[AMBER] Question of Amber_ Sasaki

From: Shiho Ohno <s.ohno.tohoku-mpu.ac.jp>
Date: Tue, 2 Nov 2021 13:57:12 +0900

 

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
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