Dear Amber Administrator
Please excuse me for asking this question.
My name is Sasaki, Tohoku Medical and Pharmaceutical University.
I have a question about Amber, so I would like to contact you.
I'm currently in the process of installing Amber Tool 19.
. /configure gnu and got the following error
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Error: NetCDF C configure returned 1
NetCDF configure failed! Check the netcdf_config.log file
Check the netcdf_config.log file in the
/home/user/amber18/AmberTools/src directory.
Check the netcdf_config.log file in the /home/user/amber18/AmberTools/src
directory.
The netcdf_config.log is as follows
configure: netCDF 4.6.1
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-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... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... no
checking whether make supports nested variables... no
checking whether to enable maintainer-specific portions of Makefiles... no
configure: checking user options
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking if fsync support is enabled... no
checking if jna bug workaround is enabledd... no
checking whether we should build netCDF-4... no
checking do we require hdf5 dynamic-loading support... yes
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 we should attempt to install netcdf-fortran
(EXPERIMENTAL)... 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 DAP client(s) are to be built... no
checking whether make supports the include directive... no
checking for gcc... gcc
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... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for curl_easy_setopt in -lcurl... no
checking whether dap remote testing should be enabled (default on)... no
checking whether dap remote authorization testing should be enabled (default
off)... no
checking whether netcdf4 group names for DAP2 hould be enabled (default
on)... yes
configure: DAP2 groups is being disabled because DAP2 support is disabled
or netcdf-4 disabled
checking which remote test server(s) to use...
remotetest.unidata.ucar.edu,jetstream.unidata.ucar.edu (defaults)
checking whether the time-consuming dap tests should be enabled (default
off)... no
checking whether to enable strict null-byte header padding when reading
(default off)... no
checking whether FFIO will be used... no
checking whether STDIO will be used... no
checking whether examples should be built... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump/nccopy should be built... yes
checking whether test should be built and run... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmarks 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... .
configure: finding C compiler
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for an ANSI C-conforming const... yes
checking whether CURLOPT_USERNAME is defined... no
checking whether CURLOPT_PASSWORD is defined... no
checking whether CURLOPT_KEYPASSWD is defined... no
checking whether CURLINFO_RESPONSE_CODE is defined... no
configure: setting up libtool
checking how to print strings... printf
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 fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to
x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain
format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver .FILE support... .
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) 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 if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
configure: finding other utilities
checking for m4... m4
checking for doxygen... no
configure: WARNING: Doxygen not found - documentation will not be built
checking for dot... no
configure: WARNING: dot not found - will use simple charts in documentation
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...
checking CC CFLAGS... gcc -fPIC -DSYSV -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ
checking type gcc... gcc is /usr/bin/gcc
checking CXX... unset
checking FC... unset
checking F90... unset
checking AR... ar
checking AR_FLAGS... cru
checking type ar... ar is /usr/bin/ar
checking NM... /usr/bin/nm -B
checking NMFLAGS...
configure: checking types, headers, and functions
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking libgen.h usability... yes
checking libgen.h presence... yes
checking for libgen.h... yes
checking for ANSI C header files... (cached) yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for sys/types.h... (cached) yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking ftw.h usability... yes
checking ftw.h presence... yes
checking for ftw.h... yes
checking for strlcat... no
checking for snprintf... yes
checking for strdup... yes
checking for strtoll... yes
checking for strtoull... yes
checking for mkstemp... yes
checking for mktemp... yes
checking for random... yes
checking for getrlimit... yes
checking for gettimeofday... yes
checking for fsync... yes
checking for MPI_Comm_f2c... no
checking whether in-memory files are enabled... yes
configure: WARNING: netcdf-4 not enabled; disabling DAP4
checking for memmove... yes
checking for getpagesize... yes
checking for sysconf... yes
checking whether mmap is enabled for in-memory files... no
checking for mremap... yes
mmap function or mremap function is not available: disabling mmap
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether isnan is declared... yes
checking whether isinf is declared... yes
checking whether isfinite is declared... yes
checking for struct stat.st_blksize... yes
checking for IEEE floating point format... yes
checking for size_t... (cached) yes
checking for ssize_t... yes
checking for schar... no
checking for uchar... no
checking for longlong... no
checking for ushort... yes
checking for uint... yes
checking for int64... no
checking for uint64... no
checking for off_t... yes
checking whether byte ordering is bigendian... no
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking size of off_t... 8
checking size of size_t... 8
checking size of unsigned long long... 8
checking whether CDF5 support should be enabled... yes
checking size of unsigned char... 1
checking size of ushort... 2
checking size of uint... 4
checking size of ushort... (cached) 2
checking size of uint... (cached) 4
checking size of ssize_t... 8
checking size of void*... 8
checking for floor in -lm... yes
checking whether parallel I/O for classic files is to be enabled... no
checking what to call the output of the ftpbin target...
binary-netcdf-4.6.1_nc3.tar
checking if libtool needs -no-undefined flag to build shared libraries... no
checking value of LIBS... -lm
checking If compilation is for use with JNA... no
checking whether filter testing should be run... yes
configure: WARNING: netCDF-4 disabled => --disable-filter-testing
./configure: line 14948: enable_filter_testing: command not found
configure: WARNING: Shared libraries are disabled =>
--disable-filter-testing
./configure: line 14954: enable_filter_testing: command not found
configure: generating header files and makefiles
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating test_common.sh
config.status: creating nc_test4/findplugin.sh
config.status: creating Makefile
config.status: creating nc-config
config.status: creating netcdf.pc
config.status: creating libnetcdf.settings
config.status: creating postinstall.sh
config.status: creating include/netcdf_meta.h
config.status: creating include/Makefile
config.status: creating h5_test/Makefile
config.status: creating hdf4_test/Makefile
config.status: creating libsrc/Makefile
config.status: creating libsrc4/Makefile
config.status: creating libsrcp/Makefile
config.status: creating ncdump/Makefile
config.status: creating ncgen3/Makefile
config.status: creating ncgen/Makefile
config.status: creating examples/Makefile
config.status: creating examples/C/Makefile
config.status: creating examples/C/hdf5plugins/Makefile
config.status: creating examples/CDL/Makefile
config.status: creating oc2/Makefile
config.status: creating libdap2/Makefile
config.status: creating libdap4/Makefile
config.status: creating libhdf4/Makefile
config.status: creating libdispatch/Makefile
config.status: creating liblib/Makefile
config.status: creating ncdump/cdl/Makefile
config.status: creating ncdump/expected/Makefile
config.status: creating docs/Makefile
config.status: creating docs/images/Makefile
config.status: creating nctest/Makefile
config.status: creating nc_test4/Makefile
config.status: creating nc_test4/hdf5plugins/Makefile
config.status: creating nc_test/Makefile
config.status: creating ncdap_test/Makefile
config.status: creating ncdap_test/testdata3/Makefile
config.status: creating ncdap_test/expected3/Makefile
config.status: creating ncdap_test/expectremote3/Makefile
config.status: creating dap4_test/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: error: in `/home/user/amber18/AmberTools/src/netcdf-4.6.1':
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. Try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log' for more details
I am using Amber18 and AmberTools19.
I would appreciate your answer.
Thank you very much for your time.
Tohoku Medical and Pharmaceutical University Sasaki
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Received on Mon Nov 01 2021 - 22:00:03 PDT
