[Nexus] General installation question.
Balamurali Ananthan
bala at txcorp.com
Thu Apr 19 17:41:38 BST 2007
Thanks Freddie,
That worked fine and now I'm struck on this seemingly simple error for
sometime:
During make:
-------------------------------
...
f95 -mismatch -I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -c
NXdump.f90
Evaluation trial version of NAGWare Fortran 95 Release 5.1(282)
/bin/sh ../libtool --mode=link --tag=CC f95 -mismatch
-I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -L/usr/local/hdf5/lib
-L/tmp/software/4.2r1-linux/4.2r1-linux//lib -L/usr/local/lib -o NXdump
NXdump.o ../bindings/f90/libNeXus90.la -lxml2 -lhdf5 -lmfhdf -ldf -lsz
-ljpeg -lz
libtool: link: warning: library
`/tmp/software/4.2r1-linux/4.2r1-linux//lib/libsz.la' was moved.
libtool: link: warning: library
`/tmp/software/4.2r1-linux/4.2r1-linux//lib/libsz.la' was moved.
f95 -mismatch -I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -o
.libs/NXdump NXdump.o -L/usr/local/hdf5/lib
-L/tmp/software/4.2r1-linux/4.2r1-linux//lib -L/usr/local/lib
../bindings/f90/.libs/libNeXus90.so
/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f77/.libs/libNeXus77.so
/tmp/software/nexus-3.0.0/nexus-3.0.0/src/.libs/libNeXus.so
/usr/lib/libxml2.so -lpthread /usr/local/hdf5-1.6.4/lib/libhdf5.so -lmfhdf
-ldf /tmp/software/4.2r1-linux/4.2r1-linux//lib/libsz.so -lm
/usr/lib/libjpeg.so -lz -Wl,--rpath -Wl,/tmp/software/nexus-3.0.0/nexus/lib
-Wl,--rpath -Wl,/usr/local/hdf5-1.6.4/lib -Wl,--rpath
-Wl,/tmp/software/4.2r1-linux/4.2r1-linux//lib
Evaluation trial version of NAGWare Fortran 95 Release 5.1(282)
gcc: /tmp/software/nexus-3.0.0/nexus/lib: No such file or directory
make[2]: *** [NXdump] Error 1
make[2]: Leaving directory
`/tmp/software/nexus-3.0.0/nexus-3.0.0/applications'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/tmp/software/nexus-3.0.0/nexus-3.0.0/applications'
make: *** [all-recursive] Error 1
[bala at grid nexus-3.0.0]$
-------------------------------
More specifically, in applications/ if I do:
-------------------------------
[bala at grid applications]$ f95 -mismatch
-I/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f90 -o .libs/NXdump
NXdump.o -L/usr/local/hdf5/lib -L/tmp/software/4.2r1-linux/4.2r1-linux//lib
-L/usr/local/lib ../bindings/f90/.libs/libNeXus90.so
/tmp/software/nexus-3.0.0/nexus-3.0.0/bindings/f77/.libs/libNeXus77.so
/tmp/software/nexus-3.0.0/nexus-3.0.0/src/.libs/libNeXus.so
/usr/lib/libxml2.so -lpthread /usr/local/hdf5-1.6.4/lib/libhdf5.so -lmfhdf
-ldf /tmp/software/4.2r1-linux/4.2r1-linux//lib/libsz.so -lm
/usr/lib/libjpeg.so -lz -Wl,--rpath -Wl,/tmp/software/nexus-3.0.0/nexus/lib
-Wl,--rpath -Wl,/usr/local/hdf5-1.6.4/lib -Wl,--rpath
-Wl,/tmp/software/4.2r1-linux/4.2r1-linux//lib
Evaluation trial version of NAGWare Fortran 95 Release 5.1(282)
gcc: /tmp/software/nexus-3.0.0/nexus/lib: No such file or directory
--------------------------------
/tmp/software/nexus-3.0.0/nexus is the prefix location that I specified
during configure. Is it not supposed to create a lib/ instead of
complaining that the directory is not found?
Am I missing something? Any help is much appreciated. Thanks.
.Bala.
> -----Original Message-----
> From: Akeroyd, FA (Freddie) [mailto:F.A.Akeroyd at rl.ac.uk]
> Sent: Wednesday, April 18, 2007 7:21 AM
> To: Balamurali Ananthan; nexus at nexusformat.org
> Subject: RE: [Nexus] General installation question.
>
> 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
> ---
>
>
> _______________________________________________
> NeXus mailing list
> NeXus at nexusformat.org
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