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fplll / g6k

The General Sieve Kernel
GNU General Public License v2.0
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G6k install in sage environment #119

Closed ndrahmani closed 1 year ago

ndrahmani commented 1 year ago

I am trying to install G6k in sage 10.0 env on a cluster using: PYTHON=python3 ./bootstrap.sh but I get the following error

`Usage: ./bootstrap.sh [ -j <#jobs> ] (uses system's python) PYTHON=python2 ./bootstrap.sh (uses python2) PYTHON=python3 ./bootstrap.sh (uses python3)

Using python version: 3.11.1 Using -j 4 created virtual environment CPython3.11.1.final.0-64 in 975ms creator CPython3Posix(dest=/home/n.rahmani/my_data/g6k/g6k/g6k-env, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/n.rahmani/.local/share/virtualenv) added seed packages: pip==23.2.1, setuptools==68.0.0, wheel==0.41.1 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator ln: failed to create symbolic link './activate': File exists Requirement already satisfied: pip in ./g6k-env/lib/python3.11/site-packages (23.2.1) fatal: destination path 'g6k-fplll' already exists and is not an empty directory. Preparing the fplll build system...please wait

Found GNU Autoconf version 2.69 Found GNU Automake version 1.16.1 Found GNU Libtool version 2.4.6

Automatically preparing build ... done

The fplll build system is now prepared. To build here, run: ./configure make checking whether to enable maintainer-specific portions of Makefiles... yes checking build system type... x86_64-conda-linux-gnu checking host system type... x86_64-conda-linux-gnu checking target system type... x86_64-conda-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... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for x86_64-conda-linux-gnu-gcc... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc 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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc accepts -g... yes checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc understands -c and -o together... yes checking dependency style of /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc... gcc3 checking for a sed that does not truncate output... /data/n.rahmani/envs/sage/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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld checking if the linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm checking the name lister (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 3458764513820540925 checking how to convert x86_64-conda-linux-gnu file names to x86_64-conda-linux-gnu format... func_convert_file_noop checking how to convert x86_64-conda-linux-gnu file names to toolchain format... func_convert_file_noop checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld option to reload object files... -r checking for x86_64-conda-linux-gnu-objdump... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-conda-linux-gnu-dlltool... no checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for x86_64-conda-linux-gnu-ar... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ar checking for archiver @FILE support... @ checking for x86_64-conda-linux-gnu-strip... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-strip checking for x86_64-conda-linux-gnu-ranlib... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ranlib checking command to parse /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm output from /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc 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 x86_64-conda-linux-gnu-mt... no checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cpp 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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -fno-rtti -fno-exceptions... no checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc option to produce PIC... -fPIC -DPIC checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc PIC flag -fPIC -DPIC works... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc static flag -static works... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -c -o file.o... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -c -o file.o... (cached) yes checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-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 whether we are using the GNU C++ compiler... yes checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ accepts -g... yes checking dependency style of /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++... gcc3 checking how to run the C++ preprocessor... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ -E checking for ld used by /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64 checking if the linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) is GNU ld... yes checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ option to produce PIC... -fPIC -DPIC checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ PIC flag -fPIC -DPIC works... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ static flag -static works... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports -c -o file.o... yes checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports -c -o file.o... (cached) yes checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for x86_64-conda-linux-gnu-gcc... (cached) /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc checking whether we are using the GNU C compiler... (cached) yes checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc accepts -g... (cached) yes checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... (cached) none needed checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc understands -c and -o together... (cached) yes checking dependency style of /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc... (cached) gcc3 checking whether make sets $(MAKE)... (cached) yes checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports C++11 features with -std=c++11... yes checking for __gmp_get_memory_functions in -lgmp... yes checking for mpfr_fms in -lmpfr... yes checking for x86_64-conda-linux-gnu-pkg-config... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBQD... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking cstdio usability... yes checking cstdio presence... yes checking for cstdio... yes checking iostream usability... yes checking iostream presence... yes checking for iostream... yes checking string usability... yes checking string presence... yes checking for string... yes checking limits usability... yes checking limits presence... yes checking for limits... yes checking vector usability... yes checking vector presence... yes checking for vector... yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking for working volatile... yes checking for working strtod... yes checking for floor... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for strtol... yes checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc is Clang... no checking whether pthreads work with "-pthread" and "-lpthread"... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... no checking whether std::atomic can be used without link library... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating fplll/Makefile config.status: creating tests/Makefile config.status: creating fplll.pc config.status: creating config.h config.status: config.h is unchanged config.status: creating fplll/fplll_config.h config.status: fplll/fplll_config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands Making clean in fplll make[1]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' rm -f fplll latticegen rm -f llldiff test -z ".gcov .libs/.gcda .libs/.gcno .gcno .gcda /.gcno /.gcda" || rm -f .gcov .libs/.gcda .libs/.gcno .gcno .gcda /.gcno /.gcda test -z "libfplll.la" || rm -f libfplll.la rm -f ./so_locations rm -rf .libs _libs rm -rf enum/.libs enum/_libs rm -rf enum-parallel/.libs enum-parallel/_libs rm -rf pruner/.libs pruner/_libs rm -f .o rm -f enum-parallel/.o rm -f enum-parallel/.lo rm -f enum/.o rm -f enum/.lo rm -f pruner/.o rm -f pruner/.lo rm -f .lo make[1]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' Making clean in tests make[1]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/tests' rm -f test_nr test_lll test_enum test_cvp test_svp test_bkz test_pruner test_gso test_lll_gram test_hlll test_svp_gram test_bkz_gram test_counter test_babai test_ceil test -z ".gcov .libs/.gcda .libs/.gcno .gcno .gcda" || rm -f .gcov .libs/.gcda .libs/.gcno .gcno .gcda rm -rf .libs _libs rm -f .o test -z "test_nr.log test_lll.log test_enum.log test_cvp.log test_svp.log test_bkz.log test_pruner.log test_gso.log test_lll_gram.log test_hlll.log test_svp_gram.log test_bkz_gram.log test_counter.log test_babai.log test_ceil.log" || rm -f test_nr.log test_lll.log test_enum.log test_cvp.log test_svp.log test_bkz.log test_pruner.log test_gso.log test_lll_gram.log test_hlll.log test_svp_gram.log test_bkz_gram.log test_counter.log test_babai.log test_ceil.log test -z "test_nr.trs test_lll.trs test_enum.trs test_cvp.trs test_svp.trs test_bkz.trs test_pruner.trs test_gso.trs test_lll_gram.trs test_hlll.trs test_svp_gram.trs test_bkz_gram.trs test_counter.trs test_babai.trs test_ceil.trs" || rm -f test_nr.trs test_lll.trs test_enum.trs test_cvp.trs test_svp.trs test_bkz.trs test_pruner.trs test_gso.trs test_lll_gram.trs test_hlll.trs test_svp_gram.trs test_bkz_gram.trs test_counter.trs test_babai.trs test_ceil.trs test -z "test-suite.log" || rm -f test-suite.log rm -f .lo make[1]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/tests' make[1]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll' test -z ".gcov .libs/.gcda .libs/.gcno .gcno .gcda" || rm -f .gcov .libs/.gcda .libs/.gcno .gcno .gcda rm -rf .libs _libs rm -f *.lo make[1]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll' make all-recursive make[1]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll' Making all in fplll make[2]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' make all-am make[3]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' CXX main.o CXX libfplll_la-fplll.lo CXX libfplll_la-util.lo CXX enum/libfplll_la-topenum.lo In file included from defs.h:38, from bkz_param.h:23, from bkz.h:21, from fplll.h:25, from main.h:21, from main.cpp:18: /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::' 80 | using ::timespec_get; | ^~~~ In file included from ../fplll/nr/../defs.h:38, from ../fplll/nr/nr.h:7, from ../fplll/nr/numvect.h:19, from nr/matrix.h:21, from util.h:23, from util.cpp:16: /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::' 80 | using ::timespec_get; | ^~~~ In file included from ../fplll/nr/../defs.h:38, from ../fplll/nr/nr.h:7, from ../fplll/nr/numvect.h:19, from enum/../nr/matrix.h:21, from enum/../util.h:23, from enum/topenum.h:19, from enum/topenum.cpp:16: /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::' 80 | using ::timespec_get; | ^~~~ In file included from defs.h:38, from bkz_param.h:23, from bkz.h:21, from fplll.h:25, from fplll.cpp:18: /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::' 80 | using ::timespec_get; | ^~~~ make[3]: [Makefile:1453: enum/libfplll_la-topenum.lo] Error 1 make[3]: Waiting for unfinished jobs.... make[3]: [Makefile:1446: libfplll_la-util.lo] Error 1 make[3]: [Makefile:1439: libfplll_la-fplll.lo] Error 1 make[3]: [Makefile:1415: main.o] Error 1 make[3]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' make[2]: [Makefile:857: all] Error 2 make[2]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll/fplll' make[1]: [Makefile:507: all-recursive] Error 1 make[1]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/g6k-fplll' make: [Makefile:395: all] Error 2 Making fplll failed. Check the logs above - they'll contain more information. `

malb commented 1 year ago

You don't need to run bootstrap in a SageMath environment, it already has FPLLL/FPyLLL.

ndrahmani commented 1 year ago

thanks Sir,

can you please tell me how to do it, I am not familiar with this things thanks in advance

ndrahmani commented 1 year ago

this is what I get after running the following command sage --python3 setup.py build_ext --inplace 

WARNING: Overriding pythran description with argspec information for: numpy.random.binomial
WARNING: Overriding pythran description with argspec information for: numpy.random.bytes
WARNING: Overriding pythran description with argspec information for: numpy.random.chisquare
WARNING: Overriding pythran description with argspec information for: numpy.random.choice
WARNING: Overriding pythran description with argspec information for: numpy.random.dirichlet
WARNING: Overriding pythran description with argspec information for: numpy.random.exponential
WARNING: Overriding pythran description with argspec information for: numpy.random.f
WARNING: Overriding pythran description with argspec information for: numpy.random.gamma
WARNING: Overriding pythran description with argspec information for: numpy.random.geometric
WARNING: Overriding pythran description with argspec information for: numpy.random.pareto
WARNING: Overriding pythran description with argspec information for: numpy.random.gumbel
WARNING: Overriding pythran description with argspec information for: numpy.random.poisson
WARNING: Overriding pythran description with argspec information for: numpy.random.negative_binomial
WARNING: Overriding pythran description with argspec information for: numpy.random.normal
WARNING: Overriding pythran description with argspec information for: numpy.random.laplace
WARNING: Overriding pythran description with argspec information for: numpy.random.logistic
WARNING: Overriding pythran description with argspec information for: numpy.random.lognormal
WARNING: Overriding pythran description with argspec information for: numpy.random.logseries
WARNING: Overriding pythran description with argspec information for: numpy.random.power
WARNING: Overriding pythran description with argspec information for: numpy.random.ranf
WARNING: Overriding pythran description with argspec information for: numpy.random.randint
WARNING: Overriding pythran description with argspec information for: numpy.random.random
WARNING: Overriding pythran description with argspec information for: numpy.random.random_integers
WARNING: Overriding pythran description with argspec information for: numpy.random.random_sample
WARNING: Overriding pythran description with argspec information for: numpy.random.rayleigh
WARNING: Overriding pythran description with argspec information for: numpy.random.sample
WARNING: Overriding pythran description with argspec information for: numpy.random.standard_exponential
WARNING: Overriding pythran description with argspec information for: numpy.random.standard_gamma
WARNING: Overriding pythran description with argspec information for: numpy.random.standard_normal
WARNING: Overriding pythran description with argspec information for: numpy.random.uniform
WARNING: Overriding pythran description with argspec information for: numpy.random.weibull
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:35: installing './compile'
configure.ac:6: installing './config.guess'
configure.ac:6: installing './config.sub'
configure.ac:11: installing './install-sh'
configure.ac:11: installing './missing'
kernel/Makefile.am: installing './depcomp'
checking build system type... x86_64-conda-linux-gnu
checking host system type... x86_64-conda-linux-gnu
checking whether to enable maintainer-specific portions of Makefiles... yes
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 make supports nested variables... (cached) yes
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for x86_64-conda-linux-gnu-gcc... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc
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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc accepts -g... yes
checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc understands -c and -o together... yes
checking dependency style of /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc... gcc3
checking for a sed that does not truncate output... /data/n.rahmani/envs/sage/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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld
checking if the linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm
checking the name lister (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking how to convert x86_64-conda-linux-gnu file names to x86_64-conda-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-conda-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld option to reload object files... -r
checking for x86_64-conda-linux-gnu-objdump... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-conda-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-conda-linux-gnu-ar... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-conda-linux-gnu-strip... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-strip
checking for x86_64-conda-linux-gnu-ranlib... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ranlib
checking command to parse /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-nm output from /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc 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 x86_64-conda-linux-gnu-mt... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cpp
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 /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -fno-rtti -fno-exceptions... no
checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc option to produce PIC... -fPIC -DPIC
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc PIC flag -fPIC -DPIC works... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc static flag -static works... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -c -o file.o... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc supports -c -o file.o... (cached) yes
checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-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 whether we are using the GNU C++ compiler... yes
checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ accepts -g... yes
checking dependency style of /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++... gcc3
checking how to run the C++ preprocessor... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ -E
checking for ld used by /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++... /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64
checking if the linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) is GNU ld... yes
checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes
checking for /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ option to produce PIC... -fPIC -DPIC
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ PIC flag -fPIC -DPIC works... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ static flag -static works... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports -c -o file.o... yes
checking if /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports -c -o file.o... (cached) yes
checking whether the /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ linker (/data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-c++ supports C++11 features with -std=c++11... yes
checking whether /data/n.rahmani/envs/sage/bin/x86_64-conda-linux-gnu-cc is Clang... no
checking whether pthreads work with "-pthread" and "-lpthread"... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... no
checking whether C++ compiler accepts -march=native... yes
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking for x86 cpuid 0x00000000 output... 16:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x80000000 output... 80000008:0:0:0
checking for x86 cpuid 0x00000001 output... 50654:200800:7ffefbf7:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:d39ffffb:18:9c002400
checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800
checking for x86-AVX xgetbv 0x00000000 output... 2ff:0
checking whether RDRND is supported by the processor... yes
checking whether RDRND is supported by the processor and OS... yes
checking whether C++ compiler accepts -mrdrnd... yes
checking whether BMI1 is supported by the processor... yes
checking whether BMI1 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mbmi... yes
checking whether BMI2 is supported by the processor... yes
checking whether BMI2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mbmi2... yes
checking whether ADX is supported by the processor... yes
checking whether ADX is supported by the processor and OS... yes
checking whether C++ compiler accepts -madx... yes
checking whether MPX is supported by the processor... yes
checking whether MPX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mmpx... yes
checking whether PREFETCHWT1 is supported by the processor... no
checking whether ABM is supported by the processor... yes
checking whether ABM is supported by the processor and OS... yes
checking whether C++ compiler accepts -mabm... yes
checking whether MMX is supported by the processor... yes
checking whether MMX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mmmx... yes
checking whether SSE is supported by the processor... yes
checking whether SSE is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse... yes
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse2... yes
checking whether SSE3 is supported by the processor... yes
checking whether SSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse3... yes
checking whether SSSE3 is supported by the processor... yes
checking whether SSSE3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mssse3... yes
checking whether SSE4.1 is supported by the processor... yes
checking whether SSE4.1 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.1... yes
checking whether SSE4.2 is supported by the processor... yes
checking whether SSE4.2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse4.2... yes
checking whether SSE4a is supported by the processor... no
checking whether SHA is supported by the processor... no
checking whether AES is supported by the processor... yes
checking whether AES is supported by the processor and OS... yes
checking whether C++ compiler accepts -maes... yes
checking whether AVX is supported by the processor... yes
checking whether AVX is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... yes
checking whether FMA3 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mfma... yes
checking whether FMA4 is supported by the processor... no
checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... yes
checking whether AVX2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx2... yes
checking whether AVX512-F is supported by the processor... yes
checking whether AVX512-F is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx512f... yes
checking whether AVX512-CD is supported by the processor... yes
checking whether AVX512-CD is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx512cd... yes
checking whether AVX512-PF is supported by the processor... no
checking whether AVX512-ER is supported by the processor... no
checking whether AVX512-VL is supported by the processor... yes
checking whether AVX512-VL is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx512vl... yes
checking whether AVX512-BW is supported by the processor... yes
checking whether AVX512-BW is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx512bw... yes
checking whether AVX512-DQ is supported by the processor... yes
checking whether AVX512-DQ is supported by the processor and OS... yes
checking whether C++ compiler accepts -mavx512dq... yes
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating kernel/Makefile
config.status: creating g6k.pc
config.status: creating kernel/g6k_config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Compiling g6k/siever.pyx because it changed.
Compiling g6k/siever_params.pyx because it changed.
[1/2] Cythonizing g6k/siever.pyx
[2/2] Cythonizing g6k/siever_params.pyx
running build_ext
Making all in kernel
make[1]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/kernel'
(CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/sh /home/n.rahmani/my_data/g6k/g6k/missing autoheader)
rm -f stamp-h1
touch g6k_config.h.in
cd .. && /bin/sh ./config.status kernel/g6k_config.h
config.status: creating kernel/g6k_config.h
config.status: kernel/g6k_config.h is unchanged
make  all-am
make[2]: Entering directory '/home/n.rahmani/my_data/g6k/g6k/kernel'
  CXX      sieving.lo
In file included from /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/chrono:42,
                 from /data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/mutex:39,
                 from siever.h:35,
                 from sieving.cpp:21:
/data/n.rahmani/envs/sage/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
   80 |   using ::timespec_get;
      |           ^~~~~~~~~~~~
make[2]: *** [Makefile:484: sieving.lo] Error 1
make[2]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/kernel'
make[1]: *** [Makefile:359: all] Error 2
make[1]: Leaving directory '/home/n.rahmani/my_data/g6k/g6k/kernel'
make: *** [Makefile:399: all-recursive] Error 1
Traceback (most recent call last):
  File "/home/n.rahmani/my_data/g6k/g6k/setup.py", line 104, in <module>
    setup(
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
    return distutils.core.setup(**attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
           ^^^^^^^^^^^^^^^^^^
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/dist.py", line 1234, in run_command
    super().run_command(command)
  File "/data/n.rahmani/envs/sage/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/home/n.rahmani/my_data/g6k/g6k/setup.py", line 62, in run
    subprocess.check_call("make")
  File "/data/n.rahmani/envs/sage/lib/python3.11/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
joerowell commented 1 year ago

Hi,

This isn't a G6K issue: this is an issue with your conda environment. In particular, it looks like your conda environment is looking to use ::timespec_get when it hasn't yet been included (see e.g this). This isn't something we can help you with, because it's an issue with your environment. For example, see this.

ndrahmani commented 1 year ago

ah got it thanks dear Joe and Martin