gmake[1]: Entering directory '/global/u2/m/madams/petsc_install/petsc' ========================================== See documentation/faq.html and documentation/bugreporting.html for help with installation problems. Please send EVERYTHING printed out below when reporting problems. Please check the mailing list archives and consider subscribing. http://www.mcs.anl.gov/petsc/miscellaneous/mailing-lists.html ========================================== Starting on cori07 at Thu Aug 16 19:14:38 PDT 2018 Machine characteristics: Linux cori07 4.4.114-94.11-default #1 SMP Thu Feb 1 19:28:26 UTC 2018 (4309ff9) x86_64 x86_64 x86_64 GNU/Linux ----------------------------------------- Using PETSc directory: /global/u2/m/madams/petsc_install/petsc Using PETSc arch: arch-cori-knl-opt64-intel ----------------------------------------- PETSC_VERSION_RELEASE 1 PETSC_VERSION_MAJOR 3 PETSC_VERSION_MINOR 7 PETSC_VERSION_SUBMINOR 5 PETSC_VERSION_PATCH 0 PETSC_VERSION_DATE "unknown" PETSC_VERSION_GIT "unknown" PETSC_VERSION_DATE_GIT "unknown" PETSC_VERSION_(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \ PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \ ----------------------------------------- Using configure Options: --with-cc=cc --with-cxx=CC --with-fc=ftn COPTFLAGS=" -g -fp-model fast -hcpu=mic-knl -qopenmp-simd" CXXOPTFLAGS="-g -fp-model fast -hcpu=mic-knl -qopenmp-simd" FOPTFLAGS=" -g -fp-model fast -hcpu=mic-knl -qopenmp-simd" --download-metis=1 --download-hypre=1 --download-parmetis=1 --download-fblaslapack --with-debugging=0 --with-mpiexec=srun --with-batch=0 --with-memalign=64 --with-64-bit-indices=1 PETSC_ARCH=arch-cori-knl-opt64-intel --with-openmp=0 --download-p4est=0 --prefix=/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel Using configuration flags: #define INCLUDED_PETSCCONF_H #define IS_COLORING_MAX 65535 #define STDC_HEADERS 1 #define MPIU_COLORING_VALUE MPI_UNSIGNED_SHORT #define PETSC_UINTPTR_T uintptr_t #define PETSC_HAVE_PTHREAD 1 #define PETSC_DEPRECATED(why) __attribute((deprecated)) #define PETSC_REPLACE_DIR_SEPARATOR '\\' #define PETSC_HAVE_SO_REUSEADDR 1 #define PETSC_HAVE_MPI 1 #define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2 #define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0 #define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1 #define PETSC_HAVE_FORTRAN 1 #define PETSC_DIR "/global/u2/m/madams/petsc_install/petsc" #define PETSC_HAVE_HYPRE 1 #define PETSC_LIB_DIR "/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel/lib" #define PETSC_HAVE_PARMETIS 1 #define PETSC_USE_SOCKET_VIEWER 1 #define PETSC_USE_ISATTY 1 #define PETSC_HAVE_SOWING 1 #define PETSC_SLSUFFIX "" #define PETSC_FUNCTION_NAME_CXX __func__ #define PETSC_HAVE_FBLASLAPACK 1 #define PETSC_HAVE_ATOLL 1 #define PETSC_HAVE_ATTRIBUTEALIGNED 1 #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1 #define PETSC_UNUSED __attribute((unused)) #define PETSC_ATTRIBUTEALIGNED(size) __attribute((aligned (size))) #define PETSC_FUNCTION_NAME_C __func__ #define PETSC_USE_SINGLE_LIBRARY 1 #define PETSC_HAVE_BUILTIN_EXPECT 1 #define PETSC_HAVE_METIS 1 #define PETSC_DIR_SEPARATOR '/' #define PETSC_PATH_SEPARATOR ':' #define PETSC_HAVE_XMMINTRIN_H 1 #define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA #define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c)) #define PETSC_HAVE_BLASLAPACK 1 #define PETSC_HAVE_GZIP 1 #define PETSC_HAVE_STRING_H 1 #define PETSC_HAVE_SYS_TYPES_H 1 #define PETSC_HAVE_ENDIAN_H 1 #define PETSC_HAVE_SYS_PROCFS_H 1 #define PETSC_HAVE_DLFCN_H 1 #define PETSC_HAVE_SCHED_H 1 #define PETSC_HAVE_STDINT_H 1 #define PETSC_HAVE_LINUX_KERNEL_H 1 #define PETSC_HAVE_TIME_H 1 #define PETSC_HAVE_MATH_H 1 #define PETSC_HAVE_INTTYPES_H 1 #define PETSC_TIME_WITH_SYS_TIME 1 #define PETSC_HAVE_SYS_PARAM_H 1 #define PETSC_HAVE_PTHREAD_H 1 #define PETSC_HAVE_UNISTD_H 1 #define PETSC_HAVE_STDLIB_H 1 #define PETSC_HAVE_SYS_WAIT_H 1 #define PETSC_HAVE_SETJMP_H 1 #define PETSC_HAVE_LIMITS_H 1 #define PETSC_HAVE_SYS_UTSNAME_H 1 #define PETSC_HAVE_NETINET_IN_H 1 #define PETSC_HAVE_SYS_SOCKET_H 1 #define PETSC_HAVE_FLOAT_H 1 #define PETSC_HAVE_SEARCH_H 1 #define PETSC_HAVE_SYS_RESOURCE_H 1 #define PETSC_HAVE_SYS_TIMES_H 1 #define PETSC_HAVE_NETDB_H 1 #define PETSC_HAVE_MALLOC_H 1 #define PETSC_HAVE_PWD_H 1 #define PETSC_HAVE_FCNTL_H 1 #define PETSC_HAVE_STRINGS_H 1 #define PETSC_HAVE_SYS_SYSINFO_H 1 #define PETSC_HAVE_SYS_TIME_H 1 #define PETSC_USING_F90 1 #define PETSC_USING_F2003 1 #define PETSC_HAVE_RTLD_NOW 1 #define PETSC_HAVE_RTLD_LOCAL 1 #define PETSC_HAVE_RTLD_LAZY 1 #define PETSC_C_STATIC_INLINE static inline #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_CXX_NAMESPACE 1 #define PETSC_HAVE_RTLD_GLOBAL 1 #define PETSC_C_RESTRICT restrict #define PETSC_CXX_RESTRICT __restrict__ #define PETSC_CXX_STATIC_INLINE static inline #define PETSC_HAVE_LIBMPICHCXX_GNU_51 1 #define PETSC_HAVE_LIBDL 1 #define PETSC_HAVE_LIBGFORTRAN 1 #define PETSC_HAVE_LIBSTDC__ 1 #define PETSC_HAVE_LIBM 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LIBHYPRE 1 #define PETSC_HAVE_LOG2 1 #define PETSC_HAVE_LIBPARMETIS 1 #define PETSC_HAVE_LIBFLAPACK 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_LIBFBLAS 1 #define PETSC_HAVE_LIBHDF5HL_FORTRAN_PARALLEL 1 #define PETSC_HAVE_LIBMETIS 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_HAVE_LIBHDF5_FORTRAN_PARALLEL 1 #define PETSC_ARCH "arch-cori-knl-opt64-intel" #define PETSC_USE_SCALAR_REAL 1 #define PETSC_HAVE_ISINF 1 #define PETSC_HAVE_ISNAN 1 #define PETSC_HAVE_ISNORMAL 1 #define PETSC_USE_REAL_DOUBLE 1 #define PETSC_SIZEOF_MPI_COMM 4 #define PETSC_BITS_PER_BYTE 8 #define PETSC_SIZEOF_MPI_FINT 4 #define PETSC_USE_VISIBILITY_C 1 #define PETSC_SIZEOF_VOID_P 8 #define PETSC_RETSIGTYPE void #define PETSC_HAVE_CXX_COMPLEX 1 #define PETSC_SIZEOF_LONG 8 #define PETSC_USE_FORTRANKIND 1 #define PETSC_USE_VISIBILITY_CXX 1 #define PETSC_SIZEOF_SIZE_T 8 #define PETSC_HAVE_SIGINFO_T 1 #define PETSC_SIZEOF_CHAR 1 #define PETSC_SIZEOF_DOUBLE 8 #define PETSC_SIZEOF_FLOAT 4 #define PETSC_HAVE_C99_COMPLEX 1 #define PETSC_SIZEOF_INT 4 #define PETSC_SIZEOF_LONG_LONG 8 #define PETSC_SIZEOF_SHORT 2 #define PETSC_CLANGUAGE_C 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_IALLREDUCE 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_HAVE_MPI_COMM_C2F 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_TYPE_GET_EXTENT 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_COMBINER_NAMED 1 #define PETSC_HAVE_MPI_COMM_F2C 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_REDUCE_SCATTER 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPICH_NUMVERSION 30200300 #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_COMM_SPAWN 1 #define PETSC_HAVE_MPI_FINT 1 #define PETSC_HAVE_MPI_IBARRIER 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_REDUCE_LOCAL 1 #define PETSC_HAVE_MPI_REPLACE 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_ALLTOALLW 1 #define PETSC_HAVE_DYNAMIC_LIBRARIES 1 #define PETSC_HAVE_SHARED_LIBRARIES 1 #define PETSC_USE_GDB_DEBUGGER 1 #define PETSC_VERSION_DATE_GIT "2017-01-01 09:58:23 -0600" #define PETSC_VERSION_BRANCH_GIT "(HEAD detached at v3.7.5)" #define PETSC_VERSION_GIT "v3.7.5" #define PETSC_USE_64BIT_INDICES 1 #define PETSC_USE_ERRORCHECKING 1 #define PETSC_HAVE_STRCASECMP 1 #define PETSC_HAVE_GET_NPROCS 1 #define PETSC_HAVE_POPEN 1 #define PETSC_HAVE_SIGSET 1 #define PETSC_HAVE_GETWD 1 #define PETSC_HAVE_VSNPRINTF 1 #define PETSC_HAVE_TIMES 1 #define PETSC_HAVE_DLSYM 1 #define PETSC_HAVE_SNPRINTF 1 #define PETSC_HAVE_GETHOSTBYNAME 1 #define PETSC_HAVE_GETCWD 1 #define PETSC_HAVE_DLERROR 1 #define PETSC_HAVE_FORK 1 #define PETSC_HAVE_RAND 1 #define PETSC_HAVE_GETTIMEOFDAY 1 #define PETSC_HAVE_DLCLOSE 1 #define PETSC_HAVE_UNAME 1 #define PETSC_HAVE_GETHOSTNAME 1 #define PETSC_HAVE_MKSTEMP 1 #define PETSC_HAVE_SIGACTION 1 #define PETSC_HAVE_DRAND48 1 #define PETSC_HAVE_MEMALIGN 1 #define PETSC_HAVE_VA_COPY 1 #define PETSC_HAVE_CLOCK 1 #define PETSC_HAVE_ACCESS 1 #define PETSC_HAVE_SIGNAL 1 #define PETSC_HAVE_USLEEP 1 #define PETSC_HAVE_GETRUSAGE 1 #define PETSC_HAVE_VFPRINTF 1 #define PETSC_HAVE_NANOSLEEP 1 #define PETSC_HAVE_GETDOMAINNAME 1 #define PETSC_HAVE_TIME 1 #define PETSC_HAVE_LSEEK 1 #define PETSC_HAVE_SOCKET 1 #define PETSC_HAVE_SYSINFO 1 #define PETSC_HAVE_READLINK 1 #define PETSC_HAVE_REALPATH 1 #define PETSC_HAVE_DLOPEN 1 #define PETSC_HAVE_MEMMOVE 1 #define PETSC_HAVE__GFORTRAN_IARGC 1 #define PETSC_SIGNAL_CAST #define PETSC_HAVE_SLEEP 1 #define PETSC_HAVE_VPRINTF 1 #define PETSC_HAVE_BZERO 1 #define PETSC_HAVE_GETPAGESIZE 1 #define PETSC_WRITE_MEMORY_BARRIER() asm volatile("sfence":::"memory") #define PETSC_MEMORY_BARRIER() asm volatile("mfence":::"memory") #define PETSC_READ_MEMORY_BARRIER() asm volatile("lfence":::"memory") #define PETSC_CPU_RELAX() asm volatile("rep; nop" ::: "memory") #define PETSC_BLASLAPACK_UNDERSCORE 1 #define PETSC_MEMALIGN 64 #define PETSC_USE_INFO 1 #define PETSC_Alignx(a,b) #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_MALLOC_COALESCED 1 #define PETSC_USE_LOG 1 #define PETSC_IS_COLOR_VALUE_TYPE_F integer2 #define PETSC_IS_COLOR_VALUE_TYPE short #define PETSC_USE_CTABLE 1 #define PETSC_LEVEL1_DCACHE_LINESIZE 64 #define PETSC_LEVEL1_DCACHE_SIZE 32768 #define PETSC_LEVEL1_DCACHE_ASSOC 8 #define PETSC__GNU_SOURCE 1 #define PETSC__BSD_SOURCE 1 #define PETSC__DEFAULT_SOURCE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_HAVE_GFORTRAN_IARGC 1 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_HAVE_SCHED_CPU_SET_T 1 #define PETSC_HAVE_PTHREAD_BARRIER_T 1 #define PETSC_HAVE_SYS_SYSCTL_H 1 ----------------------------------------- Using C/C++ compile: cc -c -I/global/u2/m/madams/petsc_install/petsc/include -I/global/u2/m/madams/petsc_install/petsc/arch-cori-knl-opt64-intel/include -I/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel/include Using Fortran compile: ftn -c -I/global/u2/m/madams/petsc_install/petsc/include -I/global/u2/m/madams/petsc_install/petsc/arch-cori-knl-opt64-intel/include -I/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel/include ----------------------------------------- Using C/C++ linker: cc Using C/C++ flags: Using Fortran linker: ftn Using Fortran flags: ----------------------------------------- Using libraries: -L/global/u2/m/madams/petsc_install/petsc/arch-cori-knl-opt64-intel/lib -lpetsc -Wl,-rpath,/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel/lib -L/global/homes/m/madams/petsc_install/petscv3.7.5-cori-knl-opt64-intel/lib -lparmetis -lmetis -lHYPRE -L/opt/cray/pe/libsci/18.03.1/GNU/7.1/x86_64/lib -L/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.7.0/gni/mpich-gnu/5.1/lib -L/usr/common/software/darshan/3.1.4/lib -L/opt/cray/rca/2.2.16-6.0.5.0_15.34__g5e09e6d.ari/lib64 -L/opt/cray/alps/6.5.28-6.0.5.0_18.6__g13a91b6.ari/lib64 -L/opt/cray/xpmem/2.2.4-6.0.5.1_8.18__g35d5e73.ari/lib64 -L/opt/cray/pe/pmi/5.0.13/lib64 -L/opt/cray/ugni/6.0.14-6.0.5.0_16.9__g19583bb.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.5.0_13.12__ga14955a.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/opt/cray/wlm_detect/1.3.2-6.0.5.0_3.1__g388ccd5.ari/lib64 -L/opt/gcc/7.3.0/snos/lib/gcc/x86_64-suse-linux/7.3.0 -L/opt/gcc/7.3.0/snos/lib64 -L/opt/gcc/7.3.0/snos/lib -lmpichcxx_gnu_51 -lstdc++ -lflapack -lfblas -lgfortran -lm -lhdf5hl_fortran_parallel -lgfortran -lm -lgfortran -lm -lhdf5_fortran_parallel -lgfortran -lm -lgfortran -lm -lgfortran -lm -lmpichcxx_gnu_51 -lstdc++ -L/opt/cray/pe/libsci/18.03.1/GNU/7.1/x86_64/lib -L/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.7.0/gni/mpich-gnu/5.1/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.7.0/gni/mpich-gnu/5.1/lib -L/usr/common/software/darshan/3.1.4/lib -L/opt/cray/rca/2.2.16-6.0.5.0_15.34__g5e09e6d.ari/lib64 -L/opt/cray/alps/6.5.28-6.0.5.0_18.6__g13a91b6.ari/lib64 -L/opt/cray/xpmem/2.2.4-6.0.5.1_8.18__g35d5e73.ari/lib64 -L/opt/cray/pe/pmi/5.0.13/lib64 -L/opt/cray/ugni/6.0.14-6.0.5.0_16.9__g19583bb.ari/lib64 -L/opt/cray/udreg/2.3.2-6.0.5.0_13.12__ga14955a.ari/lib64 -L/opt/cray/pe/atp/2.1.1/libApp -L/opt/cray/wlm_detect/1.3.2-6.0.5.0_3.1__g388ccd5.ari/lib64 -L/opt/gcc/7.3.0/snos/lib/gcc/x86_64-suse-linux/7.3.0 -L/opt/gcc/7.3.0/snos/lib64 -L/opt/gcc/7.3.0/snos/lib -ldl -lAtpSigHandler -lAtpSigHCommData -lpthread -lhugetlbfs -lfmpich -lmpichcxx -ldarshan -ldarshan-stubs -lz -lsci_gnu_71_mpi -lsci_gnu_71 -lhdf5_hl_parallel -lhdf5_parallel -lmpichf90_gnu_51 -lrt -lugni -lpmi -lmpich_gnu_51 -lalpslli -lwlm_detect -lalpsutil -lrca -lxpmem -ludreg -lgfortran -lquadmath -lmvec -lgcc_eh -ldl ------------------------------------------ Using mpiexec: srun ========================================== Building PETSc using GNU Make with 1 build threads ========================================== gmake[2]: Entering directory '/global/u2/m/madams/petsc_install/petsc' Use "/usr/bin/gmake V=1" to see the verbose compile lines. CC arch-cori-knl-opt64-intel/obj/src/sys/info/verboseinfo.o In file included from /global/u2/m/madams/petsc_install/petsc/include/petsc/private/petscimpl.h(8), from /global/u2/m/madams/petsc_install/petsc/src/sys/info/verboseinfo.c(6): /global/u2/m/madams/petsc_install/petsc/include/petscsys.h(2886): error: expected a ")" PETSC_STATIC_INLINE PetscErrorCode PetscSegBufferGetInts(PetscSegBuffer seg,PetscInt count,PetscInt *PETSC_RESTRICT *slot) {return PetscSegBufferGet(seg,(size_t)count,(void**)slot);} ^ In file included from /global/u2/m/madams/petsc_install/petsc/include/petsc/private/petscimpl.h(8), from /global/u2/m/madams/petsc_install/petsc/src/sys/info/verboseinfo.c(6): /global/u2/m/madams/petsc_install/petsc/include/petscsys.h(2886): error: identifier "slot" is undefined PETSC_STATIC_INLINE PetscErrorCode PetscSegBufferGetInts(PetscSegBuffer seg,PetscInt count,PetscInt *PETSC_RESTRICT *slot) {return PetscSegBufferGet(seg,(size_t)count,(void**)slot);} ^ compilation aborted for /global/u2/m/madams/petsc_install/petsc/src/sys/info/verboseinfo.c (code 2) gmakefile:163: recipe for target 'arch-cori-knl-opt64-intel/obj/src/sys/info/verboseinfo.o' failed gmake[2]: *** [arch-cori-knl-opt64-intel/obj/src/sys/info/verboseinfo.o] Error 2 gmake[2]: Leaving directory '/global/u2/m/madams/petsc_install/petsc' /global/u2/m/madams/petsc_install/petsc/lib/petsc/conf/rules:105: recipe for target 'gnumake' failed gmake[1]: *** [gnumake] Error 2 gmake[1]: Leaving directory '/global/u2/m/madams/petsc_install/petsc' **************************ERROR************************************* Error during compile, check arch-cori-knl-opt64-intel/lib/petsc/conf/make.log Send it and arch-cori-knl-opt64-intel/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov ******************************************************************** Finishing at: Thu Aug 16 19:14:38 PDT 2018