdf.F90
>> g77: pnetcdf.F90: linker input file unused because linking not done
>> /usr/bin/install -c -d -m 755
>> /home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1/install/include
>> /usr/bin/install -c -m 644 pnetcdf.inc pnetcdf.mod
>> /home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1/install/include
>> /usr/bin/install: cannot stat `pnetcdf.mod': No such file or directory
>> make: ***
>> [/home/mdl/yuazhang/IOTracing/benchmark/parallel-netcdf-1.1.1/install/include/pnetcdf.inc]
>> Error 1
>>
>> The error part is:
>> mpif77 -c -c pnetcdf.F90
>> g77: pnetcdf.F90: linker input file unused because linking not done
>>
>> It seems to me like fortran compiler mismatch, but in the other machine it
>> works without any error or warning. I did set environment variable correctly
>> like:
>>
>> CC=mpicc
>> FC=mpif77
>> F90=mpif90
>> MPICC=mpicc
>> MPIF77=mpif77
>> MPIF90=mpif90
>>
>> What else can I do?
>>
>> Thank you in advance.
>>
>> - Shawn
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/parallel-netcdf/attachments/20100203/0e0e210e/attachment-0001.htm>
More information about the parallel-netcdf
mailing list