Thank you very much for your suggestion. But now I got another problem about the building the package xz-5.2.2.p0. I attached the log file here. Any help will be greatly appreciated!
Isuru Fernando <isu...@gmail.com> 于2020年4月13日周一 下午8:50写道： > Looks like you are using ccache, but CCACHE_DIR is not pointing to the > scratch folder. > Delete $HOME/.ccache and set CCACHE_DIR env variable to some place like > /scratch/user/hhuang235/.ccache > > Isuru > > On Mon, Apr 13, 2020 at 8:45 PM HANG HUANG <huanghang1...@gmail.com> > wrote: > >> Thanks very much for your reply. In fact, my scratch folder has almost 1T >> of free space. So I am really confused of why I got that error message. >> >> >> Best, >> Amy >> >> >> 'Justin C. Walker' via sage-support <sage-support@googlegroups.com> >> 于2020年4月13日周一 下午6:16写道： >> >>> >>> >>> > On Apr 13, 2020, at 14:59 , HANG HUANG <huanghang1...@gmail.com> >>> wrote: >>> > >>> > I am trying to install Sage version 9.0 on the High performance >>> cluster at my university, which runs Linux (CentOS 7). I am installing to >>> my local "scratch" folder since I do not have administrative permissions. I >>> am trying to install from source code as the installing from pre-built >>> binaries also gives me some other error. I was able to run ./configure >>> without any issues and then when i did make, I received the following log >>> file (attached) and error: >>> > >>> > Error building Sage. >>> > >>> > The following package(s) may have failed to build (not necessarily >>> > during this run of 'make all-start'): >>> > >>> > * package: flint-2.5.2.p5 >>> > log file: >>> /scratch/user/hhuang235/sage-9.0/logs/pkgs/flint-2.5.2.p5.log >>> > build directory: >>> /scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/flint-2.5.2.p5 >>> > >>> > The build directory may contain configuration files and other >>> potentially >>> > helpful information. WARNING: if you now run 'make' again, the build >>> > directory will, by default, be deleted. Set the environment variable >>> > SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. >>> > >>> > make[1]: *** [all-start] Error 1 >>> > make[1]: Leaving directory `/scratch/user/hhuang235/sage-9.0' >>> > make: *** [all] Error 2 >>> >>> Checking the log file for flint that you attached, there is this: >>> >>> ccache: error: Failed to create temporary file for >>> /home/hhuang235/.ccache/2/9/8e02d78d68b9638edd65c3e5744171-2001.manifest.tmp: >>> Disk quota exceeded >>> >>> I think that should explain the problem you are having. Is the “scratch >>> folder” on a disk of small size, or does it have a small amount of free >>> space? The source build of Sage does take a lot of space. On my system, >>> Sage 9.0 uses about 7.5 GB (when complete). >>> >>> HTH >>> >>> Justin >>> >>> -- >>> Justin C. Walker >>> Curmudgeon-at-large >>> Director >>> Institute for the Absorption of Federal Funds >>> ---- >>> 186,000 Miles per Second >>> Not just a good idea: >>> it's the law! >>> ---- >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "sage-support" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to sage-support+unsubscr...@googlegroups.com. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/sage-support/8F194F5B-3706-4290-AB20-9E16425014D4%40mac.com >>> . >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "sage-support" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to sage-support+unsubscr...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-support/CADTeGQetEtmqpEKvGXQ-Y6tOHqUaVX_NMdBQnVXqwv%3Dq7Kxr7A%40mail.gmail.com >> <https://groups.google.com/d/msgid/sage-support/CADTeGQetEtmqpEKvGXQ-Y6tOHqUaVX_NMdBQnVXqwv%3Dq7Kxr7A%40mail.gmail.com?utm_medium=email&utm_source=footer> >> . >> > -- > You received this message because you are subscribed to the Google Groups > "sage-support" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-support+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-support/CA%2B01voOSBEF-8L3NkKreYmK3HTC808pjE2Ni4ss3n5DwMY%2B1HA%40mail.gmail.com > <https://groups.google.com/d/msgid/sage-support/CA%2B01voOSBEF-8L3NkKreYmK3HTC808pjE2Ni4ss3n5DwMY%2B1HA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/CADTeGQcFJSmsYZR7ViQe1iwq6-5bd8WWz_kSSQZGv%3DneGGuiSw%40mail.gmail.com.
Found local metadata for xz-5.2.2.p0 Using cached file /scratch/user/hhuang235/sage-9.0/upstream/xz-5.2.2.tar.gz xz-5.2.2.p0 ==================================================== Setting up build directory for xz-5.2.2.p0 Finished extraction No patch files found in ../patches **************************************************** Host system: Linux tlogin-0502.cluster 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=/usr/bin/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux Thread model: posix gcc version 4.8.5 20150623 (Red Hat 4.8.5-39) (GCC) **************************************************** Package 'xz' is currently not installed No legacy uninstaller found for 'xz'; nothing to do Configuring xz-5.2.2.p0 configure: WARNING: unrecognized options: --disable-maintainer-mode XZ Utils 5.2.2 System type: checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu Configure options: checking if debugging code should be compiled... no checking which encoders to build... lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc checking which decoders to build... lzma1 lzma2 delta x86 powerpc ia64 arm armthumb sparc checking which match finders to build... hc3 hc4 bt2 bt3 bt4 checking which integrity checks to build... crc32 crc64 sha256 checking if assembler optimizations should be used... x86_64 checking if small size is preferred over speed... no checking if threading support is wanted... yes, posix checking how much RAM to assume if the real amount is unknown... 128 MiB checking if library symbol versioning should be used... yes checking for a shell that conforms to POSIX... /usr/bin/bash Initializing Automake: 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 whether ln -s works... yes checking for style of include used by make... GNU 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 gcc option to accept ISO C99... -std=gnu99 checking dependency style of gcc -std=gnu99... none checking how to run the C preprocessor... gcc -std=gnu99 -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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes POSIX threading support: checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for library containing clock_gettime... none required checking for clock_gettime... yes checking for pthread_condattr_setclock... yes checking whether CLOCK_MONOTONIC is declared... yes Initializing Libtool: 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 gcc -std=gnu99... ld checking if the linker (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 the maximum length of command line arguments... 1572864 checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for 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 archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 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... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes checking if gcc -std=gnu99 static flag -static works... yes checking if gcc -std=gnu99 supports -c -o file.o... yes checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes checking whether the gcc -std=gnu99 linker (ld -m elf_x86_64) 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 for windres... no Initializing gettext: checking whether NLS is requested... yes checking for msgfmt... /usr/bin/msgfmt checking for gmsgfmt... /usr/bin/msgfmt checking for xgettext... /usr/bin/xgettext checking for msgmerge... /usr/bin/msgmerge checking for ld used by GCC... ld -m elf_x86_64 checking if the linker (ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc System headers and functions: checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking immintrin.h usability... yes checking immintrin.h presence... yes checking for immintrin.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for uint8_t... yes checking for uint16_t... yes checking for int32_t... yes checking for uint32_t... yes checking for int64_t... yes checking for uint64_t... yes checking for uintptr_t... yes checking size of size_t... 8 checking for struct stat.st_atim.tv_nsec... yes checking for struct stat.st_atimespec.tv_nsec... no checking for struct stat.st_atimensec... no checking for struct stat.st_uatime... no checking for struct stat.st_atim.st__tim.tv_nsec... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking whether byte ordering is bigendian... no checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking for getopt_long... yes checking whether optreset is declared... no checking for futimens... yes checking for posix_fadvise... yes checking whether program_invocation_name is declared... yes checking byteswap.h usability... yes checking byteswap.h presence... yes checking for byteswap.h... yes checking if bswap_16 is available... yes checking if bswap_32 is available... yes checking if bswap_64 is available... yes checking if unaligned memory access should be used... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking how to detect the amount of physical memory... sysconf checking for sys/param.h... (cached) yes checking how to detect the number of available CPU cores... sysconf checking whether mbrtowc and mbstate_t are properly declared... yes checking for wcwidth... yes checking CommonCrypto/CommonDigest.h usability... no checking CommonCrypto/CommonDigest.h presence... no checking for CommonCrypto/CommonDigest.h... no checking sha256.h usability... no checking sha256.h presence... no checking for sha256.h... no checking sha2.h usability... no checking sha2.h presence... no checking for sha2.h... no checking minix/sha2.h usability... no checking minix/sha2.h presence... no checking for minix/sha2.h... no checking whether _mm_movemask_epi8 is declared... yes GCC extensions: checking whether the -Werror option is usable... yes checking for simple visibility declarations... yes checking if gcc -std=gnu99 accepts -Wall... yes checking if gcc -std=gnu99 accepts -Wextra... yes checking if gcc -std=gnu99 accepts -Wvla... yes checking if gcc -std=gnu99 accepts -Wformat=2... yes checking if gcc -std=gnu99 accepts -Winit-self... yes checking if gcc -std=gnu99 accepts -Wmissing-include-dirs... yes checking if gcc -std=gnu99 accepts -Wstrict-aliasing... yes checking if gcc -std=gnu99 accepts -Wfloat-equal... yes checking if gcc -std=gnu99 accepts -Wundef... yes checking if gcc -std=gnu99 accepts -Wshadow... yes checking if gcc -std=gnu99 accepts -Wpointer-arith... yes checking if gcc -std=gnu99 accepts -Wbad-function-cast... yes checking if gcc -std=gnu99 accepts -Wwrite-strings... yes checking if gcc -std=gnu99 accepts -Wlogical-op... yes checking if gcc -std=gnu99 accepts -Waggregate-return... yes checking if gcc -std=gnu99 accepts -Wstrict-prototypes... yes checking if gcc -std=gnu99 accepts -Wold-style-definition... yes checking if gcc -std=gnu99 accepts -Wmissing-prototypes... yes checking if gcc -std=gnu99 accepts -Wmissing-declarations... yes checking if gcc -std=gnu99 accepts -Wmissing-noreturn... yes checking if gcc -std=gnu99 accepts -Wredundant-decls... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Doxyfile config.status: creating Makefile config.status: creating po/Makefile.in config.status: creating lib/Makefile config.status: creating src/Makefile config.status: creating src/liblzma/Makefile config.status: creating src/liblzma/api/Makefile config.status: creating src/xz/Makefile config.status: creating src/xzdec/Makefile config.status: creating src/lzmainfo/Makefile config.status: creating src/scripts/Makefile config.status: creating tests/Makefile config.status: creating debug/Makefile config.status: creating src/scripts/xzdiff config.status: creating src/scripts/xzgrep config.status: creating src/scripts/xzmore config.status: creating src/scripts/xzless config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing po-directories commands config.status: creating po/POTFILES config.status: creating po/Makefile configure: WARNING: unrecognized options: --disable-maintainer-mode Building xz-5.2.2.p0 make[4]: Entering directory `/scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0/src' CDPATH="${ZSH_VERSION+.}:" && cd . && /usr/bin/bash /scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0/src/build-aux/missing aclocal-1.15 -I m4 /scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0/src/build-aux/missing: line 81: aclocal-1.15: command not found WARNING: 'aclocal-1.15' is missing on your system. You should only need it if you modified 'acinclude.m4' or 'configure.ac' or m4 files included by 'configure.ac'. The 'aclocal' program is part of the GNU Automake package: <http://www.gnu.org/software/automake> It also requires GNU Autoconf, GNU m4 and Perl in order to run: <http://www.gnu.org/software/autoconf> <http://www.gnu.org/software/m4/> <http://www.perl.org/> make[4]: *** [aclocal.m4] Error 127 make[4]: Leaving directory `/scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0/src' ******************************************************************************** Error building xz-5.2.2.p0 ******************************************************************************** real 0m11.912s user 0m5.148s sys 0m5.376s ************************************************************************ Error installing package xz-5.2.2.p0 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /scratch/user/hhuang235/sage-9.0/logs/pkgs/xz-5.2.2.p0.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/scratch/user/hhuang235/sage-9.0/local/var/tmp/sage/build/xz-5.2.2.p0' && '/scratch/user/hhuang235/sage-9.0/sage' --sh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
