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xianghu 07-25-2010 10:51 AM

problem of install netcdf with intel fortran on CENTOS
 
hi,I will install ncetcdf4.1.1 with intel fortran 11.1 on centos,according to the readme file,"configure.."is complete,when i command "make",the following message apear:

[root@localhost ~/netcdf-4.1.1]# make
make all-recursive
make[1]: Entering directory `/home/hu/netcdf-4.1.1'
Making all in f90
make[2]: Entering directory `/home/hu/netcdf-4.1.1/f90'
make all-am
make[3]: Entering directory `/home/hu/netcdf-4.1.1/f90'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/hu/netcdf-4.1.1/f90'
make[2]: Leaving directory `/home/hu/netcdf-4.1.1/f90'
Making all in fortran
make[2]: Entering directory `/home/hu/netcdf-4.1.1/fortran'
make all-am
make[3]: Entering directory `/home/hu/netcdf-4.1.1/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DintelFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo fort-attio.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DintelFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -MT fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c -o fort-attio.o
In file included from fort-attio.c:7:
ncfortran.h:26:42: error: NF_INT_IS_C_... not defined: No such file or directory
fort-attio.c: In function ‘NF_INT_cfF’:
fort-attio.c:13: error: expected declaration specifiers before ‘NF_INTEGER’
fort-attio.c:20: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:121: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:133: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:141: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:148: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘NF_INTEGER’
fort-attio.c:148: error: expected ‘{’ at end of input
make[3]: *** [fort-attio.lo] Error 1
make[3]: Leaving directory `/home/hu/netcdf-4.1.1/fortran'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hu/netcdf-4.1.1/fortran'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/hu/netcdf-4.1.1'
make: *** [all] Error 2
[root@localhost ~/netcdf-4.1.1]#

someone tell me how to fix it please,thanks!!

colucix 07-26-2010 03:27 AM

Hi and welcome to LinuxQuestions!
Quote:

Originally Posted by xianghu (Post 4044816)
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I../libsrc -DNDEBUG -DintelFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -g -O2 -MT fort-attio.lo -MD -MP -MF $depbase.Tpo -c -o fort-attio.lo fort-attio.c &&\
mv -f $depbase.Tpo $depbase.Plo

Basically you're mixing GNU C and Intel Fortran compilers: most likely this is not safe and could be the reason of the obtained error. If you have a valid license for the Intel fortran compiler you might ask a similar one for the Intel C compiler (icc).

Then you can set your environemnt according to intel's instructions, here. This page is still related to NetCDF3 but they can be applied to NetCDF4, as well.

The only difference is related to the -x option of the intel compilers, which makes optimization for a specific CPU architecture. For Intel compiler version 11.1 the syntax is slightly different (please check the manual page). Here is a working environment for my Centos 5.5 box, equipped with an old but still performing Pentium 4:
Code:

export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xSSE2 -ip -no-prec-div -static'
export CXXFLAGS='-O3 -xSSE2 -ip -no-prec-div -static'

export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xSSE2 -ip -no-prec-div -static'

export CPP='icc -E'
export CXXCPP='icpc -E'

As you can see the only difference from the Intel's instructions is -xSSE2 in place of -xT. If in doubt, please post the output of
Code:

awk '/model name|flags/' /proc/cpuinfo | head -2
to show the CPU model and flags. Hope this helps.

knudfl 07-26-2010 04:52 AM

Welcome to LQ. .. .. :)

Yesterdays test result ...
Using this source (4.1.1) :
ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.gz

# yum remove gcc-gfortran
cd /usr/bin/
# ln -s /opt/intel/Compiler/11.0/083/bin/ia32/ifort

cd netcdf-4.1.1/ && ./configure && make : No errors.

But then again, it's ifort 11.0, not 11.1 .
.....

P.S. : 'ifort' is free to use, it's the 'icc' you have to pay ?
.....

xianghu 07-26-2010 10:00 AM

Thanks a lot!!!

i will try again according to your advice after download intel's non-commercial icc,.

thanks !

xianghu 07-27-2010 05:13 AM

HI,here is a new problem,after installing Intel Fortran and c compilers,and the environemnt has been setted according to intel's instructions
[root@localhost netcdf-4.1.1]# ./configure --prefix=/usr/local/netCDF
configure: netCDF 4.1.1
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-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
configure: checking user options
checking whether CXX is set to ''... no
checking whether FC is set to ''... no
checking whether F90 is set to ''... no
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking whether udunits is to be built... no
checking if fsync support is enabled... yes
checking whether extra valgrind tests should be run... no
checking whether libcf is to be built... no
checking whether reading of HDF4 SD files is to be enabled... no
checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)... no
checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled... no
checking whether a location for the parallel-netcdf library was specified... no
checking whether new netCDF-4 C++ API is to be built... no
checking whether extra example tests should be run... no
checking whether parallel IO tests should be run... no
checking whether a location for the HDF5 library was specified...
checking whether a location for the ZLIB library was specified...
checking whether a location for the SZLIB library was specified...
checking whether a location for the HDF4 library was specified...
checking whether a default chunk size in bytes was specified... 4194304
checking whether a maximum per-variable cache size for HDF5 was specified... 67108864
checking whether a number of chunks for the default per-variable cache was specified... 10
checking whether a default file cache size for HDF5 was specified... 4194304
checking whether a default file cache maximum number of elements for HDF5 was specified... 1009
checking whether a default cache preemption for HDF5 was specified... 0.75
checking whether netCDF-4 logging is enabled... no
checking whether a path for curl-config was specified... no
checking whether a location for curl installation was specified... no
configure: checking whether a location for curl-config is in PATH... no
checking whether DAP client is to be built... no
checking whether dap remote testing should be enabled (default on)... no
checking whether the time-consuming dap tests should be enabled (default off)... no
checking whether a location for liboc was specified... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether Fortran compiler(s) should be tested during configure... yes
checking whether FFIO will be used... no
checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes
checking whether only the C library is desired... no
checking whether examples should be built... yes
checking whether F77 API is desired... yes
checking whether any Fortran API is desired... yes
checking whether F90 API is desired... yes
checking whether fortran type sizes should be checked... yes
checking whether C API is desired... yes
checking where to get netCDF C-only library for separate fortran libraries...
checking whether CXX API is desired... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump should be built... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking whether extreme numbers should be used in tests... yes
checking where to put large temp files if large file tests are run... .
checking whether a win32 DLL is desired... no
checking whether separate fortran libs are desired... no
configure: finding C compiler
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... configure: error: in `/home/hu/netcdf-4.1.1':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
[root@localhost netcdf-4.1.1]#

and the config.log is here:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by netCDF configure 4.1.1, which was
generated by GNU Autoconf 2.65. Invocation command line was

$ ./configure --prefix=/usr/local/netCDF

## --------- ##
## Platform. ##
## --------- ##

hostname = localhost.localdomain
uname -m = i686
uname -r = 2.6.18-194.el5
uname -s = Linux
uname -v = #1 SMP Tue Mar 16 21:52:43 EDT 2010

/usr/bin/uname -p = unknown
/bin/uname -X = unknown

/bin/arch = i686
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /opt/intel/Compiler/11.1/072/bin/ia32
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /sbin
PATH: /bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /usr/X11R6/bin
PATH: /home/hu/bin
PATH: /home/hu/bin
PATH: /home/hu/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:3262: netCDF 4.1.1
configure:3296: checking build system type
configure:3310: result: i686-pc-linux-gnu
configure:3330: checking host system type
configure:3343: result: i686-pc-linux-gnu
configure:3388: checking for a BSD-compatible install
configure:3456: result: /usr/bin/install -c
configure:3467: checking whether build environment is sane
configure:3517: result: yes
configure:3658: checking for a thread-safe mkdir -p
configure:3697: result: /bin/mkdir -p
configure:3710: checking for gawk
configure:3726: found /bin/gawk
configure:3737: result: gawk
configure:3748: checking whether make sets $(MAKE)
configure:3770: result: yes
configure:3854: checking user options
configure:3897: checking whether CXX is set to ''
configure:3901: result: no
configure:3905: checking whether FC is set to ''
configure:3909: result: no
configure:3913: checking whether F90 is set to ''
configure:3917: result: no
configure:3921: checking whether a NCIO_MINBLOCKSIZE was specified
configure:3931: result: 256
configure:3939: checking whether udunits is to be built
configure:3948: result: no
configure:3951: checking if fsync support is enabled
configure:3959: result: yes
configure:3968: checking whether extra valgrind tests should be run
configure:3976: result: no
configure:3999: checking whether libcf is to be built
configure:4008: result: no
configure:4012: checking whether reading of HDF4 SD files is to be enabled
configure:4020: result: no
configure:4024: checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)
configure:4037: result: no
configure:4041: checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled
configure:4049: result: no
configure:4053: checking whether a location for the parallel-netcdf library was specified
configure:4062: result: no
configure:4072: checking whether new netCDF-4 C++ API is to be built
configure:4083: result: no
configure:4090: checking whether extra example tests should be run
configure:4098: result: no
configure:4102: checking whether parallel IO tests should be run
configure:4110: result: no
configure:4114: checking whether a location for the HDF5 library was specified
configure:4122: result:
configure:4128: checking whether a location for the ZLIB library was specified
configure:4136: result:
configure:4142: checking whether a location for the SZLIB library was specified
configure:4150: result:
configure:4156: checking whether a location for the HDF4 library was specified
configure:4164: result:
configure:4170: checking whether a default chunk size in bytes was specified
configure:4180: result: 4194304
configure:4189: checking whether a maximum per-variable cache size for HDF5 was specified
configure:4199: result: 67108864
configure:4208: checking whether a number of chunks for the default per-variable cache was specified
configure:4218: result: 10
configure:4227: checking whether a default file cache size for HDF5 was specified
configure:4237: result: 4194304
configure:4246: checking whether a default file cache maximum number of elements for HDF5 was specified
configure:4256: result: 1009
configure:4265: checking whether a default cache preemption for HDF5 was specified
configure:4275: result: 0.75
configure:4284: checking whether netCDF-4 logging is enabled
configure:4292: result: no
configure:4307: checking whether a path for curl-config was specified
configure:4316: result: no
configure:4332: checking whether a location for curl installation was specified
configure:4355: result: no
configure:4367: checking whether a location for curl-config is in PATH... no
configure:4405: checking whether DAP client is to be built
configure:4428: result: no
configure:4437: checking whether dap remote testing should be enabled (default on)
configure:4448: result: no
configure:4451: checking whether the time-consuming dap tests should be enabled (default off)
configure:4462: result: no
configure:4466: checking whether a location for liboc was specified
configure:4478: result: no
configure:4507: checking whether netCDF extra tests should be run (developers only)
configure:4515: result: no
configure:4532: checking whether Fortran compiler(s) should be tested during configure
configure:4540: result: yes
configure:4544: checking whether FFIO will be used
configure:4552: result: no
configure:4568: checking whether to skip C++, F77, or F90 APIs if compiler is broken
configure:4576: result: yes
configure:4580: checking whether only the C library is desired
configure:4588: result: no
configure:4607: checking whether examples should be built
configure:4615: result: yes
configure:4627: checking whether F77 API is desired
configure:4636: result: yes
configure:4641: checking whether any Fortran API is desired
configure:4649: result: yes
configure:4654: checking whether F90 API is desired
configure:4664: result: yes
configure:4668: checking whether fortran type sizes should be checked
configure:4676: result: yes
configure:4682: checking whether C API is desired
configure:4690: result: yes
configure:4697: checking where to get netCDF C-only library for separate fortran libraries
configure:4713: result:
configure:4725: checking whether CXX API is desired
configure:4734: result: yes
configure:4743: checking whether v2 netCDF API should be built
configure:4751: result: yes
configure:4770: checking whether the ncgen/ncdump should be built
configure:4779: result: yes
configure:4791: checking whether large file (> 2GB) tests should be run
configure:4799: result: no
configure:4816: checking whether benchmaks should be run (experimental)
configure:4824: result: no
configure:4836: checking whether extreme numbers should be used in tests
configure:4851: result: yes
configure:4863: checking where to put large temp files if large file tests are run
configure:4872: result: .
configure:4883: checking whether a win32 DLL is desired
configure:4891: result: no
configure:4913: checking whether separate fortran libs are desired
configure:4922: result: no
configure:4956: finding C compiler
configure:5071: checking for C compiler version
configure:5080: icc --version >&5
icc (ICC) 11.1 20100414
Copyright (C) 1985-2010 Intel Corporation. All rights reserved.

configure:5091: $? = 0
configure:5080: icc -v >&5
Version 11.1
configure:5091: $? = 0
configure:5080: icc -V >&5
Intel(R) C Compiler Professional for applications running on IA-32, Version 11.1 Build 20100414 Package ID: l_cproc_p_11.1.072
Copyright (C) 1985-2010 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY

configure:5091: $? = 0
configure:5080: icc -qversion >&5
icc: command line warning #10006: ignoring unknown option '-qversion'
icc: command line error: no files specified; for help type "icc -help"
configure:5091: $? = 1
configure:5111: checking whether the C compiler works
configure:5133: icc -O3 -xT -ip -no-prec-div -static conftest.c >&5
configure:5137: $? = 0
configure:5186: result: yes
configure:5189: checking for C compiler default output file name
configure:5191: result: a.out
configure:5197: checking for suffix of executables
configure:5204: icc -o conftest -O3 -xT -ip -no-prec-div -static conftest.c >&5
configure:5208: $? = 0
configure:5230: result:
configure:5252: checking whether we are cross compiling
configure:5260: icc -o conftest -O3 -xT -ip -no-prec-div -static conftest.c >&5
configure:5264: $? = 0
configure:5271: ./conftest

Fatal Error: This program was not built to run on the processor in your system.
The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support.

configure:5275: $? = 1
configure:5282: error: in `/home/hu/netcdf-4.1.1':
configure:5286: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=i686-pc-linux-gnu
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=icc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-O3 -xT -ip -no-prec-div -static'
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=set
ac_cv_env_CPP_value='icc -E'
ac_cv_env_CXXCPP_set=set
ac_cv_env_CXXCPP_value='icpc -E'
ac_cv_env_CXXFLAGS_set=set
ac_cv_env_CXXFLAGS_value='-O3 -xT -ip -no-prec-div -static'
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=icpc
ac_cv_env_F77_set=set
ac_cv_env_F77_value=ifort
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=ifort
ac_cv_env_FFLAGS_set=set
ac_cv_env_FFLAGS_value='-O3 -xT -ip -no-prec-div -static'
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_host=i686-pc-linux-gnu
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/bin/mkdir
ac_cv_prog_AWK=gawk
ac_cv_prog_make_make_set=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /home/hu/netcdf-4.1.1/missing --run aclocal-1.11'
ALLOCA=''
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR='${SHELL} /home/hu/netcdf-4.1.1/missing --run tar'
AR=''
AUTOCONF='${SHELL} /home/hu/netcdf-4.1.1/missing --run autoconf'
AUTOHEADER='${SHELL} /home/hu/netcdf-4.1.1/missing --run autoheader'
AUTOMAKE='${SHELL} /home/hu/netcdf-4.1.1/missing --run automake-1.11'
AWK='gawk'
BINFILE_NAME=''
BUILD_BENCHMARKS_FALSE=''
BUILD_BENCHMARKS_TRUE='#'
BUILD_CXX4_FALSE=''
BUILD_CXX4_TRUE=''
BUILD_CXX_FALSE=''
BUILD_CXX_TRUE=''
BUILD_C_FALSE=''
BUILD_C_TRUE=''
BUILD_DAP_FALSE=''
BUILD_DAP_TRUE=''
BUILD_DLL_FALSE=''
BUILD_DLL_TRUE='#'
BUILD_EXAMPLES_FALSE='#'
BUILD_EXAMPLES_TRUE=''
BUILD_F77_FALSE=''
BUILD_F77_TRUE=''
BUILD_F90_FALSE=''
BUILD_F90_TRUE=''
BUILD_LIBCF_FALSE=''
BUILD_LIBCF_TRUE=''
BUILD_PARALLEL_FALSE=''
BUILD_PARALLEL_TRUE=''
BUILD_SEPARATE_FORTRAN_FALSE=''
BUILD_SEPARATE_FORTRAN_TRUE='#'
BUILD_UDUNITS_FALSE=''
BUILD_UDUNITS_TRUE=''
BUILD_UTILITIES_FALSE='#'
BUILD_UTILITIES_TRUE=''
BUILD_V2_FALSE='#'
BUILD_V2_TRUE=''
CC='icc'
CCDEPMODE=''
CFLAGS='-O3 -xT -ip -no-prec-div -static'
CPP='icc -E'
CPPFLAGS=''
CROSS_COMPILING_FALSE=''
CROSS_COMPILING_TRUE=''
CURLDIR=''
CURL_CFLAGS='-lcurl'
CURL_FCFLAGS='-lcurl'
CURL_FFLAGS='-lcurl'
CURL_LIBS=''
CXX='icpc'
CXXCPP='icpc -E'
CXXDEPMODE=''
CXXFLAGS='-O3 -xT -ip -no-prec-div -static'
CYGPATH_W='echo'
DEFS=''
DEPDIR=''
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
ENABLE_DAP_LONG_TESTS_FALSE=''
ENABLE_DAP_LONG_TESTS_TRUE=''
ENABLE_DAP_REMOTE_TESTS_FALSE=''
ENABLE_DAP_REMOTE_TESTS_TRUE=''
EXEEXT=''
EXTRA_EXAMPLE_TESTS_FALSE=''
EXTRA_EXAMPLE_TESTS_TRUE=''
EXTRA_TESTS_FALSE=''
EXTRA_TESTS_TRUE='#'
F77='ifort'
FC='ifort'
FCFLAGS=''
FCFLAGS_f90=''
FFLAGS='-O3 -xT -ip -no-prec-div -static'
FGREP=''
FTPBINDIR=''
GREP=''
HAS_CXX=''
HAS_DAP=''
HAS_F77=''
HAS_F90=''
HAS_HDF4=''
HAS_HDF5=''
HAS_NC2=''
HAS_NC4=''
HAS_SZLIB=''
HDF4DIR=''
HDF5DIR=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
INTERNAL_OCLIB_FALSE='#'
INTERNAL_OCLIB_TRUE=''
LARGE_FILE_TESTS_FALSE=''
LARGE_FILE_TESTS_TRUE='#'
LD=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL=''
LIPO=''
LN_S=''
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/hu/netcdf-4.1.1/missing --run makeinfo'
MAKEWHATIS_CMD=''
MKDIR_P='/bin/mkdir -p'
MOD_FLAG=''
NC_FLIBS=''
NC_LIBS=''
NETCDF_C_LIB=''
NM=''
NMEDIT=''
NMFLAGS=''
OBJEXT=''
OCLIB_CFLAGS='-I/include'
OCLIB_LIBS='-L/lib -loc'
OTOOL64=''
OTOOL=''
PACKAGE='netcdf'
PACKAGE_BUGREPORT='support-netcdf@unidata.ucar.edu'
PACKAGE_NAME='netCDF'
PACKAGE_STRING='netCDF 4.1.1'
PACKAGE_TARNAME='netcdf'
PACKAGE_URL=''
PACKAGE_VERSION='4.1.1'
PATH_SEPARATOR=':'
PNETCDFDIR=''
RANLIB=''
SED=''
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
SZLIBDIR=''
TEST_F77_FALSE=''
TEST_F77_TRUE=''
TEST_PARALLEL_FALSE=''
TEST_PARALLEL_TRUE=''
UPPER_CASE_MOD_FALSE=''
UPPER_CASE_MOD_TRUE=''
USE_DAP_FALSE=''
USE_DAP_TRUE=''
USE_DISPATCH_FALSE=''
USE_DISPATCH_TRUE=''
USE_FFIO_FALSE=''
USE_FFIO_TRUE='#'
USE_HDF4_DIR_FALSE=''
USE_HDF4_DIR_TRUE=''
USE_HDF4_FALSE=''
USE_HDF4_FILE_TESTS_FALSE=''
USE_HDF4_FILE_TESTS_TRUE=''
USE_HDF4_TRUE=''
USE_HDF5_DIR_FALSE=''
USE_HDF5_DIR_TRUE=''
USE_LOGGING_FALSE=''
USE_LOGGING_TRUE=''
USE_NETCDF4_FALSE=''
USE_NETCDF4_TRUE=''
USE_NETCDF_C_LIB_DIR_FALSE=''
USE_NETCDF_C_LIB_DIR_TRUE='#'
USE_PNETCDF_DIR_FALSE=''
USE_PNETCDF_DIR_TRUE=''
USE_PNETCDF_FALSE=''
USE_PNETCDF_TRUE=''
USE_RENAMEV3_FALSE=''
USE_RENAMEV3_TRUE=''
USE_SZIP_FALSE=''
USE_SZIP_TRUE=''
USE_SZLIB_DIR_FALSE=''
USE_SZLIB_DIR_TRUE=''
USE_VALGRIND_TESTS_FALSE=''
USE_VALGRIND_TESTS_TRUE=''
USE_ZLIB_DIR_FALSE=''
USE_ZLIB_DIR_TRUE=''
VERSION='4.1.1'
WHATIS=''
ZLIBDIR=''
ac_ct_CC=''
ac_ct_CXX=''
ac_ct_DUMPBIN=''
ac_ct_F77=''
ac_ct_FC=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE=''
am__fastdepCXX_TRUE=''
am__include=''
am__isrc=''
am__leading_dot='.'
am__quote=''
am__tar='${AMTAR} chof - "$$tardir"'
am__untar='${AMTAR} xf -'
bindir='${exec_prefix}/bin'
build='i686-pc-linux-gnu'
build_alias=''
build_cpu='i686'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='i686-pc-linux-gnu'
host_alias=''
host_cpu='i686'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/hu/netcdf-4.1.1/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
lt_ECHO='echo'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local/netCDF'
prog=''
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
subdirs=''
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "netCDF"
#define PACKAGE_TARNAME "netcdf"
#define PACKAGE_VERSION "4.1.1"
#define PACKAGE_STRING "netCDF 4.1.1"
#define PACKAGE_BUGREPORT "support-netcdf@unidata.ucar.edu"
#define PACKAGE_URL ""
#define PACKAGE "netcdf"
#define VERSION "4.1.1"
#define NCIO_MINBLOCKSIZE 256
#define USE_FSYNC 1
#define DEFAULT_CHUNK_SIZE 4194304
#define MAX_DEFAULT_CACHE_SIZE 67108864
#define DEFAULT_CHUNKS_IN_CACHE 10
#define CHUNK_CACHE_SIZE 4194304
#define CHUNK_CACHE_NELEMS 1009
#define CHUNK_CACHE_PREEMPTION 0.75
#define USE_EXTREME_NUMBERS 1
#define TEMP_LARGE "."

configure: exit 1

at the same time,i command:

awk '/model name|flags/' /proc/cpuinfo | head -2

[root@localhost netcdf-4.1.1]# awk '/model name|flags/' /proc/cpuinfo | head -2
model name : AMD Athlon(tm) 64 X2 Dual Core Processor 4400+
flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext fxsr_opt rdtscp lm 3dnowext 3dnow constant_tsc up nonstop_tsc pni cx16 lahf_lm extapic 3dnowprefetch ts fid vid ttp tm stc 100mhzsteps

so i can't use intel's compiler because of my computer equipped with AMD CPU?

Thanks very much!!!

xianghu 07-27-2010 05:19 AM

I am a novice in the LINUX,thanks!!

colucix 07-27-2010 06:27 AM

Quote:

Originally Posted by xianghu (Post 4046658)
so i can't use intel's compiler because of my computer equipped with AMD CPU?

Yes, you can. The problem is related to the processor optimization -xT which requires the SSSE3 instruction set capability. This option is not compatible with this specific AMD CPU.

As I previously mentioned, please check the ifort or icc man page to see the new syntax rules of the -x option. Looking at the flags associated with your processor, you can see it supports at most the SSE2 instruction set:
Code:

flags : <omitted> sse sse2 <omitted>
so that you can try with -xSSE2 in place of -xT (see the CFLAGS, CXXFLAGS, FFLAGS environment variables).

If it still doesn't work you can try to remove the -x option completely. This means that no additional optimization related to the kind of processor will be performed, but you can live without it.

Good luck! :)

xianghu 07-29-2010 04:02 AM

thanks a lot !!!
netcdf has been installed acording to your's suggestion!
and ,a new problem appear in compiling ICON,i'll write a new post,thanks for all!!!

colucix 07-29-2010 05:34 AM

You're welcome! :)


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