[mpich-discuss] Fwd: Installation error in ubuntu

Wed Feb 22 10:29:13 CST 2012

---------- Forwarded message ----------
From: Balaji S <balaji.ceg.13 at gmail.com>
Date: Wed, Feb 22, 2012 at 9:55 PM
Subject: Installation error in ubuntu
To: mpich-discuss at mcs.anl.gov

* *Hi,
          I am new to mpich2, i try installing it in ubuntu 10.04. i have
gcc,g++ and gfortran. i used the option
 ./configure --prefix=/home/balaji/mpich2-install 2>&1 | tee c.txt

But i am getting some errors,
 checking for rand... yes
checking for srand... yes
checking for OpenPA atomic primitive availability... no
configure: error:
The nemesis channel was selected yet a set of working OpenPA headers
were not found.  Please check the OpenPA configure step for errors.
configure: error: channels/nemesis configure failed
configure: error: src/mpid/ch3 configure failed

I hav attached the c.txt and config.log files along with this mail.

Please help and clarify my doubt.

-- 
With Regards,
    Balaji.S

-- 
With Regards,
    Balaji.S
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Configuring MPICH2 version 1.4.1p1 with  '--prefix=/home/balaji/mpich2-install'
Running on system: Linux ubuntu 2.6.32-33-generic #70-Ubuntu SMP Thu Jul 7 21:13:52 UTC 2011 x86_64 GNU/Linux
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 how to run the C preprocessor... gcc -E
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for grep that handles long lines and -e... /bin/grep
checking for fgrep... /bin/grep -F
Executing mpich2prereq in /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3 with 
Executing mpich2prereq in /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis
configure: ===== configuring src/mpl =====
configure: WARNING: /home/balaji/fyp/mpich2-1.4.1p1/src/mpl/configure exists but is not executable
configure: ===== done with src/mpl configure =====
configure: ===== configuring src/openpa =====
configure: WARNING: /home/balaji/fyp/mpich2-1.4.1p1/src/openpa/configure exists but is not executable
configure: ===== done with src/openpa configure =====
sourcing /home/balaji/fyp/mpich2-1.4.1p1/src/pm/hydra/mpich2prereq
configure: WARNING: pmi simple has no configure or Makefile
checking whether the compiler defines __func__... yes
checking whether the compiler defines __FUNC__... no
checking whether the compiler sets __FUNCTION__... yes
checking whether C compiler accepts option -O2... yes
checking whether C compiler option -O2 works with an invalid prototype program... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes
checking for type of weak symbol alias support... pragma weak
checking whether __attribute__ ((weak)) allowed... yes
checking whether __attribute__ ((weak_import)) allowed... yes
checking whether __attribute__((weak,alias(...))) allowed... no
checking for multiple weak symbol support... yes
checking for ifort... no
checking for pgf77... no
checking for af77... no
checking for xlf... no
checking for frt... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for fort... no
checking for ifc... no
checking for efc... no
checking for ftn... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking whether Fortran 77 compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../.. -L/usr/lib/x86_64-linux-gnu -lgfortranbegin -lgfortran -lm
checking whether gfortran accepts the FLIBS found by autoconf... yes
checking whether gcc links with FLIBS found by autoconf... yes
checking whether Fortran 77 and C objects are compatible... yes
checking for linker for Fortran main program... Use Fortran to link programs
checking for Fortran 77 name mangling... lower uscore
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for libraries to link Fortran main with C stdio routines... none
checking whether Fortran init will work with C... yes
checking for ifort... no
checking for pgf90... no
checking for pathf90... no
checking for pathf95... no
checking for xlf90... no
checking for xlf95... no
checking for xlf2003... no
checking for f90... no
checking for epcf90... no
checking for f95... f95
checking whether we are using the GNU Fortran compiler... yes
checking whether f95 accepts -g... yes
checking for extension for Fortran 90 programs... f90
checking whether the Fortran 90 compiler (f95    ) works... yes
checking whether the Fortran 90 compiler (f95    ) is a cross-compiler... no
checking whether Fortran 90 compiler works with Fortran 77 compiler... yes
checking whether Fortran 77 accepts ! for comments... yes
checking for include directory flag for Fortran... -I
checking for Fortran 77 flag for library directories... -L
checking whether Fortran 77 compiler processes .F files with C preprocessor... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking whether the Fortran 90 compiler (f95    ) works... yes
checking whether the Fortran 90 compiler (f95    ) is a cross-compiler... no
checking for Fortran 90 module extension... mod
checking for Fortran 90 module include flag... -I
checking whether Fortran 90 compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes
checking whether Fortran 90 compiler processes .F90 files with C preprocessor... yes
checking what libraries are needed to link Fortran90 programs with C routines that use stdio... none
checking for Fortran 90 compiler vendor... gnu
checking for c++... c++
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking whether the C++ compiler c++ can build an executable... yes
checking whether C++ compiler works with string... yes
checking whether the compiler supports exceptions... yes
checking whether the compiler recognizes bool as a built-in type... yes
checking whether the compiler implements namespaces... yes
checking whether <iostream> available... yes
checking whether the compiler implements the namespace std... yes
checking whether <math> available... no
checking for GNU g++ version... 4 . 4
checking whether C++ compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes
checking for perl... /usr/bin/perl
checking for ar... ar
checking for ranlib... ranlib
checking for killall... killall
checking for a BSD-compatible install... /usr/bin/install -c
checking whether install works... yes
checking whether install breaks libraries... no
checking whether mkdir -p works... yes
checking for make... make
checking whether clock skew breaks make... no
checking whether make supports include... yes
checking whether make allows comments in actions... yes
checking for virtual path format... VPATH
checking whether make sets CFLAGS... yes
checking for bash... /bin/bash
checking whether /bin/bash supports arrays... yes
checking for doctext... false
checking for location of doctext style files... unavailable
checking for an ANSI C-conforming const... yes
checking for working volatile... yes
checking for C/C++ restrict keyword... __restrict
checking for inline... inline
checking whether __attribute__ allowed... yes
checking whether __attribute__((format)) allowed... yes
checking whether byte ordering is bigendian... no
checking whether C compiler allows unaligned doubles... yes
checking whether gcc supports __func__... yes
Using gcc to determine dependencies
checking whether long double is supported... yes
checking whether long long is supported... yes
checking for max C struct integer alignment... eight
checking for max C struct floating point alignment... sixteen
checking for max C struct alignment of structs with doubles... eight
checking for max C struct floating point alignment with long doubles... sixteen
configure: WARNING: Structures containing long doubles may be aligned differently from structures with floats or longs.  MPICH2 does not handle this case automatically and you should avoid assumed extents for structures containing float types.
checking if alignment of structs with doubles is based on position... no
checking if alignment of structs with long long ints is based on position... no
checking if double alignment breaks rules, find actual alignment... no
checking for alignment restrictions on pointers... int or better
checking size of char... 1
checking size of unsigned char... 1
checking size of short... 2
checking size of unsigned short... 2
checking size of int... 4
checking size of unsigned int... 4
checking size of long... 8
checking size of unsigned long... 8
checking size of long long... 8
checking size of unsigned long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of void *... 8
checking for ANSI C header files... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking size of wchar_t... 4
checking size of float_int... 8
checking size of double_int... 16
checking size of long_int... 16
checking size of short_int... 8
checking size of two_int... 8
checking size of long_double_int... 32
checking sys/bitypes.h usability... yes
checking sys/bitypes.h presence... yes
checking for sys/bitypes.h... yes
checking inttypes.h usability... yes
checking inttypes.h presence... yes
checking for inttypes.h... yes
checking stdint.h usability... yes
checking stdint.h presence... yes
checking for stdint.h... yes
checking for int8_t... yes
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking size of _Bool... 1
checking size of float _Complex... 8
checking size of double _Complex... 16
checking size of long double _Complex... 32
checking for _Bool... yes
checking for float _Complex... yes
checking for double _Complex... yes
checking for long double _Complex... yes
checking for size of Fortran type integer... 4
checking for size of Fortran type real... 4
checking for size of Fortran type double precision... 8
checking whether integer*1 is supported... yes
checking whether integer*2 is supported... yes
checking whether integer*4 is supported... yes
checking whether integer*8 is supported... yes
checking whether integer*16 is supported... yes
checking whether real*4 is supported... yes
checking whether real*8 is supported... yes
checking whether real*16 is supported... no
checking for C type matching Fortran integer... int
checking for size of MPI_Status... 20
checking for values of Fortran logicals... True is 1 and False is 0
checking for BSD/POSIX style global symbol lister... BSD style,/usr/bin/nm -g -B
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for multiple __attribute__((alias)) support... yes
checking the minimum alignment of Fortran common block of 1 integers... 16
checking the minimum alignment of Fortran common block of 5 integers... 16, too small! reset to 32
checking for Fortran 90 integer kind for 8-byte integers... 8
checking if real*8 is supported in Fortran 90... yes
checking size of bool... 1
checking how to run the C++ preprocessor... c++ -E
checking complex usability... yes
checking complex presence... yes
checking for complex... yes
checking size of Complex... 8
checking size of DoubleComplex... 16
checking size of LongDoubleComplex... 32
checking if char * pointers use byte addresses... yes
checking for alignment restrictions on ... no
checking for alignment restrictions on int32_t... no
checking size of MPIR_Bsend_data_t... 88
checking for gcc __asm__ and pentium cmpxchgl instruction... no
checking for gcc __asm__ and AMD x86_64 cmpxchgq instruction... yes
checking for gcc __asm__ and IA64 xchg4 instruction... no
checking for ANSI C header files... (cached) yes
checking stdlib.h usability... yes
checking stdlib.h presence... yes
checking for stdlib.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking sys/types.h usability... yes
checking sys/types.h presence... yes
checking for sys/types.h... yes
checking string.h usability... yes
checking string.h presence... yes
checking for string.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stddef.h... (cached) yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking unistd.h usability... yes
checking unistd.h presence... yes
checking for unistd.h... yes
checking endian.h usability... yes
checking endian.h presence... yes
checking for endian.h... yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/uio.h... yes
checking for size_t... yes
checking for setitimer... yes
checking for alarm... yes
checking for vsnprintf... yes
checking for vsprintf... yes
checking whether vsnprintf needs a declaration... no
checking for strerror... yes
checking for strncasecmp... yes
checking whether strerror_r is declared... yes
checking for strerror_r... yes
checking whether strerror_r returns char *... no
checking whether strerror_r needs a declaration... no
checking for snprintf... yes
checking whether snprintf needs a declaration... no
checking for qsort... yes
checking for va_copy... yes
checking for variable argument list macro functionality... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for strdup... yes
checking whether strdup needs a declaration... no
checking for mkstemp... yes
checking whether mkstemp needs a declaration... no
checking for fdopen... yes
checking whether fdopen needs a declaration... yes
checking for putenv... yes
checking whether putenv needs a declaration... no
checking for clock_gettime... no
checking for clock_getres... no
checking for gethrtime... no
checking for mach_absolute_time... no
checking for gettimeofday... yes
sourcing /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/setup_device
RUNNING SETUP_DEVICE FOR THE CH3 DEVICE
sourcing /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/setup_channel
RUNNING SETUP_CHANNEL FOR THE NEMESIS CHANNEL
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for pthread_key_create in -lpthread... yes
checking for pthread_yield... yes
checking for pthread_key_create... yes
checking for pthread_cleanup_push... no
checking whether pthread_cleanup_push is available (may be a macro in pthread.h)... no
checking whether pthread.h defines PTHREAD_MUTEX_RECURSIVE_NP... yes
checking whether pthread.h defines PTHREAD_MUTEX_RECURSIVE... no
checking whether pthread.h defines PTHREAD_MUTEX_ERRORCHECK_NP... yes
checking whether pthread.h defines PTHREAD_MUTEX_ERRORCHECK... no
checking for thread local storage specifier... __thread
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for sched_yield... yes
checking for yield... no
checking for usleep... yes
checking for sleep... yes
checking for select... yes
checking for getpid... yes
checking for sched_setaffinity... yes
checking for sched_getaffinity... yes
checking for bindprocessor... no
checking for thread_policy_set... no
checking whether cpu_set_t available... yes
checking whether the CPU_SET and CPU_ZERO macros are defined... no
configure: ===== configuring src/mpid/ch3 =====
configure: executing: /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/configure  '--prefix=/home/balaji/mpich2-install' --disable-option-checking
RUNNING CONFIGURE FOR CH3 DEVICE
checking for make... make
checking whether clock skew breaks make... no
checking whether make supports include... yes
checking whether make allows comments in actions... yes
checking for virtual path format... VPATH
checking whether make sets CFLAGS... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for string.h... (cached) yes
checking for sys/types.h... (cached) yes
checking sys/uio.h usability... yes
checking sys/uio.h presence... yes
checking for sys/uio.h... yes
checking uuid/uuid.h usability... no
checking uuid/uuid.h presence... no
checking for uuid/uuid.h... no
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking for unistd.h... (cached) yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for net/if.h... yes
checking for pid_t... yes
checking for inet_pton... yes
checking for gethostname... yes
checking whether gethostname needs a declaration... no
checking for CFUUIDCreate... no
checking for uuid_generate... no
checking for time... yes
checking whether CPP accepts variable length argument lists... yes
checking whether byte ordering is bigendian... no
checking whether we can use struct ifconf... yes
configure: ===== configuring channels/nemesis =====
configure: executing: /home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/configure  '--prefix=/home/balaji/mpich2-install' '--disable-option-checking' 'CC=gcc' 'CFLAGS=   -O2' 'LDFLAGS= ' 'LIBS=-lpthread  ' 'CPPFLAGS=  -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpl/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpl/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/openpa/src -I/home/balaji/fyp/mpich2-1.4.1p1/src/openpa/src -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/common/datatype -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/common/datatype -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/common/locks -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/common/locks -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/nemesis/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/nemesis/include -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/nemesis/utils/monitor -I/home/balaji/fyp/mpich2-1.4.1p1/src/mpid/ch3/channels/nemesis/nemesis/utils/monitor -I/home/balaji/fyp/mpich2-1.4.1p1/src/util/wrappers -I/home/balaji/fyp/mpich2-1.4.1p1/src/util/wrappers' --disable-option-checking
RUNNING CONFIGURE FOR THE NEMESIS CHANNEL
checking for make... make
checking whether clock skew breaks make... no
checking whether make supports include... yes
checking whether make allows comments in actions... yes
checking for virtual path format... VPATH
checking whether make sets CFLAGS... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
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 for inline... inline
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /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 for pid_t... yes
checking for net/if.h... yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for unistd.h... (cached) yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/sockio.h usability... no
checking sys/sockio.h presence... no
checking for sys/sockio.h... no
checking for sys/types.h... (cached) yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking sys/ipc.h usability... yes
checking sys/ipc.h presence... yes
checking for sys/ipc.h... yes
checking sys/shm.h usability... yes
checking sys/shm.h presence... yes
checking for sys/shm.h... yes
checking for netinet/in.h... yes
checking signal.h usability... yes
checking signal.h presence... yes
checking for signal.h... yes
checking for signal... yes
checking for mkstemp... yes
checking for rand... yes
checking for srand... yes
checking for OpenPA atomic primitive availability... no
configure: error:
The nemesis channel was selected yet a set of working OpenPA headers
were not found.  Please check the OpenPA configure step for errors.
configure: error: channels/nemesis configure failed
configure: error: src/mpid/ch3 configure failed
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