Hi
After successfully installing ambertools at 5th step of Ambertools manual in
section 1.2, I think I should not go to 6th and 7th step if dont need mpi
run or should I?
When I am trying to go to install amber10 distribution, it is giving me
following error
*Configuring netcdf; (may be time-consuming)
./configure_amber: line 1211: cd: netcdf/src: No such file or directory
netcdf configure returned 1
NETCDF configure failed! Check the netcdf_config.log file*
As both directories amber10 and amber11 are in /home/ssa. How should I go
ahead in environemnt setting as I am suspecting some error here?
log file is
configure: netCDF 3.6.2
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
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 whether to enable maintainer-specific portions of Makefiles... no
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 documentation is to be installed... no
checking whether Fortran compiler(s) should be tested during configure...
yes
checking whether configure should try to set compiler flags... 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 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... no
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump should be built... yes
checking whether gfortran accepts -g... yes
configure: setting up Fortran 90
checking for Fortran flag to compile .f90 files... none
checking fortran 90 modules inclusion flag... -I
checking if Fortran compiler can handle Fortran-90... yes
configure: finding C++ compiler (will not be used if C++ API is not desired)
checking for cl... no
checking for KCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for xlC... no
checking for aCC... no
checking for c++... c++
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ld used by gcc... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking for /usr/x86_64-suse-linux/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 recognize dependent libraries... pass_all
checking how to run the C preprocessor... 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... c++ -E
checking the maximum length of command line arguments... 1572864
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking for correct ltmain.sh version... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/x86_64-suse-linux/bin/ld -m
elf_x86_64) suppo
rts 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 if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by c++... /usr/x86_64-suse-linux/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) is GNU
ld... y
es
checking whether the c++ linker (/usr/x86_64-suse-linux/bin/ld -m
elf_x86_64) suppo
rts shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/usr/x86_64-suse-linux/bin/ld -m
elf_x86_64) suppo
rts shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
(cached) (cached) checking how to hardcode library paths into programs...
immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking whether the gfortran linker (/usr/x86_64-suse-linux/bin/ld -m
elf_x86_64)
supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
(cached) (cached) checking how to hardcode library paths into programs...
immediate
configure: finding other utilities
checking for a BSD-compatible install... /usr/bin/install -c
configure: trying to set fortran flags for this platform
configure: trying to set flags for this platform
checking if _HPUX_SOURCE should be set... no
checking if Solaris -Xa option is needed... CFLAGS= -D_FILE_OFFSET_BITS=64
-D_LARGE
FILE_SOURCE
configure: trying to set fortran 90 flags for this platform
checking if we need to add to FFLAGS for ifort compiler... FFLAGS= -O3
-mtune=gener
ic
checking if we need to set _LARGE_FILES despite results of previous tests...
_LARGE
_FILES=
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
configure: displaying some results
checking CPPFLAGS... -DNDEBUG
checking CC CFLAGS... gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
checking type gcc... gcc is /usr/bin/gcc
checking CXX... c++
checking CXXFLAGS... -g -O2
checking type c++... c++ is /usr/bin/c++
checking FC... gfortran
checking FFLAGS... -O3 -mtune=generic
checking type gfortran... gfortran is /usr/bin/gfortran
checking F90... gfortran
checking F90FLAGS... -O3 -mtune=generic
checking type gfortran... gfortran is /usr/bin/gfortran
checking AR... ar
checking ARFLAGS...
checking type ar... ar is /usr/bin/ar
checking NM... /usr/bin/nm -B
checking NMFLAGS...
checking for /usr/bin/nm... /usr/bin/nm -B
checking nm flags...
checking for C-equivalent to Fortran routine "SUB"... sub_
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 if Fortran 90 compiler capitalizes .mod filenames... no
configure: checking types, headers, and functions
checking for stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for strlcat... no
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 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... 8
checking for float... yes
checking size of float... 4
checking for double... yes
checking size of double... 8
checking for off_t... (cached) yes
checking size of off_t... 8
checking for size_t... (cached) yes
checking size of size_t... 8
checking for manual-page index command...
checking binary distribution directory... /home/ftp/pub/binary/dummy_system
configure: generating header files and makefiles
configure: creating ./config.status
config.status: creating Makefile
config.status: creating man/Makefile
config.status: creating fortran/Makefile
config.status: creating libsrc/Makefile
config.status: creating nctest/Makefile
config.status: creating nc_test/Makefile
config.status: creating ncdump/Makefile
config.status: creating ncgen/Makefile
config.status: creating nf_test/Makefile
config.status: creating cxx/Makefile
config.status: creating f90/Makefile
config.status: creating examples/Makefile
config.status: creating examples/C/Makefile
config.status: creating examples/CDL/Makefile
config.status: creating examples/CXX/Makefile
config.status: creating examples/F90/Makefile
netcdf_config.log lines 203-229/234 98%
On Tue, Jan 26, 2010 at 12:11 AM, David Watson <dewatson.olemiss.edu> wrote:
> On Jan 25, 2010, at 10:49 PM, sikander azam wrote:
> [snip]
> >> ESC[?1034h[gtkleap]$ set default echo on
> [snip]
> >> ESC[?1034h[gtkleap]$ set default echo on
> [snip]
> >> ESC[?1034h[gtkleap]$ set default echo on
> [snip]
> >> ESC[?1034h[gtkleap]$ set default echo on
> [snip]
> >> ESC[?1034h[gtkleap]$ set default echo on
>
> [snip]
>
> Try the following:
> export TERM="vt100"
> then rerun the tests.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 27 2010 - 07:00:03 PST
