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ICTP / RegCM

ICTP Regional Climate Model
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Error while compiling RegCM4 #3

Closed mada0007 closed 4 years ago

mada0007 commented 4 years ago

Dear all I have having this error after successfull submission

What am I doing wrong?

bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure CC=gcc FC=gfortran CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 --no-create --no-recursion checking build system type... x86_64-apple-darwin18.7.0 checking host system type... x86_64-apple-darwin18.7.0 checking how to print strings... printf 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 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... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ld checking if the linker (/Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-nm checking the name lister (/Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop checking for /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-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... no checking for strip... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-strip checking for ranlib... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ranlib checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking command to parse /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-nm output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-nmedit checking for lipo... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-lipo checking for otool... /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... 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... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld 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 a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking for ranlib... (cached) /Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ranlib 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 whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fno-common checking if gfortran PIC flag -fno-common works... yes checking if gfortran static flag -static works... no checking if gfortran supports -c -o file.o... yes checking if gfortran supports -c -o file.o... (cached) yes checking whether the gfortran linker (/Users/mada0007/anaconda3/bin/x86_64-apple-darwin13.4.0-ld) supports shared libraries... yes checking dynamic linker characteristics... darwin18.7.0 dyld checking how to hardcode library paths into programs... immediate checking if nf-config program is present... no checking if nc-config program is present... yes checking whether byte ordering is bigendian... no checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore configure: checking for NetCDF... configure: checking for netcdf.h... checking netcdf.h usability... yes checking netcdf.h presence... yes checking for netcdf.h... yes configure: checking for libnetcdf.a... checking for nc_close in -lnetcdf... yes configure: checking for libnetcdff.a... checking for nf_close in -lnetcdf... no configure: checking for libnetcdff.a... checking for nf_close in -lnetcdff... yes configure: checking for NetCDF module file... checking for mpifort... mpifort checking for MPI_Init... no checking for MPI_Init in -lfmpi... no checking for MPI_Init in -lmpichf90... no checking for MPI_Init in -lmpi... no checking for MPI_Init in -lmpich... no checking that generated files are newer than configure... done configure: creating ./config.status /bin/sh ./config.status config.status: creating Makefile config.status: creating external/Makefile config.status: creating Share/Makefile config.status: creating PreProc/Makefile config.status: creating PreProc/Terrain/Makefile config.status: creating PreProc/ICBC/Makefile config.status: creating PreProc/CH_EMISSIONS/Makefile config.status: creating PreProc/CH_EMISSIONS/interpolation/Makefile config.status: creating PreProc/CH_EMISSIONS/interpolation/tools/Makefile config.status: creating PreProc/CH_EMISSIONS/interpolation/tools/REGCM_grid/Makefile config.status: creating PreProc/CLM/Makefile config.status: creating PreProc/CLM45/Makefile config.status: creating PostProc/Makefile config.status: creating Main/mpplib/Makefile config.status: creating Main/netlib/Makefile config.status: creating Main/Makefile config.status: creating Main/batslib/Makefile config.status: creating Main/clmlib/Makefile config.status: creating Main/ocnlib/Makefile config.status: creating Main/clmlib/clm4.5/Makefile config.status: creating Main/chemlib/Makefile config.status: creating Main/chemlib/GAS_CBMZ_NEW/Makefile config.status: creating Main/cumlib/Makefile config.status: creating Main/radlib/Makefile config.status: creating Main/radlib/RRTMG_SW/Makefile config.status: creating Main/pbllib/Makefile config.status: creating Tools/Programs/CheckSun/Makefile config.status: creating Tools/Programs/RegCM_read/Makefile config.status: creating Tools/Programs/timeseries/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing libtool commands config.status: executing depfiles commands Making install in external make[1]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/external' make[2]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/external' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/external' make[1]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/external' Making install in Share make[1]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share' make[2]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share' make[1]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share' Making install in PreProc make[1]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/PreProc' Making install in Terrain make[2]: Entering directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/PreProc/Terrain' /bin/sh ../../libtool --tag=FC --mode=link gfortran -O3 -mtune=native -march=native -fconvert=big-endian -fno-range-check -finline-functions -L/Users/mada0007/Documents/softwares/RegCM-4.5.0/external -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -o terrain mod_header.o mod_block.o mod_fudge.o mod_maps.o mod_write.o mod_smooth.o mod_maputils.o mod_intldtr.o mod_rdldtr.o mod_moist.o terrain.o -L/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share -lrcmlib -lnetcdff -L/usr/local/Cellar/netcdf/4.7.4/lib -lnetcdf libtool: link: gfortran -O3 -mtune=native -march=native -fconvert=big-endian -fno-range-check -finline-functions -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -o terrain mod_header.o mod_block.o mod_fudge.o mod_maps.o mod_write.o mod_smooth.o mod_maputils.o mod_intldtr.o mod_rdldtr.o mod_moist.o terrain.o -L/Users/mada0007/Documents/softwares/RegCM-4.5.0/external -L/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share -lrcmlib -lnetcdff -L/usr/local/Cellar/netcdf/4.7.4/lib -lnetcdf collect2: fatal error: ld terminated with signal 11 [Segmentation fault: 11] compilation terminated. ld: archive has no table of contents file '/Users/mada0007/Documents/softwares/RegCM-4.5.0/Share/librcmlib.a' for architecture x86_64 make[2]: [Makefile:400: terrain] Error 1 make[2]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/PreProc/Terrain' make[1]: [Makefile:385: install-recursive] Error 1 make[1]: Leaving directory '/Users/mada0007/Documents/softwares/RegCM-4.5.0/PreProc' make: *** [Makefile:431: install-recursive] Error 1

graziano-giuliani commented 4 years ago

This looks like a compiler bug or a system resources issue on the compiling OS. For the latter check user resources using limits or ulimit -a and try to increase the stack space or ask system administrator to do this for your user if the limit is a hard one. If the error persist, try upgrading the compiler. What is the exact OS/compiler you are using?

graziano-giuliani commented 4 years ago

Closed a compiler bug.