(partial) EasyBuild log for failed build of /gpfs0/users/rescomp/adamh/src/github/easybuild-easyconfigs/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb (PR #5577)

OpenMPI-2.1.2-GCC-6.4.0-2.28_partial.log

checking for sys/param.h... yes
checking sys/queue.h usability... yes
checking sys/queue.h presence... yes
checking for sys/queue.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.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/stat.h... (cached) yes
checking sys/statfs.h usability... yes
checking sys/statfs.h presence... yes
checking for sys/statfs.h... yes
checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/tree.h usability... no
checking sys/tree.h presence... no
checking for sys/tree.h... no
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 sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking net/uio.h usability... no
checking net/uio.h presence... no
checking for net/uio.h... no
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking sys/vfs.h usability... yes
checking sys/vfs.h presence... yes
checking for sys/vfs.h... yes
checking sys/wait.h usability... yes
checking sys/wait.h presence... yes
checking for sys/wait.h... yes
checking syslog.h usability... yes
checking syslog.h presence... yes
checking for syslog.h... yes
checking termios.h usability... yes
checking termios.h presence... yes
checking for termios.h... yes
checking ulimit.h usability... yes
checking ulimit.h presence... yes
checking for ulimit.h... yes
checking for unistd.h... (cached) yes
checking util.h usability... no
checking util.h presence... no
checking for util.h... no
checking utmp.h usability... yes
checking utmp.h presence... yes
checking for utmp.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking ifaddrs.h usability... yes
checking ifaddrs.h presence... yes
checking for ifaddrs.h... yes
checking crt_externs.h usability... no
checking crt_externs.h presence... no
checking for crt_externs.h... no
checking regex.h usability... yes
checking regex.h presence... yes
checking for regex.h... yes
checking mntent.h usability... yes
checking mntent.h presence... yes
checking for mntent.h... yes
checking paths.h usability... yes
checking paths.h presence... yes
checking for paths.h... yes
checking ioLib.h usability... no
checking ioLib.h presence... no
checking for ioLib.h... no
checking sockLib.h usability... no
checking sockLib.h presence... no
checking for sockLib.h... no
checking hostLib.h usability... no
checking hostLib.h presence... no
checking for hostLib.h... no
checking shlwapi.h usability... no
checking shlwapi.h presence... no
checking for shlwapi.h... no
checking sys/synch.h usability... no
checking sys/synch.h presence... no
checking for sys/synch.h... no
checking db.h usability... yes
checking db.h presence... yes
checking for db.h... yes
checking ndbm.h usability... no
checking ndbm.h presence... no
checking for ndbm.h... no
checking for sys/mount.h... yes
checking for sys/sysctl.h... yes
checking for net/if.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking if <stdbool.h> works... yes

============================================================================
== Type tests
============================================================================
checking for socklen_t... yes
checking for struct sockaddr_in... (cached) yes
checking for struct sockaddr_in6... yes
checking for struct sockaddr_storage... yes
checking whether AF_UNSPEC is declared... yes
checking whether PF_UNSPEC is declared... yes
checking whether AF_INET6 is declared... yes
checking whether PF_INET6 is declared... yes
checking if SA_RESTART defined in signal.h... yes
checking for struct sockaddr.sa_len... no
checking for struct dirent.d_type... yes
checking for siginfo_t.si_fd... yes
checking for siginfo_t.si_band... yes
checking for struct statfs.f_type... yes
checking for struct statfs.f_fstypename... no
checking for struct statvfs.f_basetype... no
checking for struct statvfs.f_fstypename... no
checking for pointer diff type... ptrdiff_t (size: 8)
checking for type of MPI_Aint... ptrdiff_t (size: 8)
checking for type of MPI_Count... long long (size: 8)
checking for type of MPI_Offset... long long (size: 8)
checking for an MPI datatype for MPI_Offset... MPI_LONG_LONG
checking for MPI_INTEGER_KIND... 4
checking for MPI_ADDRESS_KIND... 8
checking for MPI_COUNT_KIND... 8
checking for MPI_OFFSET_KIND... 8
checking the linker for support for the -fini option... yes

============================================================================
== Library and Function tests
============================================================================
checking for library containing openpty... -lutil
checking for library containing gethostbyname... none required
checking for library containing socket... none required
checking for library containing sched_yield... none required
checking for library containing dirname... none required
checking for library containing ceil... none required
checking for library containing clock_gettime... -lrt
checking for asprintf... yes
checking for snprintf... yes
checking for vasprintf... yes
checking for vsnprintf... yes
checking for openpty... yes
checking for isatty... yes
checking for getpwuid... yes
checking for fork... yes
checking for waitpid... yes
checking for execve... yes
checking for pipe... yes
checking for ptsname... yes
checking for setsid... yes
checking for mmap... yes
checking for tcgetpgrp... yes
checking for posix_memalign... yes
checking for strsignal... yes
checking for sysconf... yes
checking for syslog... yes
checking for vsyslog... yes
checking for regcmp... no
checking for regexec... yes
checking for regfree... yes
checking for _NSGetEnviron... no
checking for socketpair... yes
checking for strncpy_s... no
checking for usleep... yes
checking for mkfifo... yes
checking for dbopen... no
checking for dbm_open... no
checking for statfs... yes
checking for statvfs... yes
checking for setpgid... yes
checking for setenv... yes
checking for __malloc_initialize_hook... yes
checking for htonl define... no
checking for htonl... yes
checking whether va_copy is declared... yes
checking whether __va_copy is declared... yes
checking whether __func__ is declared... yes

============================================================================
== System-specific tests
============================================================================
checking for _SC_NPROCESSORS_ONLN... yes
checking whether byte ordering is bigendian... no
checking for broken qsort... no
checking if C compiler and POSIX threads work as is... yes
checking if C++ compiler and POSIX threads work as is... yes
checking if Fortran compiler and POSIX threads work as is... yes
checking for pthread_mutexattr_setpshared... yes
checking for pthread_condattr_setpshared... yes
checking for PTHREAD_MUTEX_ERRORCHECK_NP... yes
checking for PTHREAD_MUTEX_ERRORCHECK... yes
checking for working POSIX threads package... yes
checking if threads have different pids (pthreads on linux)... no
checking if want MPI_THREAD_MULTIPLE support... Enabled
checking whether ln -s works... yes
checking for grep that handles long lines and -e... (cached) /bin/grep
checking for egrep... (cached) /bin/grep -E
checking dependency style of gcc... (cached) gcc3
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... none needed
checking whether yytext is a pointer... no
checking for flavor of ps to use... ps -A -o fname,pid,uid
checking if build filesystem is case sensitive... yes
checking if configuring for case sensitive filesystem... yes
checking whether RLIMIT_NPROC is declared... yes
checking whether RLIMIT_MEMLOCK is declared... yes
checking whether RLIMIT_NOFILE is declared... yes
checking whether RLIMIT_FSIZE is declared... yes
checking whether RLIMIT_CORE is declared... yes
checking whether RLIMIT_STACK is declared... yes
checking whether RLIMIT_AS is declared... yes

============================================================================
== Modular Component Architecture (MCA) setup
============================================================================
checking for subdir args...  '--prefix=/well/rescomp/eb/software/OpenMPI/2.1.2-GCC-6.4.0-2.28' '--enable-shared' '--enable-mpi-thread-multiple' '--with-verbs' '--enable-mpirun-prefix-by-default' '--with-hwloc=/well/rescomp/eb/software/hwloc/1.11.8-GCCcore-6.4.0' '--disable-dlopen' 'CC=gcc' 'CFLAGS=-O2 -march=native' 'LDFLAGS=-L/well/rescomp/eb/software/GCCcore/6.4.0/lib64 -L/well/rescomp/eb/software/GCCcore/6.4.0/lib -L/well/rescomp/eb/software/hwloc/1.11.8-GCCcore-6.4.0/lib' 'LIBS=-lm -lpthread' 'CPPFLAGS=-I/well/rescomp/eb/software/hwloc/1.11.8-GCCcore-6.4.0/include' 'CXX=g++' 'CXXFLAGS=-O2 -march=native' 'FC=gfortran' 'FCFLAGS=-O2 -march=native' 'PKG_CONFIG_PATH=/well/rescomp/eb/software/hwloc/1.11.8-GCCcore-6.4.0/lib/pkgconfig:/apps/well/python/2.7.11/lib/pkgconfig'
checking --with-verbs value... simple ok (unspecified)
checking --with-verbs-libdir value... simple ok (unspecified)
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for pkg-config... (cached) /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for X... libraries , headers 
 
==> Pre-emptively configuring the hwloc framework to satisfy dependencies.
checking whether to enable hwloc PCI device support... yes (default)

+++ Configuring MCA framework hwloc
checking for no configure components in framework hwloc... 
checking for m4 configure components in framework hwloc... external, hwloc1112

--- MCA component hwloc:external (m4 configuration macro, priority 90)
checking for MCA component hwloc:external compile mode... static
checking --with-hwloc-libdir value... simple ok (unspecified)
checking looking for external hwloc in... (/well/rescomp/eb/software/hwloc/1.11.8-GCCcore-6.4.0)
checking hwloc.h usability... yes
checking hwloc.h presence... yes
checking for hwloc.h... yes
looking for library in lib
checking for library containing hwloc_topology_init... -lhwloc
checking if external hwloc supports XML... yes
checking infiniband/verbs.h usability... no
checking infiniband/verbs.h presence... no
checking for infiniband/verbs.h... no
checking if external hwloc version is 1.8 or greater... yes
checking if MCA component hwloc:external can compile... yes

--- MCA component hwloc:hwloc1112 (m4 configuration macro, priority 90)
checking for MCA component hwloc:hwloc1112 compile mode... static
checking hwloc building mode... embedded
configure: hwloc builddir: /dev/shm/OpenMPI/2.1.2/GCC-6.4.0-2.28/openmpi-2.1.2/opal/mca/hwloc/hwloc1112/hwloc
configure: hwloc srcdir: /dev/shm/OpenMPI/2.1.2/GCC-6.4.0-2.28/openmpi-2.1.2/opal/mca/hwloc/hwloc1112/hwloc
checking for hwloc version... 1.11.2
checking if want hwloc maintainer support... disabled (embedded mode)
checking for hwloc directory prefix... opal/mca/hwloc/hwloc1112/hwloc/
checking for hwloc symbol prefix... hwloc_
checking size of void *... (cached) 8
checking which OS support to include... Linux
checking which CPU support to include... x86_64
checking size of unsigned long... 8
checking size of unsigned int... 4
checking for the C compiler vendor... gnu
checking for __attribute__... yes
checking for __attribute__(aligned)... yes
checking for __attribute__(always_inline)... yes
checking for __attribute__(cold)... yes
checking for __attribute__(const)... yes
checking for __attribute__(deprecated)... yes
checking for __attribute__(format)... yes
checking for __attribute__(hot)... yes
checking for __attribute__(malloc)... yes
checking for __attribute__(may_alias)... yes
checking for __attribute__(no_instrument_function)... yes
checking for __attribute__(nonnull)... yes
checking for __attribute__(noreturn)... yes
checking for __attribute__(packed)... yes
checking for __attribute__(pure)... yes
checking for __attribute__(sentinel)... yes
checking for __attribute__(unused)... yes
checking for __attribute__(warn_unused_result)... yes
checking for __attribute__(weak_alias)... yes
checking if gcc supports -fvisibility=hidden... yes
checking whether to enable symbol visibility... yes (via -fvisibility=hidden)
configure: WARNING: "-fvisibility=hidden" has been added to the hwloc CFLAGS
checking whether the C compiler rejects function calls with too many arguments... yes
checking whether the C compiler rejects function calls with too few arguments... yes
checking for unistd.h... (cached) yes
checking for dirent.h... (cached) yes
checking for strings.h... (cached) yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking for strncasecmp... yes
checking whether function strncasecmp is declared... yes
checking for strftime... yes
checking for setlocale... yes
checking for stdint.h... (cached) yes
checking for sys/mman.h... (cached) yes
checking for KAFFINITY... no
checking for PROCESSOR_CACHE_TYPE... no
checking for CACHE_DESCRIPTOR... no
checking for LOGICAL_PROCESSOR_RELATIONSHIP... no
checking for RelationProcessorPackage... no
checking for SYSTEM_LOGICAL_PROCESSOR_INFORMATION... no
checking for GROUP_AFFINITY... no
checking for PROCESSOR_RELATIONSHIP... no
checking for NUMA_NODE_RELATIONSHIP... no
checking for CACHE_RELATIONSHIP... no
checking for PROCESSOR_GROUP_INFO... no
checking for GROUP_RELATIONSHIP... no
checking for SYSTEM_LOGICAL_PROCESSOR_INFORMATION_EX... no
checking for PSAPI_WORKING_SET_EX_BLOCK... no
checking for PSAPI_WORKING_SET_EX_INFORMATION... no
checking for PROCESSOR_NUMBER... no
checking for main in -lgdi32... no
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking sys/lgrp_user.h usability... no
checking sys/lgrp_user.h presence... no
checking for sys/lgrp_user.h... no
checking kstat.h usability... no
checking kstat.h presence... no
checking for kstat.h... no
checking whether fabsf is declared... yes
checking for fabsf in -lm... yes
checking picl.h usability... no
checking picl.h presence... no
checking for picl.h... no
checking whether _SC_NPROCESSORS_ONLN is declared... yes
checking whether _SC_NPROCESSORS_CONF is declared... yes
checking whether _SC_NPROC_ONLN is declared... no
checking whether _SC_NPROC_CONF is declared... no
checking whether _SC_PAGESIZE is declared... yes
checking whether _SC_PAGE_SIZE is declared... yes
checking whether _SC_LARGE_PAGESIZE is declared... no
checking mach/mach_host.h usability... no
checking mach/mach_host.h presence... no
checking for mach/mach_host.h... no
checking mach/mach_init.h usability... no
checking mach/mach_init.h presence... no
checking for mach/mach_init.h... no
checking for sys/param.h... (cached) yes
checking for sys/sysctl.h... (cached) yes
checking whether CTL_HW is declared... no
checking whether HW_NCPU is declared... no
checking whether strtoull is declared... yes
checking whether getprogname is declared... no
checking whether getexecname is declared... no
checking whether GetModuleFileName is declared... no
checking for program_invocation_name... yes
checking for __progname... yes
checking for pthread_t... yes
checking whether function sched_setaffinity is declared... yes
checking for old prototype of sched_setaffinity... no
checking for working CPU_SET... yes
checking for working CPU_SET_S... yes
checking for working syscall... yes
checking for KERRIGHED... no
checking for lib... no
checking for bash... /bin/sh
checking for ffs... yes
checking whether function ffs is declared... yes
checking for ffsl... yes
checking whether function ffsl is declared... yes
checking for fls... no
checking for flsl... no
checking for clz... no
checking for clzl... no
checking for openat... yes
checking for malloc.h... (cached) yes
checking for getpagesize... yes
checking for memalign... yes
checking for posix_memalign... (cached) yes
checking for sys/utsname.h... (cached) yes
checking for uname... yes
checking pthread_np.h usability... no
checking pthread_np.h presence... no
checking for pthread_np.h... no
checking whether pthread_setaffinity_np is declared... yes
checking whether pthread_getaffinity_np is declared... yes
checking for sched_setaffinity... yes
checking for sys/cpuset.h... no
checking for cpuset_setaffinity... no
checking for library containing pthread_getthrds_np... no
checking for cpuset_setid... no
checking numaif.h usability... yes
checking numaif.h presence... yes
checking for numaif.h... yes
checking for numa_available in -lnuma... yes
checking for set_mempolicy in -lnuma... yes
checking for mbind in -lnuma... yes
checking for migrate_pages in -lnuma... yes
checking libudev.h usability... no
checking libudev.h presence... no
checking for libudev.h... no
checking for PCIACCESS... no
checking pciaccess.h usability... no
checking pciaccess.h presence... no
checking for pciaccess.h... no
checking CL/cl_ext.h usability... no
checking CL/cl_ext.h presence... no
checking for CL/cl_ext.h... no
checking cuda.h usability... no
checking cuda.h presence... no
checking for cuda.h... no
checking cuda_runtime_api.h usability... no
checking cuda_runtime_api.h presence... no
checking for cuda_runtime_api.h... no
checking nvml.h usability... no
checking nvml.h presence... no
checking for nvml.h... no
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Xlib.h usability... yes
checking X11/Xlib.h presence... yes
checking for X11/Xlib.h... yes
checking for XOpenDisplay in -lX11... yes
checking for X11/Xutil.h... yes
checking X11/keysym.h usability... yes
checking X11/keysym.h presence... yes
checking for X11/keysym.h... yes
checking NVCtrl/NVCtrl.h usability... no
checking NVCtrl/NVCtrl.h presence... no
checking for NVCtrl/NVCtrl.h... no
checking for x86 cpuid... yes
checking for pthread_mutex_lock... yes
checking if plugin support is enabled... no
checking components to build statically...  noos xml synthetic custom xml_nolibxml linux linuxpci x86
checking components to build as plugins... 
checking whether hwloc configure succeeded... yes
checking for infiniband/verbs.h... (cached) no
configure: WARNING: using an external hwloc; disqualifying this component
checking if MCA component hwloc:hwloc1112 can compile... no
 
checking for winning hwloc component header file... opal/mca/hwloc/external/external.h
 
<== Pre-emptive hwloc framework configuration complete.
<== We now return you to your regularly scheduled programming.
 
checking if user requested PMI support... no
checking which components should be disabled... 
checking which components should be direct-linked into the library... 
checking which components should be run-time loadable... none
checking which components should be static... all
checking for projects containing MCA frameworks... opal, orte, ompi, oshmem

*** Configuring MCA for opal
checking for frameworks for opal... common, allocator, backtrace, btl, dl, event, hwloc, if, installdirs, memchecker, memcpy, memory, mpool, patcher, pmix, pstat, rcache, sec, shmem, timer

+++ Configuring MCA framework common
checking for no configure components in framework common... 
checking for m4 configure components in framework common... verbs_usnic, verbs, sm, libfabric, cuda, ugni

--- MCA component common:verbs_usnic (m4 configuration macro)
checking for MCA component common:verbs_usnic compile mode... static
checking if MCA component common:verbs_usnic can compile... no

--- MCA component common:verbs (m4 configuration macro)
checking for MCA component common:verbs compile mode... static
checking if want to add padding to the openib BTL control header... no
checking for fcntl.h... (cached) yes
checking sys/poll.h usability... yes
checking sys/poll.h presence... yes
checking for sys/poll.h... yes
checking infiniband/verbs.h usability... no
checking infiniband/verbs.h presence... no
checking for infiniband/verbs.h... no
checking if ConnectX XRC support is enabled... no
checking if ConnectIB XRC support is enabled... no
checking if dynamic SL is enabled... no
configure: WARNING: Verbs support requested (via --with-verbs) but not found.
configure: WARNING: If you are using libibverbs v1.0 (i.e., OFED v1.0 or v1.1), you *MUST* have both the libsysfs headers and libraries installed.  Later versions of libibverbs do not require libsysfs.
configure: error: Aborting.
 (at easybuild/tools/run.py:481 in parse_cmd_output)
== 2018-01-12 17:57:33,846 easyblock.py:2685 WARNING build failed (first 300 chars): cmd " ./configure --prefix=/well/rescomp/eb/software/OpenMPI/2.1.2-GCC-6.4.0-2.28 --enable-shared --enable-mpi-thread-multiple --with-verbs --enable-mpirun-prefix-by-default --with-hwloc=$EBROOTHWLOC --disable-dlopen " exited with exit code 1 and output:
checking for perl... perl

==================
== 2018-01-12 17:57:33,846 easyblock.py:279 INFO Closing log for application name OpenMPI version 2.1.2