tan2
commented
1 year ago Hi Lily,
You have successfully compiled CitcomS. You don't need to run "make install". You can find the executable in the directory "~/software/CitcomS-3.3.1/bin/".
On Tue, Aug 8, 2023 at 10:51 AM zbc1508 @.***> wrote:
Dear developers： I have tried many times on installing CitcomS on my Mac M2 these months, but still can't use it. I installed centOS7 virtual machine, and now I tried to use ubuntu 20.04 virtual machine, and it seemed still did't work. And I copy the terminal txt, could help me find the problems? Thank you very much!
@.:/software/CitcomS-3.3.1$ ls aclocal.m4 ChangeLog COPYING lib NEWS visual AUTHORS config.h.in etc m4 Py2C aux-config configure examples Makefile.am README bin configure.ac INSTALL Makefile.in tests @.:/software/CitcomS-3.3.1$ ./configure 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... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for mpicc... mpicc 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 mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of mpicc... gcc3 checking for mpicxx... mpicxx checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking dependency style of mpicxx... gcc3 checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -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 malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by mpicc... /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 whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-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 https://github.com/file support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from mpicc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC -DPIC checking if mpicc PIC flag -fPIC -DPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking if mpicc supports -c -o file.o... (cached) yes checking whether the mpicc 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 checking how to run the C++ preprocessor... mpicxx -E checking for ld used by mpicxx... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the mpicxx linker (/usr/bin/ld) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -DPIC works... yes checking if mpicxx static flag -static works... no checking if mpicxx supports -c -o file.o... yes checking if mpicxx supports -c -o file.o... (cached) yes checking whether the mpicxx linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for library containing MPI_Init... none required checking for library containing H5Fopen... no configure: WARNING: HDF5 library not found; disabling HDF5 support checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for library containing gzopen... -lz checking for library containing sqrt... -lm checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating etc/Makefile config.status: creating examples/Makefile config.status: creating lib/Makefile config.status: creating tests/Makefile config.status: creating Py2C/Makefile config.status: creating visual/Makefile config.status: creating visual/OpenDXMacro/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands
================ Configuration Summary ================ CC: mpicc CFLAGS: -g -O2 CPPFLAGS: -DUSE_GZDIR LDFLAGS: LIBS: -lm -lz with-hdf5: no with-ggrd: no @.:/software/CitcomS-3.3.1$ make make all-recursive make[1]: Entering directory '/home/lily/software/CitcomS-3.3.1' Making all in Py2C make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' Making all in etc make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/etc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/etc' Making all in examples make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/examples' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/examples' Making all in tests make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/tests' Making all in visual make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual' Making all in OpenDXMacro make[3]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual/OpenDXMacro' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual/OpenDXMacro' make[3]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual' make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual' Making all in lib make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/lib' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/lib' Making all in bin make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/bin' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/bin' make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1' make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1' make[1]: Leaving directory '/home/lily/software/CitcomS-3.3.1' @.:/software/CitcomS-3.3.1$ make install Making install in Py2C make[1]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' /usr/bin/mkdir -p '/usr/local/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c Py2C '/usr/local/bin' libtool: install: /usr/bin/install -c Py2C /usr/local/bin/Py2C /usr/bin/install: cannot create regular file '/usr/local/bin/Py2C': Permission denied make[2]: [Makefile:377: install-binPROGRAMS] Error 1 make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[1]: [Makefile:595: install-am] Error 2 make[1]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' make: [Makefile:400: install-recursive] Error 1 @.:~/software/CitcomS-3.3.1$
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zbc1508
Dear developers： I have tried many times on installing CitcomS on my Mac M2 these months, but still can't use it. I installed centOS7 virtual machine, and now I tried to use ubuntu 20.04 virtual machine, and it seemed still did't work. And I copy the terminal txt, could help me find the problems? Thank you very much!
lily@lily:~/software/CitcomS-3.3.1$ ls aclocal.m4 ChangeLog COPYING lib NEWS visual AUTHORS config.h.in etc m4 Py2C aux-config configure examples Makefile.am README bin configure.ac INSTALL Makefile.in tests lily@lily:~/software/CitcomS-3.3.1$ ./configure 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... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for mpicc... mpicc 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 mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of mpicc... gcc3 checking for mpicxx... mpicxx checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking dependency style of mpicxx... gcc3 checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -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 malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by mpicc... /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 whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-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 mpicc object... ok checking for sysroot... no checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC -DPIC checking if mpicc PIC flag -fPIC -DPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking if mpicc supports -c -o file.o... (cached) yes checking whether the mpicc 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 checking how to run the C++ preprocessor... mpicxx -E checking for ld used by mpicxx... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the mpicxx linker (/usr/bin/ld) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -DPIC works... yes checking if mpicxx static flag -static works... no checking if mpicxx supports -c -o file.o... yes checking if mpicxx supports -c -o file.o... (cached) yes checking whether the mpicxx linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for library containing MPI_Init... none required checking for library containing H5Fopen... no configure: WARNING: HDF5 library not found; disabling HDF5 support checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for library containing gzopen... -lz checking for library containing sqrt... -lm checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bin/Makefile config.status: creating etc/Makefile config.status: creating examples/Makefile config.status: creating lib/Makefile config.status: creating tests/Makefile config.status: creating Py2C/Makefile config.status: creating visual/Makefile config.status: creating visual/OpenDXMacro/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands
================ Configuration Summary ================ CC: mpicc CFLAGS: -g -O2 CPPFLAGS: -DUSE_GZDIR LDFLAGS: LIBS: -lm -lz with-hdf5: no with-ggrd: no lily@lily:~/software/CitcomS-3.3.1$ make make all-recursive make[1]: Entering directory '/home/lily/software/CitcomS-3.3.1' Making all in Py2C make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' Making all in etc make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/etc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/etc' Making all in examples make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/examples' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/examples' Making all in tests make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/tests' Making all in visual make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual' Making all in OpenDXMacro make[3]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual/OpenDXMacro' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual/OpenDXMacro' make[3]: Entering directory '/home/lily/software/CitcomS-3.3.1/visual' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual' make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/visual' Making all in lib make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/lib' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/lib' Making all in bin make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/bin' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/bin' make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1' make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1' make[1]: Leaving directory '/home/lily/software/CitcomS-3.3.1' lily@lily:~/software/CitcomS-3.3.1$ make install Making install in Py2C make[1]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[2]: Entering directory '/home/lily/software/CitcomS-3.3.1/Py2C' /usr/bin/mkdir -p '/usr/local/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c Py2C '/usr/local/bin' libtool: install: /usr/bin/install -c Py2C /usr/local/bin/Py2C /usr/bin/install: cannot create regular file '/usr/local/bin/Py2C': Permission denied make[2]: [Makefile:377: install-binPROGRAMS] Error 1 make[2]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' make[1]: [Makefile:595: install-am] Error 2 make[1]: Leaving directory '/home/lily/software/CitcomS-3.3.1/Py2C' make: *** [Makefile:400: install-recursive] Error 1 lily@lily:~/software/CitcomS-3.3.1$