[Nexus] General installation question.

Akeroyd, FA (Freddie) F.A.Akeroyd at rl.ac.uk
Wed Apr 18 14:21:14 BST 2007 

Balamurali,

The NXIGETDATA and NXIGETSLAB function are both C functions called
directly from FORTRAN. They are declared as EXTERNAL to Fortran and the
compilers we had used so far (g95, gfortran, Intel Fortran) seem to have
allowed them to be called with different argument types; however it
looks like the NAG compiler is more strict about doing this.

I don't have the NAG Fortran compiler installed, but according to the
web documentation passing the

  -mismatch

option to the compiler will make it less strict and should solve the
problem ... to do this you would need to rerun configure as

  env F90FLAGS=-mismatch ./configure

and then "make clean" and "make" again

Regards,

Freddie

-----Original Message-----
From: nexus-bounces at nexusformat.org
[mailto:nexus-bounces at nexusformat.org] On Behalf Of Balamurali Ananthan
Sent: 17 April 2007 00:42
To: nexus at nexusformat.org
Subject: [Nexus] General installation question.

Hello all,

I am newbie, trying to build nexus api 3.0.0 on my Linux machine.

During 'make' in bindings/f90, I get the following error:

...
Making all in f90
make[2]: Entering directory
`/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90'
/bin/sh ../../libtool --mode=compile --tag=F77 f95
-I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -c -o NXmodule.lo
`test
-f 'NXmodule.f90' || echo './'`NXmodule.f90
mkdir .libs
 f95 -I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -c
NXmodule.f90
-fPIC -o .libs/NXmodule.o
Unrecognised option -fPIC passed to ld
Evaluation trial version of NAGWare Fortran 95 Release 5.1(282)
Warning: NXmodule.f90, line 733: Unused dummy variable ATTR_TYPE
         detected at NXGETI1ATTR@<end-of-statement>
Warning: NXmodule.f90, line 733: Unused dummy variable ATTR_LENGTH
         detected at NXGETI1ATTR@<end-of-statement>
Warning: NXmodule.f90, line 751: Unused dummy variable ATTR_TYPE
         detected at NXGETI2ATTR@<end-of-statement>
Warning: NXmodule.f90, line 751: Unused dummy variable ATTR_LENGTH
         detected at NXGETI2ATTR@<end-of-statement>
Warning: NXmodule.f90, line 769: Unused dummy variable ATTR_TYPE
         detected at NXGETI4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 769: Unused dummy variable ATTR_LENGTH
         detected at NXGETI4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 787: Unused dummy variable ATTR_TYPE
         detected at NXGETR4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 787: Unused dummy variable ATTR_LENGTH
         detected at NXGETR4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 805: Unused dummy variable ATTR_TYPE
         detected at NXGETR8ATTR@<end-of-statement>
Warning: NXmodule.f90, line 805: Unused dummy variable ATTR_LENGTH
         detected at NXGETR8ATTR@<end-of-statement>
Warning: NXmodule.f90, line 826: Unused dummy variable ATTR_TYPE
         detected at NXGETCHARATTR@<end-of-statement>
Warning: NXmodule.f90, line 826: Unused dummy variable ATTR_LENGTH
         detected at NXGETCHARATTR@<end-of-statement>
Warning: NXmodule.f90, line 1001: Unused dummy variable VALUE_TYPE
         detected at NXPUTI1ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1001: Unused dummy variable VALUE_LENGTH
         detected at NXPUTI1ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1017: Unused dummy variable VALUE_TYPE
         detected at NXPUTI2ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1017: Unused dummy variable VALUE_LENGTH
         detected at NXPUTI2ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1033: Unused dummy variable VALUE_TYPE
         detected at NXPUTI4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1033: Unused dummy variable VALUE_LENGTH
         detected at NXPUTI4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1049: Unused dummy variable VALUE_TYPE
         detected at NXPUTR4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1049: Unused dummy variable VALUE_LENGTH
         detected at NXPUTR4ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1065: Unused dummy variable VALUE_TYPE
         detected at NXPUTR8ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1065: Unused dummy variable VALUE_LENGTH
         detected at NXPUTR8ATTR@<end-of-statement>
Warning: NXmodule.f90, line 1082: Unused dummy variable VALUE_TYPE
         detected at NXPUTCHARATTR@<end-of-statement>
Warning: NXmodule.f90, line 1082: Unused dummy variable VALUE_LENGTH
         detected at NXPUTCHARATTR@<end-of-statement>
Warning: NXmodule.f90, line 1099: Unused symbol J
         detected at NXGETINFO@<end-of-statement>
Warning: NXmodule.f90, line 1099: Unused symbol I
         detected at NXGETINFO@<end-of-statement>
Warning: NXmodule.f90, line 1115: Unused symbol I
         detected at NXGETNEXTENTRY@<end-of-statement>
Warning: NXmodule.f90, line 1115: Unused symbol J
         detected at NXGETNEXTENTRY@<end-of-statement>
Warning: NXmodule.f90, line 1207: Unused symbol NEW_ID
         detected at NXGETGROUPINFO@<end-of-statement>
Warning: NXmodule.f90, line 1207: Unused symbol GROUP_ID
         detected at NXGETGROUPINFO@<end-of-statement>
[f95 continuing despite warning messages]
Error: NXmodule.f90, line 295: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 305: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 342: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 347: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 384: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 389: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 421: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 453: Inconsistent datatype for arg 2 in call
to
NXIGETDATA
Error: NXmodule.f90, line 523: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 534: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 574: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 580: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 620: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 626: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 661: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
Error: NXmodule.f90, line 701: Inconsistent datatype for arg 2 in call
to
NXIGETSLAB
[f95 error termination]
make[2]: *** [NXmodule.lo] Error 1
make[2]: Leaving directory
`/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings'
make: *** [all-recursive] Error 1

Here is the version of f95 that I use:

[bala at grid nexus-3.0.0]$ f95 -version
NAGWare Fortran 95 compiler Release 5.1(282)
Copyright 1990-2006 The Numerical Algorithms Group Ltd., Oxford, U.K.
[bala at grid nexus-3.0.0]$

And here is the configuration information:

[bala at grid nexus-3.0.0]$ ./configure
--prefix=/tmp/software/nexus-3.0.0/nexus
--with-hdf4=/tmp/software/4.2r1-linux/4.2r1-linux/
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 egrep... grep -E
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... /usr/bin/gcc
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 /usr/bin/gcc accepts -g... yes
checking for /usr/bin/gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of /usr/bin/gcc... gcc3
checking for C compiler option -fno-common... yes
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/bin/g++ accepts -g... yes
checking dependency style of /usr/bin/g++... gcc3
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking for Fortran 77 compiler option
-I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f77... yes
checking how to get verbose linking output from g77... -v
checking for Fortran libraries of g77...
-L/usr/lib/gcc/i386-redhat-linux/3.4.6
-L/usr/lib/gcc/i386-redhat-linux/3.4.6/../../.. -lfrtbegin -lg2c -lm
-lgcc_s
checking for f90... no
checking for f95... f95
configure: Java SDK home is /usr/local/jdk1.5.0_06/bin/..
checking for javac... /usr/local/jdk1.5.0_06/bin/../bin/javac
checking for javadoc... /usr/local/jdk1.5.0_06/bin/../bin/javadoc
checking for jar... /usr/local/jdk1.5.0_06/bin/../bin/jar
checking for java... /usr/local/jdk1.5.0_06/bin/../bin/java
checking for javah... /usr/local/jdk1.5.0_06/bin/../bin/javah
checking for a sed that does not truncate output... /bin/sed
checking for ld used by /usr/bin/gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... /usr/bin/gcc -E
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... /usr/bin/g++ -E
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from /usr/bin/gcc
object...
ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if /usr/bin/gcc static flag  works... yes
checking if /usr/bin/gcc supports -fno-rtti -fno-exceptions... no
checking for /usr/bin/gcc option to produce PIC... -fPIC
checking if /usr/bin/gcc PIC flag -fPIC works... yes
checking if /usr/bin/gcc supports -c -o file.o... yes
checking whether the /usr/bin/gcc linker (/usr/bin/ld) 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
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by /usr/bin/g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld) supports shared
libraries... yes
checking for /usr/bin/g++ option to produce PIC... -fPIC
checking if /usr/bin/g++ PIC flag -fPIC works... yes
checking if /usr/bin/g++ supports -c -o file.o... yes
checking whether the /usr/bin/g++ linker (/usr/bin/ld) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/bin/ld) supports shared
libraries...
yes
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 whether make sets $(MAKE)... (cached) yes
checking for ranlib... (cached) ranlib
checking for swig... swig
checking for docbook2pdf... docbook2pdf
checking for docbook2txt... docbook2txt
checking for location of HDF5 libraries... /usr/local/hdf5
checking for location of mxml package... unknown
checking for xdr_float in -lrpc... no
checking for gzopen in -lz... yes
checking for jpeg_CreateCompress in -ljpeg... yes
checking for SZ_Compress in -lsz... yes
checking for Hopen in -ldf... yes
checking for ncopen in -lmfhdf... yes
checking for H5open in -lhdf5... yes
checking for xmlParseDocument in -lxml2... yes
checking for ANSI C header files... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for working memcmp... no
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for alarm... yes
checking for working mktime... no
checking for strftime... yes
checking for ftime... yes
checking for memset... yes
checking for strchr... yes
checking for strdup... yes
checking for strrchr... yes
checking for strstr... yes
checking for tzset... yes
configure: creating ./config.status
config.status: creating test/Makefile
config.status: creating test/atlocal
config.status: creating Makefile
config.status: creating nexus.spec
config.status: creating build_rpm
config.status: creating include/Makefile
config.status: creating src/Makefile
config.status: creating applications/Makefile
config.status: creating applications/NXdir/Makefile
config.status: creating applications/NXtranslate/Makefile
config.status: creating applications/NXtranslate/IPNS_CPP/Makefile
config.status: creating applications/NXtranslate/docs/Makefile
config.status: creating examples/Makefile
config.status: creating doc/Makefile
config.status: creating doc/api/Makefile
config.status: creating doc/nxdict/Makefile
config.status: creating doc/tech_ref/Makefile
config.status: creating bindings/Makefile
config.status: creating bindings/f77/Makefile
config.status: creating bindings/f90/Makefile
config.status: creating bindings/java/Makefile
config.status: creating contrib/Makefile
config.status: creating contrib/applications/Makefile
config.status: creating scripts/Makefile
config.status: creating scripts/nexus.pc
config.status: creating scripts/nxbuild
config.status: creating include/nxconfig.h
config.status: executing depfiles commands
config.status: executing test/atconfig commands


Configuration (NeXus):

        Source code location:  .
        Version:               3.0.0
        Compiler:              /usr/bin/gcc,/usr/bin/g++,g77,f95

build:
        NeXus with:
                HDF4 support:  yes
                HDF5 support:  yes
                XML support:   no

        bindings:
                F77 :          yes
                F90 :          yes
                JAVA:          yes

Please check whether the configuration I detected matches what you
would like to have.

Any clues on how do I get past this error?

Thanks much.
---
Balamurali Ananthan (bala at txcorp.com) (720-974-1843)
Tech-X Corporation, 5621 Arapahoe Ave, Suite A, Boulder, CO - 80303
---
 

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