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netcdf build problem

 
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LeeE



Joined: 06 Jul 2012
Posts: 2

PostPosted: Fri Jul 06, 2012 2:43 pm    Post subject: netcdf build problem Reply with quote

I'm trying to build netcdf-4.1.3 with PGI compilers. I set env variables as follows:

export PATH=$PATH:/opt/pgi/linux86/9.0-4/bin
export PGI=/opt/pgi
export MANPATH=$MANPATH:$PGI/man
export LM_LICENSE_FILE=$PGI/license.dat
export CC=/opt/pgi/linux86/9.0-4/bin/pgcc
export FC=/opt/pgi/linux86/9.0-4/bin/pgf90
export F90=/opt/pgi/linux86/9.0-4/bin/pgf90
export CXX=/opt/pgi/linux86/9.0-4/bin/pgCC
export CPPFLAGS="-DpgiFortran"
export LD=/opt/pgi/linux86/9.0-4/bin/pgfortran
export LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib:/opt/pgi/linux86/9.0-4/lib
export INCLUDE=/usr/include:/usr/local/include:/opt/pgi/linux86/9.0-4/include

When I run the configure script:

./configure --prefix=/usr/local --disable-netcdf-4

I get the following:


configure: netCDF 4.1.3
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target 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 we should try to build netCDF-4... 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 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 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 cdmremote client is to be built... no
checking whether DAP client is to be built... yes
checking for style of include used by make... GNU
checking for gcc... /opt/pgi/linux86/9.0-4/bin/pgcc
checking whether the C compiler works... no
configure: error: in `/home/wrf/netcdf/netcdf-4.1.3':
configure: error: C compiler cannot create executables
See `config.log' for more details

Here is config.log:


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 4.1.3, which was
generated by GNU Autoconf 2.68. Invocation command line was

$ ./configure --prefix=/usr/local --disable-netcdf-4

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

hostname = earth3.surflinedc.tld
uname -m = i686
uname -r = 2.6.18-308.8.2.el5
uname -s = Linux
uname -v = #1 SMP Tue May 29 11:58:36 EDT 2012

/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: /usr/kerberos/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /home/wrf/bin
PATH: /opt/pgi/linux86/9.0-4/bin


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

configure:3070: netCDF 4.1.3
configure:3110: checking build system type
configure:3124: result: i686-pc-linux-gnu
configure:3144: checking host system type
configure:3157: result: i686-pc-linux-gnu
configure:3179: checking target system type
configure:3192: result: i686-pc-linux-gnu
configure:3243: checking for a BSD-compatible install
configure:3311: result: /usr/bin/install -c
configure:3322: checking whether build environment is sane
configure:3372: result: yes
configure:3513: checking for a thread-safe mkdir -p
configure:3552: result: /bin/mkdir -p
configure:3565: checking for gawk
configure:3581: found /bin/gawk
configure:3592: result: gawk
configure:3603: checking whether make sets $(MAKE)
configure:3625: result: yes
configure:3709: checking user options
configure:3719: checking whether CXX is set to ''
configure:3723: result: no
configure:3727: checking whether FC is set to ''
configure:3731: result: no
configure:3735: checking whether F90 is set to ''
configure:3739: result: no
configure:3743: checking whether a NCIO_MINBLOCKSIZE was specified
configure:3753: result: 256
configure:3761: checking whether udunits is to be built
configure:3770: result: no
configure:3773: checking if fsync support is enabled
configure:3781: result: yes
configure:3790: checking whether extra valgrind tests should be run
configure:3798: result: no
configure:3802: checking whether we should try to build netCDF-4
configure:3810: result: no
configure:3827: checking whether libcf is to be built
configure:3836: result: no
configure:3840: checking whether reading of HDF4 SD files is to be enabled
configure:3848: result: no
configure:3852: checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)
configure:3865: result: no
configure:3869: checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled
configure:3877: result: no
configure:3881: checking whether new netCDF-4 C++ API is to be built
configure:3892: result: no
configure:3896: checking whether extra example tests should be run
configure:3904: result: no
configure:3908: checking whether parallel IO tests should be run
configure:3916: result: no
configure:3920: checking whether a default chunk size in bytes was specified
configure:3930: result: 4194304
configure:3939: checking whether a maximum per-variable cache size for HDF5 was specified
configure:3949: result: 67108864
configure:3958: checking whether a number of chunks for the default per-variable cache was specified
configure:3968: result: 10
configure:3977: checking whether a default file cache size for HDF5 was specified
configure:3987: result: 4194304
configure:3996: checking whether a default file cache maximum number of elements for HDF5 was specified
configure:4006: result: 1009
configure:4015: checking whether a default cache preemption for HDF5 was specified
configure:4025: result: 0.75
configure:4034: checking whether netCDF-4 logging is enabled
configure:4042: result: no
configure:4046: checking whether cdmremote client is to be built
configure:4056: result: no
configure:4060: checking whether DAP client is to be built
configure:4068: result: yes
configure:4095: checking for style of include used by make
configure:4123: result: GNU
configure:4193: checking for gcc
configure:4220: result: /opt/pgi/linux86/9.0-4/bin/pgcc
configure:4449: checking for C compiler version
configure:4458: /opt/pgi/linux86/9.0-4/bin/pgcc --version >&5
pgcc-Error-Unknown switch: --version
configure:4469: $? = 1
configure:4458: /opt/pgi/linux86/9.0-4/bin/pgcc -v >&5
pgcc-Warning-No files to process
configure:4469: $? = 0
configure:4458: /opt/pgi/linux86/9.0-4/bin/pgcc -V >&5

pgcc 9.0-4 32-bit target on x86 Linux -tp nehalem
Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
Copyright 2000-2009, STMicroelectronics, Inc. All Rights Reserved.
configure:4469: $? = 0
configure:4458: /opt/pgi/linux86/9.0-4/bin/pgcc -qversion >&5
pgcc-Error-Unknown switch: -qversion
configure:4469: $? = 1
configure:4489: checking whether the C compiler works
configure:4511: /opt/pgi/linux86/9.0-4/bin/pgcc -DpgiFortran conftest.c >&5
pgi-cc-lin32: LICENSE MANAGER PROBLEM: No such feature exists.
Feature: pgi-cc-lin32
License path: /opt/pgi/license.dat:
FLEXnet Licensing error:-5,357
For further information, refer to the FLEXnet Licensing documentation,
available at "www.acresso.com".
configure:4515: $? = 2
configure:4553: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "netCDF"
| #define PACKAGE_TARNAME "netcdf"
| #define PACKAGE_VERSION "4.1.3"
| #define PACKAGE_STRING "netCDF 4.1.3"
| #define PACKAGE_BUGREPORT "support-netcdf@unidata.ucar.edu"
| #define PACKAGE_URL ""
| #define PACKAGE "netcdf"
| #define VERSION "4.1.3"
| #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
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:4558: error: in `/home/wrf/netcdf/netcdf-4.1.3':
configure:4560: error: C compiler cannot create executables
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=/opt/pgi/linux86/9.0-4/bin/pgcc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-DpgiFortran
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=/opt/pgi/linux86/9.0-4/bin/pgCC
ac_cv_env_F77_set=
ac_cv_env_F77_value=
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=/opt/pgi/linux86/9.0-4/bin/pgf90
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
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_ac_ct_CC=/opt/pgi/linux86/9.0-4/bin/pgcc
ac_cv_prog_make_make_set=yes
ac_cv_target=i686-pc-linux-gnu

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

ACLOCAL='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run aclocal-1.11'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run tar'
AR=''
AS=''
AUTOCONF='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run autoconf'
AUTOHEADER='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run autoheader'
AUTOMAKE='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run automake-1.11'
AWK='gawk'
BINFILE_NAME=''
BUILD_BENCHMARKS_FALSE=''
BUILD_BENCHMARKS_TRUE=''
BUILD_CDMREMOTE_FALSE=''
BUILD_CDMREMOTE_TRUE=''
BUILD_CXX4_FALSE=''
BUILD_CXX4_TRUE=''
BUILD_CXX_FALSE=''
BUILD_CXX_TRUE=''
BUILD_C_FALSE=''
BUILD_C_TRUE=''
BUILD_DAP_FALSE=''
BUILD_DAP_TRUE=''
BUILD_DLL_FALSE=''
BUILD_DLL_TRUE=''
BUILD_EXAMPLES_FALSE=''
BUILD_EXAMPLES_TRUE=''
BUILD_F77_FALSE=''
BUILD_F77_TRUE=''
BUILD_F90_FALSE=''
BUILD_F90_TRUE=''
BUILD_LIBCF_FALSE=''
BUILD_LIBCF_TRUE=''
BUILD_PARALLEL_FALSE=''
BUILD_PARALLEL_TRUE=''
BUILD_UDUNITS_FALSE=''
BUILD_UDUNITS_TRUE=''
BUILD_UTILITIES_FALSE=''
BUILD_UTILITIES_TRUE=''
BUILD_V2_FALSE=''
BUILD_V2_TRUE=''
CC='/opt/pgi/linux86/9.0-4/bin/pgcc'
CCDEPMODE=''
CFLAGS=''
CPP=''
CPPFLAGS='-DpgiFortran'
CROSS_COMPILING_FALSE=''
CROSS_COMPILING_TRUE=''
CXX='/opt/pgi/linux86/9.0-4/bin/pgCC'
CXXCPP=''
CXXDEPMODE=''
CXXFLAGS=''
CYGPATH_W='echo'
DEFS=''
DEPDIR='.deps'
DLLTOOL=''
DSYMUTIL=''
DUMPBIN=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
ENABLE_DAP_LONG_TESTS_FALSE=''
ENABLE_DAP_LONG_TESTS_TRUE=''
ENABLE_DAP_REMOTE_TESTS_FALSE=''
ENABLE_DAP_REMOTE_TESTS_TRUE=''
EXEEXT=''
EXTRA_EXAMPLE_TESTS_FALSE=''
EXTRA_EXAMPLE_TESTS_TRUE=''
EXTRA_TESTS_FALSE=''
EXTRA_TESTS_TRUE=''
F77=''
FC='/opt/pgi/linux86/9.0-4/bin/pgf90'
FCFLAGS=''
FCFLAGS_f90=''
FFLAGS=''
FGREP=''
FTPBINDIR=''
GREP=''
HAS_CXX=''
HAS_DAP=''
HAS_F77=''
HAS_F90=''
HAS_HDF4=''
HAS_HDF5=''
HAS_NC2=''
HAS_NC4=''
HAS_PNETCDF=''
HAS_SZLIB=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
INTERNAL_OCLIB_FALSE=''
INTERNAL_OCLIB_TRUE=''
LARGE_FILE_TESTS_FALSE=''
LARGE_FILE_TESTS_TRUE=''
LD='/opt/pgi/linux86/9.0-4/bin/pgfortran'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL=''
LIPO=''
LN_S=''
LTLIBOBJS=''
MAKEINFO='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/missing --run makeinfo'
MANIFEST_TOOL=''
MKDIR_P='/bin/mkdir -p'
MOD_FLAG=''
NC_FLIBS=''
NC_LIBS=''
NM=''
NMEDIT=''
NMFLAGS=''
OBJDUMP=''
OBJEXT=''
OTOOL64=''
OTOOL=''
PACKAGE='netcdf'
PACKAGE_BUGREPORT='support-netcdf@unidata.ucar.edu'
PACKAGE_NAME='netCDF'
PACKAGE_STRING='netCDF 4.1.3'
PACKAGE_TARNAME='netcdf'
PACKAGE_URL=''
PACKAGE_VERSION='4.1.3'
PATH_SEPARATOR=':'
RANLIB=''
SED=''
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
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_FALSE=''
USE_HDF4_FILE_TESTS_FALSE=''
USE_HDF4_FILE_TESTS_TRUE=''
USE_HDF4_TRUE=''
USE_LOGGING_FALSE=''
USE_LOGGING_TRUE=''
USE_NETCDF4_FALSE=''
USE_NETCDF4_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_VALGRIND_TESTS_FALSE=''
USE_VALGRIND_TESTS_TRUE=''
VERSION='4.1.3'
ac_ct_AR=''
ac_ct_CC='/opt/pgi/linux86/9.0-4/bin/pgcc'
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='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='${SHELL} /home/wrf/netcdf/netcdf-4.1.3/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='/bin/mkdir -p'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
subdirs=''
sysconfdir='${prefix}/etc'
target='i686-pc-linux-gnu'
target_alias=''
target_cpu='i686'
target_os='linux-gnu'
target_vendor='pc'

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

/* confdefs.h */
#define PACKAGE_NAME "netCDF"
#define PACKAGE_TARNAME "netcdf"
#define PACKAGE_VERSION "4.1.3"
#define PACKAGE_STRING "netCDF 4.1.3"
#define PACKAGE_BUGREPORT "support-netcdf@unidata.ucar.edu"
#define PACKAGE_URL ""
#define PACKAGE "netcdf"
#define VERSION "4.1.3"
#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

configure: exit 77

Thanks,
LeeE
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mkcolg



Joined: 30 Jun 2004
Posts: 6208
Location: The Portland Group Inc.

PostPosted: Mon Jul 09, 2012 11:21 am    Post subject: Reply with quote

Hi LeeE,

Quote:
configure:4489: checking whether the C compiler works
configure:4511: /opt/pgi/linux86/9.0-4/bin/pgcc -DpgiFortran conftest.c >&5
pgi-cc-lin32: LICENSE MANAGER PROBLEM: No such feature exists.
Feature: pgi-cc-lin32
License path: /opt/pgi/license.dat:
FLEXnet Licensing error:-5,357
For further information, refer to the FLEXnet Licensing documentation,
available at "www.acresso.com".


This error indicates that your license does not include support for the Linux 32-bit C compilers. This can mean that you don't have a license to use pgcc, but I've also seen this error when using a pre-7.2 license with a post 7.2 PGI release. We changed the compiler package names at this time.

Please send a note to PGI Customer Service (license@pgroup.com) and include your PIN number (the PIN number is the 6 digit number after VENDOR_STRING in your /opt/pgi/license.dat file). This will give us a better idea as to the exact cause of the license issue.

Best Regards,
Mat
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