---------- Forwarded message ---------- From: Kai Song <[email protected]> Date: Fri, Aug 29, 2014 at 9:32 AM Subject: Re: [petsc-users] PETSC-3.5.0 with SuperLU and Hypre To: Jed Brown <[email protected]> Cc: Matthew Knepley <[email protected]>, petsc-users < [email protected]>, Evan Um <[email protected]>, Evan Um <[email protected]>
Hi Satish and Jed, I did a "make allclean", and reconfigured with "-with-shared-libraries=0". I am still seeing the same error. Then I deleted arch-linux2-c-debug/conf/files, and remake. The "make test" failed again. I have attached the new configure.log, make.log, and rch-linux2-c-debug/conf/files in this email. Thanks, Kai On Fri, Aug 29, 2014 at 9:25 AM, Jed Brown <[email protected]> wrote: > Matthew Knepley <[email protected]> writes: > > > On Fri, Aug 29, 2014 at 10:59 AM, Kai Song <[email protected]> wrote: > > > >> Hi Matt, > >> > >> Thanks for the quick response. Both logs are included in the attachment. > >> Let me know if more log files are needed. > >> > > > > Jed, why does this not enter src/mat/impls/aij/seq/superlu? > > Kai, can you delete > > arch-linux2-c-debug/conf/files > > and re-run make (it should regenerate this file). If superlu is not > compiled, please send the contents of that file. > -- Kai Song <[email protected]> 1.510.495.2180 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209 High Performance Computing Services (HPCS) Lawrence Berkeley National Laboratory - http://scs.lbl.gov -- Kai Song <[email protected]> 1.510.495.2180 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209 High Performance Computing Services (HPCS) Lawrence Berkeley National Laboratory - http://scs.lbl.gov
gmake[1]: Entering directory `/clusterfs/voltaire/home/software/source/petsc-3.5.0' ========================================== 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 n0004.scs00 at Fri Aug 29 09:27:24 PDT 2014 Machine characteristics: Linux n0004.scs00 2.6.32-358.11.1.el6.x86_64 #1 SMP Tue Jun 11 17:23:30 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux ----------------------------------------- Using PETSc directory: /clusterfs/voltaire/home/software/source/petsc-3.5.0 Using PETSc arch: arch-linux2-c-debug ----------------------------------------- PETSC_VERSION_RELEASE 1 PETSC_VERSION_MAJOR 3 PETSC_VERSION_MINOR 5 PETSC_VERSION_SUBMINOR 0 PETSC_VERSION_PATCH 0 PETSC_VERSION_DATE "Jun, 30, 2014" PETSC_VERSION_GIT "v3.5-3-gf0a0590" PETSC_VERSION_DATE_GIT "2014-06-30 15:05:11 -0500" 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: --prefix=/clusterfs/voltaire/home/software/modules/petsc/3.5.0 --download-fblaslapack=1 --download-mumps=1 --download-parmetis=1 --download-scalapack --download-metis=1 --download-superlu=1 --download-superlu_dist=1 --download-hypre=1 --with-mpi-dir=/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/ --with-shared-libraries=0 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_HAVE_SSL 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_USE_SOCKET_VIEWER 1 #define PETSC_DIR "/clusterfs/voltaire/home/software/source/petsc-3.5.0" #define PETSC_HAVE_X 1 #define PETSC_HAVE_HYPRE 1 #define PETSC_LIB_DIR "/clusterfs/voltaire/home/software/modules/petsc/3.5.0/lib" #define PETSC_HAVE_SUPERLU_DIST 1 #define PETSC_HAVE_PARMETIS 1 #define PETSC_HAVE_FORTRAN 1 #define PETSC_USE_ISATTY 1 #define PETSC_SLSUFFIX "" #define PETSC_HAVE_SUPERLU 1 #define PETSC_FUNCTION_NAME_CXX __func__ #define PETSC_HAVE_MUMPS 1 #define PETSC_HAVE_FBLASLAPACK 1 #define PETSC_HAVE_ATOLL 1 #define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1 #define PETSC_UNUSED __attribute((unused)) #define PETSC_FUNCTION_NAME_C __func__ #define PETSC_HAVE_VALGRIND 1 #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_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_C_STATIC_INLINE static inline #define PETSC_HAVE_FORTRAN_UNDERSCORE 1 #define PETSC_HAVE_CXX_NAMESPACE 1 #define PETSC_C_RESTRICT __restrict__ #define PETSC_CXX_RESTRICT __restrict__ #define PETSC_CXX_STATIC_INLINE static inline #define PETSC_HAVE_LIBZ 1 #define PETSC_HAVE_LIBDL 1 #define PETSC_HAVE_LIBGFORTRAN 1 #define PETSC_HAVE_LIBSCALAPACK 1 #define PETSC_HAVE_LIBMETIS 1 #define PETSC_HAVE_LIBCRYPTO 1 #define PETSC_HAVE_LIBMPI_CXX 1 #define PETSC_HAVE_LIBM 1 #define PETSC_HAVE_LIBSUPERLU_4 1 #define PETSC_HAVE_LIBDMUMPS 1 #define PETSC_HAVE_LIBMUMPS_COMMON 1 #define PETSC_HAVE_LIBPTHREAD 1 #define PETSC_HAVE_LIBMPI_F77 1 #define PETSC_HAVE_LIBPARMETIS 1 #define PETSC_HAVE_LIBFBLAS 1 #define PETSC_HAVE_LIBSUPERLU_DIST_3 1 #define PETSC_HAVE_LIBSTDC__ 1 #define PETSC_HAVE_LIBZMUMPS 1 #define PETSC_HAVE_LIBMPI_F90 1 #define PETSC_HAVE_LIBSSL 1 #define PETSC_HAVE_FENV_H 1 #define PETSC_HAVE_LIBHYPRE 1 #define PETSC_HAVE_LIBPORD 1 #define PETSC_HAVE_LIBSMUMPS 1 #define PETSC_HAVE_LIBCMUMPS 1 #define PETSC_HAVE_LIBFLAPACK 1 #define PETSC_HAVE_ERF 1 #define PETSC_HAVE_LIBX11 1 #define PETSC_HAVE_TGAMMA 1 #define PETSC_ARCH "arch-linux2-c-debug" #define PETSC_CLANGUAGE_C 1 #define PETSC_USE_ERRORCHECKING 1 #define PETSC_MISSING_DREAL 1 #define PETSC_SIZEOF_MPI_COMM 8 #define PETSC_BITS_PER_BYTE 8 #define PETSC_SIZEOF_MPI_FINT 4 #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_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_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_HAVE_MPI_COMM_C2F 1 #define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1 #define PETSC_HAVE_MPI_EXSCAN 1 #define PETSC_HAVE_MPI_LONG_DOUBLE 1 #define PETSC_HAVE_MPI_COMM_F2C 1 #define PETSC_HAVE_MPI_FINT 1 #define PETSC_HAVE_MPI_F90MODULE 1 #define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1 #define PETSC_HAVE_MPI_ALLTOALLW 1 #define PETSC_HAVE_MPI_FINALIZED 1 #define PETSC_HAVE_MPI_COMM_SPAWN 1 #define PETSC_HAVE_MPI_TYPE_GET_EXTENT 1 #define PETSC_HAVE_MPI_COMBINER_DUP 1 #define PETSC_HAVE_MPI_WIN_CREATE 1 #define PETSC_HAVE_MPI_REPLACE 1 #define PETSC_HAVE_MPI_TYPE_DUP 1 #define PETSC_HAVE_MPIIO 1 #define PETSC_HAVE_MPI_INIT_THREAD 1 #define PETSC_HAVE_MPI_INT64_T 1 #define PETSC_HAVE_MPI_IN_PLACE 1 #define PETSC_BLASLAPACK_UNDERSCORE 1 #define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1 #define PETSC_HAVE_GFORTRAN_IARGC 1 #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_MEMALIGN 16 #define PETSC_USE_PROC_FOR_SIZE 1 #define PETSC_HAVE_SHARED_LIBRARIES 1 #define PETSC_USE_GDB_DEBUGGER 1 #define PETSC__GNU_SOURCE 1 #define PETSC__BSD_SOURCE 1 #define PETSC_USE_INFO 1 #define PETSC_Alignx(a,b) #define PETSC_USE_BACKWARD_LOOP 1 #define PETSC_USE_DEBUG 1 #define PETSC_IS_COLOR_VALUE_TYPE_SIZE PETSC_SIZEOF_SHORT #define PETSC_USE_LOG 1 #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_HAVE_SCHED_CPU_SET_T 1 #define PETSC_HAVE_PTHREAD_BARRIER_T 1 #define PETSC_HAVE_SYS_SYSCTL_H 1 ----------------------------------------- Using C/C++ compile: /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpicc -c -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0 -I/clusterfs/voltaire/home/software/source/petsc-3.5.0/include -I/clusterfs/voltaire/home/software/source/petsc-3.5.0/arch-linux2-c-debug/include -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include mpicc -show: gcc -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include -pthread -L/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib -lmpi -ldl -lm -lnuma -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl Using Fortran compile: /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpif90 -c -Wall -Wno-unused-variable -ffree-line-length-0 -g -O0 -I/clusterfs/voltaire/home/software/source/petsc-3.5.0/include -I/clusterfs/voltaire/home/software/source/petsc-3.5.0/arch-linux2-c-debug/include -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include mpif90 -show: gfortran -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/include -pthread -I/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib -L/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib -lmpi_f90 -lmpi_f77 -lmpi -ldl -lm -lnuma -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl ----------------------------------------- Using C/C++ linker: /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpicc Using C/C++ flags: -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -O0 Using Fortran linker: /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpif90 Using Fortran flags: -Wall -Wno-unused-variable -ffree-line-length-0 -g -O0 ----------------------------------------- Using libraries: -L/clusterfs/voltaire/home/software/source/petsc-3.5.0/arch-linux2-c-debug/lib -lpetsc -Wl,-rpath,/clusterfs/voltaire/home/software/source/petsc-3.5.0/arch-linux2-c-debug/lib -lHYPRE -L/global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -lmpi_cxx -lstdc++ -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lsuperlu_dist_3.3 -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lX11 -lssl -lcrypto -lpthread -lmpi_f90 -lmpi_f77 -lgfortran -lm -lmpi_cxx -lstdc++ -lmpi_cxx -lstdc++ -ldl -lmpi -lnuma -lrt -lnsl -lutil -lgcc_s -lpthread -ldl ------------------------------------------ Using mpiexec: /global/software/sl-6.x86_64/modules/gcc/4.4.7/openmpi/1.6.5-gcc/bin/mpiexec ========================================== Building PETSc using GNU Make with 7 build threads ========================================== gmake[2]: Entering directory `/clusterfs/voltaire/home/software/source/petsc-3.5.0' gmake[2]: Nothing to be done for `all'. gmake[2]: Leaving directory `/clusterfs/voltaire/home/software/source/petsc-3.5.0' ========================================= gmake[1]: Leaving directory `/clusterfs/voltaire/home/software/source/petsc-3.5.0' Now to install the libraries do: make PETSC_DIR=/clusterfs/voltaire/home/software/source/petsc-3.5.0 PETSC_ARCH=arch-linux2-c-debug install ========================================= Finishing at: Fri Aug 29 09:27:25 PDT 2014
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