[mpich-discuss] Failure to install MPICH2 in OS X High Sierra due to missing clock_gettime

Sun Feb 18 12:25:05 CST 2018

You're building a 5 year old version of MPICH (1.2.1p1). Can you try again with something a little more recent? The latest stable version is 3.2.1.

On Feb 18, 2018, at 10:36 AM, Dennis Fisher <fisher at plessthan.com<mailto:fisher at plessthan.com>> wrote:

Dear MPICH team

I am trying to install MPICH2 in OS X (High Sierra; XCODE and Command Line Tools both installed).
The installation proceeds per the output below until it reports:
configure: error: Requested timer clock_gettime (POSIX) is not available
Full output appended below.

Unfortunately, the MPICH2 Installer’s Guide does not provide any instructions for how to deal with this, with the exception of:
Problems should be self-explanatory, but if not, send c.txt to mpich-discuss at mcs.anl.gov<mailto:mpich-discuss at mcs.anl.gov>
It appears that the message is coming from ~ line 37903 of the configure script.  Can you direct me?

The command that I executed was:
./configure -prefix=/opt/mpich2-install & tee c.txt
I also tried (same result):
./configure -prefix=/opt/mpich2-install --enable-sharedlibs=osx-gcc & tee c.txt

Dennis

Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com<http://www.plessthan.com/>

PET694> ./configure -prefix=/opt/mpich2-install & tee c.txt
[2] 56222
Configuring MPICH2 version 1.2.1p1 with  '-prefix=/opt/mpich2-install'
Running on system: Darwin Denniss-iMac.local 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64
Executing mpich2prereq in /opt/mpich2-1.2.1p1/src/mpid/ch3 with
Executing mpich2prereq in /opt/mpich2-1.2.1p1/src/mpid/ch3/channels/nemesis
sourcing /opt/mpich2-1.2.1p1/src/pm/mpd/mpich2prereq
sourcing /opt/mpich2-1.2.1p1/src/pm/hydra/mpich2prereq
sourcing /opt/mpich2-1.2.1p1/src/pm/gforker/mpich2prereq
sourcing /opt/mpich2-1.2.1p1/src/pm/mpd/setup_pm
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 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 routines compiled with -O2 can be linked with ones compiled without -O2... yes
checking for type of weak symbol alias support... no
checking whether __attribute__ ((weak)) allowed... yes
checking whether __attribute ((weak_import)) allowed... yes
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... 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/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../.. -lgfortran -lquadmath -lm
checking whether gfortran accepts the FLIBS found by autoconf... yes
checking whether C can link with  -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/../../.. -lgfortran -lquadmath -lm... yes
checking for linker for Fortran main programs... Use Fortran to link programs
checking whether Fortran 77 and C objects are compatible... yes
checking for Fortran 77 name mangling... lower underscore
checking what libraries are needed to link Fortran programs with C routines that use stdio... none
checking whether Fortran init will work with C... yes
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for ifort... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for lf95... no
checking for pathf95... no
checking for pathf90... no
checking for g95... no
checking for gfortran... gfortran
checking that f works as the extension for Fortran 90 program... yes
checking whether we are using the GNU Fortran 90 compiler... yes
checking whether gfortran accepts -g... yes
checking for extension for Fortran 90 programs... f90
checking whether the Fortran 90 compiler (gfortran  ) works... yes
checking whether the Fortran 90 compiler (gfortran  ) is a cross-compiler... no
checking whether Fortran 90 works with Fortran 77... yes
checking whether Fortran accepts ! for comments... yes
checking for include directory flag for Fortran... -I
checking for Fortran 77 flag for library directories... `-L
checking for which Fortran libraries are needed to link C with Fortran... none
checking whether Fortran compiler processes .F files with C preprocessor... yes
checking that f works as the extension for Fortran 90 program... yes
checking whether we are using the GNU Fortran 90 compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking for extension for Fortran 90 programs... f90
checking whether the Fortran 90 compiler (gfortran  ) works... yes
checking whether the Fortran 90 compiler (gfortran  ) is a cross-compiler... no
checking for Fortran 90 module extension... mod
checking for Fortran 90 module include flag... -I
checking whether Fortran 90 accepts f90 suffix... yes
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 f90 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 . 2
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... no
checking for bash... /Users/fisher/bin/bash
checking whether /Users/fisher/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... no
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... no
checking sys/bitypes.h presence... no
checking for sys/bitypes.h... no
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 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... yes
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 Fortran 90 integer kind for 8-byte integers... 8
checking whether 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) no
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... no
checking endian.h presence... no
checking for endian.h... no
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 for snprintf... yes
checking whether snprintf needs a declaration... no
checking for va_copy... yes
checking for variable argument list macro functionality... yes
checking valgrind.h usability... no
checking valgrind.h presence... no
checking for valgrind.h... no
checking memcheck.h usability... no
checking memcheck.h presence... no
checking for memcheck.h... no
checking valgrind/valgrind.h usability... no
checking valgrind/valgrind.h presence... no
checking for valgrind/valgrind.h... no
checking valgrind/memcheck.h usability... no
checking valgrind/memcheck.h presence... no
checking for valgrind/memcheck.h... no
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... yes
checking for clock_getres... yes
checking for gethrtime... no
checking for gettimeofday... yes
checking for clock_gettime in -lrt... no
configure: error: Requested timer clock_gettime (POSIX) is not available
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