[mvapich-discuss] Link error with PGI

[Christopher W.Harrop]

Hi,

I’m not sure why, but I did not receive Hari’s reply to this question in my email Inbox, so I’m replying this way. I hope it doesn’t mess up the thread.

I am building inside a script that creates a new directory for every build and does a fresh untar of the *.tar.gz file (and it works fine for all my other builds).  However, to eliminate possibilities for error, I manually did a fresh untar and build using those same configure options and got the same error.  It’s absolutely baffling where that -pthread option is coming from.  I even tried patching libtool (not the best idea, I know) to get rid of it, and it didn’t help.  The binutils has been a problem in the past, but the machine I’m building on current has binutils-2.27-34, and I’m pretty sure that’s new enough.

Does anyone spot anything in my ./configure output that looks suspicious?

+ ./configure --prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5 --enable-fortran=yes --enable-cxx --with-pmi=pmi2 --with-pm=slurm --with-slurm=/apps/slurm/default --with-device=ch3:psm --enable-romio
Configuring MVAPICH2 version 2.3.1 with  '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5' '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '--with-device=ch3:psm' '--
enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran'
Running on system: Linux tfe03 3.10.0-957.10.1.el7.x86_64 #1 SMP Thu Feb 7 07:12:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
checking whether to enable header caching... yes
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking how to run the C preprocessor... pgcc -E
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking whether make supports nested variables... yes
checking dependency style of pgcc... pgcc
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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 dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... yes
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... (cached) yes
checking whether we are using the GNU C++ compiler... yes
checking whether pgc++ accepts -g... yes
checking dependency style of pgc++... none
checking how to run the C++ preprocessor... pgc++ -E
checking for ld used by pgc++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
pgc++-Error-Unknown switch: -print-prog-name=ld
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for pgc++ option to produce PIC... -fPIC -DPIC
checking if pgc++ PIC flag -fPIC -DPIC works... yes
checking if pgc++ static flag -static works... no
checking if pgc++ supports -c -o file.o... yes
checking if pgc++ supports -c -o file.o... (cached) yes
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether we are using the GNU Fortran compiler... no
checking whether pgfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pgfortran option to produce PIC... -fpic
checking if pgfortran PIC flag -fpic works... yes
checking if pgfortran static flag -Bstatic works... yes
checking if pgfortran supports -c -o file.o... yes
checking if pgfortran supports -c -o file.o... (cached) yes
checking whether the pgfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether we are using the GNU Fortran 77 compiler... no
checking whether pgfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pgfortran option to produce PIC... -fpic
checking if pgfortran PIC flag -fpic works... yes
checking if pgfortran static flag -Bstatic works... yes
checking if pgfortran supports -c -o file.o... yes
checking if pgfortran supports -c -o file.o... (cached) yes
checking whether the pgfortran linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking hcoll/api/hcoll_api.h usability... no
checking hcoll/api/hcoll_api.h presence... no
checking for hcoll/api/hcoll_api.h... no
checking for hcoll_init in -lhcoll... no
sourcing /scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/mpid/ch3/channels/psm/setup_channel
RUNNING SETUP_CHANNEL FOR THE PSM CHANNEL
configure: RUNNING PREREQ FOR ch3:psm
configure: ===== configuring src/mpl =====
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5' --disable-versioning '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/ap
ps/slurm/default' '--with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking the archiver (ar) interface... ar
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... pgcc -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 dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... yes
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... (cached) yes
checking for an ANSI C-conforming const... yes
checking for C/C++ restrict keyword... __restrict
checking for inline... inline
checking for variable argument list macro functionality... yes
checking for gcov... gcov
checking whether the compiler supports __typeof(variable)... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking search.h usability... yes
checking search.h presence... yes
checking for search.h... 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 for inttypes.h... (cached) yes
checking for stdint.h... (cached) 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 helgrind.h usability... no
checking helgrind.h presence... no
checking for helgrind.h... no
checking valgrind/helgrind.h usability... no
checking valgrind/helgrind.h presence... no
checking for valgrind/helgrind.h... no
checking drd.h usability... no
checking drd.h presence... no
checking for drd.h... no
checking valgrind/drd.h usability... no
checking valgrind/drd.h presence... no
checking for valgrind/drd.h... no
checking whether the valgrind headers are broken or too old... yes
checking for strdup... yes
checking whether strdup needs a declaration... no
checking for snprintf... yes
checking whether snprintf needs a declaration... no
checking for strncmp... yes
checking whether strncmp needs a declaration... no
checking for putenv... yes
checking whether putenv needs a declaration... no
checking for strerror... yes
checking whether strerror needs a declaration... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating localdefs
config.status: creating include/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing include/mplconfig.h commands
config.status: creating include/mplconfig.h - prefix MPL for include/config.h defines
configure: ===== done with src/mpl configure =====
configure: sourcing src/mpl/localdefs
configure: ===== configuring src/openpa =====
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5' --disable-versioning --with-atomic-primitives=auto_allow_emulation '--enable-fortran=yes' '--enable-cxx' '--with
-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '--with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... pgcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking the archiver (ar) interface... ar
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... pgcc -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 dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... yes
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... (cached) yes
checking for gcc... (cached) pgcc
checking whether we are using the GNU C compiler... (cached) no
checking whether pgcc accepts -g... (cached) yes
checking for pgcc option to accept ISO C89... (cached) none needed
checking whether pgcc understands -c and -o together... (cached) yes
checking dependency style of pgcc... (cached) pgcc
checking whether to enable assertions... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking atomic.h usability... no
checking atomic.h presence... no
checking for atomic.h... no
checking intrin.h usability... no
checking intrin.h presence... no
checking for intrin.h... no
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for C/C++ restrict keyword... __restrict
checking for inline... inline
checking for an ANSI C-conforming const... yes
checking for pthread_create in -lpthread... yes
checking for pthread_yield... yes
checking if 100 threads can be run at once... yes
checking size of void *... 8
checking size of int... 4
checking if compiler rejects bogus asm statements... yes
checking for support for gcc x86/x86_64 primitives... yes
checking for support for gcc x86 primitives for pre-Pentium 4... yes
checking for support for gcc ia64 primitives... no
checking for support for gcc PowerPC atomics... no
checking for support for gcc ARM atomics... no
checking for support for gcc SiCortex atomics... no
checking for support for gcc atomic intrinsics... no
checking for support for Windows NT atomic intrinsics... no
checking for support for Sun atomic operations library... no
checking whether to enable strict fairness checks... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating openpa.pc
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing src/opa_config.h commands
config.status: creating src/opa_config.h - prefix OPA for src/config.h defines
configure: ===== done with src/openpa configure =====
sourcing /scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/pm/slurm/mpichprereq
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
configure: ===== configuring osu_benchmarks =====
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5' --enable-embedded --enable-mpi --enable-mpi2 --enable-mpi3 '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi
2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '--with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... pgcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... pgcc -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 dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... yes
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether we are using the GNU C compiler... (cached) no
checking whether pgcc accepts -g... (cached) yes
checking for pgcc option to accept ISO C89... (cached) none needed
checking whether pgcc understands -c and -o together... (cached) yes
checking dependency style of pgcc... (cached) pgcc
checking whether we are using the GNU C++ compiler... yes
checking whether pgc++ accepts -g... yes
checking dependency style of pgc++... none
checking how to run the C++ preprocessor... pgc++ -E
checking for ld used by pgc++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
pgc++-Error-Unknown switch: -print-prog-name=ld
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for pgc++ option to produce PIC... -fPIC -DPIC
checking if pgc++ PIC flag -fPIC -DPIC works... yes
checking if pgc++ static flag -static works... no
checking if pgc++ supports -c -o file.o... yes
checking if pgc++ supports -c -o file.o... (cached) yes
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for library containing sqrt... none required
checking for library containing pthread_join... none required
checking for library containing clock_gettime... none required
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for inline... inline
checking for getpagesize... yes
checking for gettimeofday... yes
checking for memset... yes
checking for sqrt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating mpi/Makefile
config.status: creating mpi/pt2pt/Makefile
config.status: creating mpi/startup/Makefile
config.status: creating mpi/one-sided/Makefile
config.status: creating mpi/collective/Makefile
config.status: creating openshmem/Makefile
config.status: creating upc/Makefile
config.status: creating upcxx/Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
configure: ===== done with osu_benchmarks configure =====
checking for shared library (esp. rpath) characteristics of CC... done (results in src/env/cc_shlib.conf)
checking whether Fortran 77 compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... no
checking how to get verbose linking output from pgfortran... -v
checking for Fortran 77 libraries of pgfortran...  -L/apps/pgi/linux86-64/18.5/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -lpgf90rtl -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgftnrtl -lpgmp -lnuma -lpthread -
lpgmath -lnspgc -lpgc -lrt -lm
checking whether pgfortran accepts the FLIBS found by autoconf... yes
checking whether pgcc 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 libraries to link Fortran main with C stdio routines... none
checking whether Fortran init will work with C... no
checking for extension for Fortran 90 programs... f90
checking whether the Fortran 90 compiler (pgfortran   ) works... yes
checking whether the Fortran 90 compiler (pgfortran   ) is a cross-compiler... no
checking whether Fortran 90 compiler works with Fortran 77 compiler... yes
checking for shared library (esp. rpath) characteristics of F77... done (results in src/env/f77_shlib.conf)
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 pgfortran allows mismatched arguments... yes
checking for Fortran 2008 support... no
checking for shared library (esp. rpath) characteristics of FC... done (results in src/env/fc_shlib.conf)
checking whether the Fortran 90 compiler (pgfortran   ) works... yes
checking whether the Fortran 90 compiler (pgfortran   ) is a cross-compiler... no
checking for Fortran 90 module extension... mod
checking for Fortran 90 module include flag... -I
checking for Fortran 90 module output directory flag... -module 
checking whether Fortran 90 compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... no
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 whether TRUE has been defined... no
checking whether the C++ compiler pgc++ 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 . 8
checking for shared library (esp. rpath) characteristics of CXX... done (results in src/env/cxx_shlib.conf)
checking whether C++ compiler accepts option -O2... yes
checking whether routines compiled with -O2 can be linked with ones compiled without -O2... no
checking for perl... /bin/perl
checking for ar... ar
checking for ranlib... ranlib
checking for killall... killall
checking whether install works... yes
checking whether mkdir -p works... yes
checking for make... make
checking whether clock skew breaks make... no
checking whether make supports include... no
checking whether make allows comments in actions... no
configure: WARNING: Your make does not allow comments in target code.
Using this make may cause problems when building programs.
You should consider using gnumake instead.
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 an ANSI C-conforming const... yes
checking for working volatile... yes
checking for C/C++ restrict keyword... __restrict
checking for inline... inline
checking if C compiler supports __builtin_expect... yes
checking whether byte ordering is bigendian... no
checking whether C compiler allows unaligned doubles... yes
checking whether pgcc supports __func__... yes
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.  MVAPICH2 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 for inttypes.h... (cached) yes
checking for stdint.h... (cached) 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... yes
checking for C type matching Fortran real... float
checking for C type matching Fortran double... double
checking for C type matching Fortran integer... int
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 for Fortran 90 integer kind for 4-byte integers... 4
checking if real*8 is supported in Fortran 90... yes
checking size of bool... 1
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 for alignment restrictions on int64_t... no
checking for alignment restrictions on int32_t... no
checking for gcov... gcov
checking for ANSI C header files... (cached) yes
checking for stdlib.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking for sys/types.h... (cached) yes
checking for string.h... (cached) 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 for unistd.h... (cached) 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... yes
checking for clock_getres... yes
checking for gethrtime... no
checking for mach_absolute_time... no
checking for gettimeofday... yes
checking for library containing clock_gettime... none required
checking for library containing clock_getres... none required
checking whether struct timespec is defined in time.h... yes
checking for CLOCK_REALTIME defined in time.h... yes
checking size of MPIR_Bsend_data_t... 96
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_ERRORCHECK_NP... yes
checking whether pthread.h defines PTHREAD_MUTEX_ERRORCHECK... yes
checking whether pthread_mutexattr_settype needs a declaration... no
checking for thread local storage specifier... none
checking for getpid... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for unistd.h... (cached) yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sched_yield... yes
checking for yield... no
checking for usleep... yes
checking for sleep... yes
checking for select... yes
checking whether usleep needs a declaration... no
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... yes
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
configure: RUNNING CONFIGURE FOR src/pm/slurm
checking slurm/pmi2.h usability... yes
checking slurm/pmi2.h presence... yes
checking for slurm/pmi2.h... yes
checking for PMI2_Init in -lpmi2... yes
checking for PMI2_KVS_Ifence... no
checking for PMI2_KVS_Wait... no
checking for PMI2_Iallgather... no
checking for PMI2_Iallgather_wait... no
checking for PMI2_SHMEM_Iallgather... no
checking for PMI2_SHMEM_Iallgather_wait... no
configure: RUNNING CONFIGURE FOR F90 CODE
checking whether ln -s works... yes
checking for extension for Fortran 90 programs... f90
checking for the precision and range of reals...  6 , 37
checking for the precision and range of double precision...  15 , 307
checking for the range of integer...  9
checking for available integer kinds...  2 , 1, 4 , 2, 9 , 4, 18 , 8,
checking for available integer ranges...  {  2 , 1 , 1 }, {  4 , 2 , 2 }, {  9 , 4 , 4 }, {  18 , 8 , 8 },
checking for unistd.h... (cached) yes
checking for string.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for sys/socket.h... (cached) yes
checking for strings.h... (cached) yes
checking for assert.h... (cached) yes
checking for snprintf... (cached) yes
checking whether snprintf needs a declaration... (cached) no
checking for strncasecmp... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/param.h... (cached) yes
checking for sys/socket.h... (cached) yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking netinet/tcp.h usability... yes
checking netinet/tcp.h presence... yes
checking for netinet/tcp.h... yes
checking sys/un.h usability... yes
checking sys/un.h presence... yes
checking for sys/un.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for library containing socket... none required
checking for library containing gethostbyname... none required
checking for socket... yes
checking for setsockopt... yes
checking for gethostbyname... yes
checking whether socklen_t is defined (in sys/socket.h if present)... yes
checking whether struct hostent contains h_addr_list... yes
configure: RUNNING CONFIGURE FOR CH3 DEVICE
checking for assert.h... (cached) yes
checking for limits.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/uio.h... (cached) yes
checking uuid/uuid.h usability... yes
checking uuid/uuid.h presence... yes
checking for uuid/uuid.h... yes
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 for sys/socket.h... (cached) 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 for OpenPA atomic primitive availability... yes
checking whether byte ordering is bigendian... (cached) no
configure: RUNNING CONFIGURE FOR ch3:psm
checking for netdb.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/socket.h... (cached) 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 for errno.h... (cached) yes
checking psm.h usability... yes
checking psm.h presence... yes
checking for psm.h... yes
checking psm2.h usability... yes
checking psm2.h presence... yes
checking for psm2.h... yes
checking for psm2_init in -lpsm2... yes
checking infiniband/verbs.h usability... yes
checking infiniband/verbs.h presence... yes
checking for infiniband/verbs.h... yes
checking for ibv_open_device in -libverbs... yes
checking for mmap... yes
checking for munmap... yes
configure: Using a memory-mapped file for shared memory
configure: ===== configuring src/mpi/romio =====
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5'  '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '-
-with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for style of include used by make... GNU
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking the archiver (ar) interface... ar
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for GNU ld... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld -m elf_x86_64 option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... pgcc -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 dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... no
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether make supports nested variables... (cached) yes
Configuring with args dummy mt
checking whether clock skew breaks make... no
checking whether make supports include... no
checking whether make allows comments in actions... no
configure: WARNING: Your make does not allow comments in target code.
Using this make may cause problems when building programs.
You should consider using gnumake instead.
checking for virtual path format... VPATH
checking whether make sets CFLAGS... yes
checking for architecture... LINUX
ROMIO home directory is /scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/mpi/romio
checking whether we are using the GNU Fortran 77 compiler... no
checking whether pgfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pgfortran option to produce PIC... -fpic
checking if pgfortran PIC flag -fpic works... yes
checking if pgfortran static flag -Bstatic works... no
checking if pgfortran supports -c -o file.o... yes
checking if pgfortran supports -c -o file.o... (cached) yes
checking whether the pgfortran linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether we are using the GNU Fortran compiler... no
checking whether pgfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for pgfortran option to produce PIC... -fpic
checking if pgfortran PIC flag -fpic works... yes
checking if pgfortran static flag -Bstatic works... no
checking if pgfortran supports -c -o file.o... yes
checking if pgfortran supports -c -o file.o... (cached) yes
checking whether the pgfortran linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for long long... yes
checking size of long long... 8
checking for memalign... yes
checking Fortran external names
Fortran externals have a trailing underscore and are lowercase
checking for inline... inline
checking for size_t... yes
checking for ssize_t... yes
checking for off_t... yes
checking how to run the C preprocessor... pgcc -E
checking for unistd.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for sys/types.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for mpix.h... no
checking for u_char... yes
checking for u_short... yes
checking for u_int... yes
checking for u_long... yes
checking sys/attr.h usability... no
checking sys/attr.h presence... no
checking for sys/attr.h... no
checking size of int... 4
checking size of void *... 8
checking for int large enough for pointers... no
checking size of long long... (cached) 8
checking for extension for Fortran 90 programs... f90
checking for Fortran 90 KIND parameter for 8-byte integers...             8
checking that we can use integer*8 to declare MPI_DISPLACMENT_CURRENT... yes
Overriding Array test for MVAPICH2
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 whether struct flock compatible with MPI_Offset... yes
checking for pvfs2-config... notfound
checking configured file systems... testfs ufs nfs
configure: WARNING: File locks may not work with NFS.  See the Installation and
users manual for instructions on testing and if necessary fixing this
checking for library containing aio_write... -lrt
checking signal.h usability... yes
checking signal.h presence... yes
checking for signal.h... yes
checking aio.h usability... yes
checking aio.h presence... yes
checking for aio.h... yes
checking sys/aio.h usability... no
checking sys/aio.h presence... no
checking for sys/aio.h... no
checking whether aio routines can be used... yes
checking for obsolete two-argument aio_write... no
checking for obsolete two-argument aio_suspend... no
checking for struct aiocb.aio_fildes... yes
checking for struct aiocb.aio_whence... no
checking for struct aiocb.aio_handle... no
checking for struct aiocb.aio_reqprio... yes
checking for struct aiocb.aio_sigevent... yes
checking sys/vfs.h usability... yes
checking sys/vfs.h presence... yes
checking for sys/vfs.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/mount.h usability... yes
checking sys/mount.h presence... yes
checking for sys/mount.h... yes
checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking for statfs... yes
checking whether struct statfs properly defined... yes
checking for f_fstypename member of statfs structure... no
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stat... yes
checking for st_fstype member of stat structure... no
checking for sys/types.h... (cached) yes
checking for sys/statvfs.h... (cached) yes
checking for sys/vfs.h... (cached) yes
checking for statvfs... yes
checking for f_basetype member of statvfs structure... no
checking for blksize_t... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking whether pwrite is declared... yes
checking for strerror... yes
checking for doctext... false
checking for strdup... yes
checking whether strdup needs a declaration... no
checking for snprintf... yes
checking whether snprintf needs a declaration... no
checking for lstat... yes
checking whether lstat needs a declaration... no
checking for readlink... yes
checking whether readlink needs a declaration... no
checking for fsync... yes
checking whether fsync needs a declaration... no
checking for ftruncate... yes
checking whether ftruncate needs a declaration... no
checking for lseek64... yes
checking whether lseek64 needs a declaration... yes
checking for usleep... yes
checking whether usleep needs a declaration... no
setting SYSDEP_INC to 
checking for C/C++ restrict keyword... __restrict
checking for gcov... gcov
setting CC to pgcc
setting F77 to pgfortran
setting TEST_CC to $(bindir)/mpicc
setting TEST_F77 to $(bindir)/mpifort
setting CFLAGS to    -DNDEBUG -DNVALGRIND -O2  -DFORTRANUNDERSCORE -DHAVE_ROMIOCONF_H
setting USER_CFLAGS to 
setting USER_FFLAGS to 
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating localdefs
config.status: creating mpi2-other/info/Makefile
config.status: creating mpi2-other/array/Makefile
config.status: creating test/Makefile
config.status: creating test/misc.c
config.status: creating test/large_file.c
config.status: creating test/runtests
config.status: creating test-internal/Makefile
config.status: creating util/romioinstall
config.status: creating include/mpio.h
config.status: creating include/mpiof.h
config.status: creating mpi2-other/info/fortran/Makefile
config.status: creating mpi2-other/array/fortran/Makefile
config.status: creating test/fmisc.f
config.status: creating test/fcoll_test.f
config.status: creating test/pfcoll_test.f
config.status: creating test/fperf.f
config.status: creating adio/include/romioconf.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default-1 commands
configure: ===== done with src/mpi/romio configure =====
configure: sourcing src/mpi/romio/localdefs
checking size of OPA_ptr_t... 8
checking the sizeof MPI_Offset... 8
checking whether the Fortran Offset type works with Fortran 77... yes
checking whether the Fortran Offset type works with Fortran 90... yes
checking for size of MPI_Status... 20
checking for BSD/POSIX style global symbol lister... BSD style,/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... no
configure: WARNING: The ch3:psm device did not set the maximum size of an error string, 512 being used.
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/binding/fortran/use_mpi/mpif90model.h
config.status: creating Makefile
config.status: creating examples/Makefile
config.status: creating test/Makefile
config.status: creating test/commands/Makefile
config.status: creating src/include/mpichinfo.h
config.status: creating mpich-doxygen
config.status: creating src/include/glue_romio.h
config.status: creating src/binding/cxx/mpicxx.h
config.status: creating src/binding/fortran/mpif_h/mpif.h
config.status: creating src/binding/fortran/mpif_h/setbotf.f
config.status: creating src/binding/fortran/mpif_h/setbot.c
config.status: creating src/binding/fortran/use_mpi/mpi_sizeofs.f90
config.status: creating src/binding/fortran/use_mpi/mpi_base.f90
config.status: creating src/binding/fortran/use_mpi/mpi_constants.f90
config.status: creating src/binding/fortran/use_mpi_f08/mpi_f08_compile_constants.f90
config.status: creating src/binding/fortran/use_mpi_f08/mpi_c_interface_types.f90
config.status: creating src/packaging/pkgconfig/mvapich2.pc
config.status: creating src/packaging/envmods/mvapich2.module
config.status: WARNING:  'src/packaging/envmods/mvapich2.module.in' seems to ignore the --datarootdir setting
config.status: creating src/env/mpixxx_opts.conf
config.status: creating src/env/mpicc.sh
config.status: creating src/env/mpicc.bash
config.status: creating src/env/mpicxx.sh
config.status: creating src/env/mpicxx.bash
config.status: creating src/env/mpif77.sh
config.status: creating src/env/mpif77.bash
config.status: creating src/env/mpifort.sh
config.status: creating src/env/mpifort.bash
config.status: creating src/env/parkill
config.status: creating src/env/mpiname/Makefile
config.status: creating src/pm/mpirun/mpirun_rsh.h
config.status: creating src/util/mv2_ckpt_rebuild/Makefile
config.status: creating src/util/dbg/getfuncstack
config.status: creating src/util/timers/mpiu_timer.h
config.status: creating src/include/mpi.h
config.status: creating doc/design/Makefile
config.status: creating doc/installguide/Makefile
config.status: creating doc/logging/Makefile
config.status: creating doc/refman/Makefile
config.status: creating doc/userguide/Makefile
config.status: creating test/commands/cmdtests
config.status: creating src/include/mpichconf.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default-1 commands
config.status: executing default-2 commands
config.status: executing default-3 commands
config.status: executing default-4 commands
config.status: executing default-5 commands
=== configuring in test/mpi (/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/test/mpi)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5'  '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '-
-with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.
RUNNING CONFIGURE FOR MPI TESTS
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking whether make supports nested variables... (cached) yes
checking for make... make
checking whether clock skew breaks make... no
checking whether make supports include... no
checking whether make allows comments in actions... no
configure: WARNING: Your make does not allow comments in target code.
Using this make may cause problems when building programs.
You should consider using gnumake instead.
checking for virtual path format... VPATH
checking whether make sets CFLAGS... yes
checking for style of include used by make... GNU
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking whether long double is supported... yes
checking whether long long is supported... yes
checking for an ANSI C-conforming const... yes
checking for C/C++ restrict keyword... __restrict
checking for ranlib... ranlib
checking the archiver (ar) interface... ar
checking for grep that handles long lines and -e... /bin/grep
checking for fgrep... /bin/grep -F
checking how to run the C preprocessor... pgcc -E
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 stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.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 for _Bool... yes
checking for float _Complex... yes
checking for double _Complex... yes
checking for long double _Complex... yes
checking size of void *... 8
checking for library containing socket... none required
checking for library containing gethostbyname... none required
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for library containing pthread_create... none required
checking for library containing pthread_barrier_init... none required
checking for pthread_create... yes
checking for pthread_yield... yes
checking for pthread_barrier_init... yes
checking for pthread_barrier_wait... yes
checking whether struct hostent contains h_addr_list... yes
checking for getrusage... yes
checking whether we are using the GNU Fortran 77 compiler... no
checking whether pgfortran accepts -g... yes
checking whether integer*4 is supported... yes
checking whether integer*8 is supported... yes
checking whether integer*16 is supported... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to get verbose linking output from pgfortran... -v
checking for Fortran 77 libraries of pgfortran...  -L/apps/pgi/linux86-64/18.5/lib -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -lpgf90rtl -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgftnrtl -lpgmp -lnuma -lpthread -
lpgmath -lnspgc -lpgc -lrt -lm
checking for Fortran 77 name mangling... lower uscore
checking whether pgfortran allows mismatched arguments... yes
checking for Fortran libraries needed for getarg... none needed
checking whether Fortran 77 supports Cray-style pointer... yes
checking for Fortran 77 compiler flag for Cray-style pointer... none
checking whether we are using the GNU Fortran compiler... no
checking whether pgfortran accepts -g... yes
checking for extension for Fortran 90 programs... f90
checking whether the Fortran 90 compiler (pgfortran  ) works... yes
checking whether the Fortran 90 compiler (pgfortran  ) is a cross-compiler... no
checking for Fortran flag needed to accept free-form source... none
checking whether Fortran 90 supports Cray-style pointer... yes
checking for Fortran 90 compiler flag for Cray-style pointer... none
checking whether pgfortran supports the Fortran 2003 routines to access the commandline... yes
checking for Fortran 90 module extension... mod
checking for Fortran 90 module include flag... -I
checking for Fortran 90 module output directory flag... -module 
checking whether we are using the GNU C++ compiler... yes
checking whether pgc++ accepts -g... yes
checking dependency style of pgc++... none
checking whether <iostream> available... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler implements the namespace std... yes
checking whether MPI_2DOUBLE_COMPLEX is available... no
checking whether MPI_2COMPLEX is available... no
checking size of void *... (cached) 8
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of short... 2
checking for C integer type of address size... long
checking for perl... /bin/perl
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating maint/testmerge
config.status: creating runtests
config.status: creating checktests
config.status: creating Makefile
config.status: creating basic/Makefile
config.status: creating attr/Makefile
config.status: creating util/Makefile
config.status: creating coll/Makefile
config.status: creating coll/testlist
config.status: creating comm/Makefile
config.status: creating datatype/Makefile
config.status: creating datatype/testlist
config.status: creating errhan/Makefile
config.status: creating group/Makefile
config.status: creating info/Makefile
config.status: creating init/Makefile
config.status: creating pt2pt/Makefile
config.status: creating mpi_t/Makefile
config.status: creating rma/Makefile
config.status: creating rma/testlist
config.status: creating spawn/Makefile
config.status: creating spawn/testlist
config.status: creating topo/Makefile
config.status: creating io/Makefile
config.status: creating io/testlist
config.status: creating f77/Makefile
config.status: creating f77/attr/Makefile
config.status: creating f77/attr/attraints.h
config.status: creating f77/pt2pt/attr1aints.h
config.status: creating f77/ext/add1size.h
config.status: creating f77/datatype/Makefile
config.status: creating f77/datatype/typeaints.h
config.status: creating f77/util/Makefile
config.status: creating f77/coll/Makefile
config.status: creating f77/comm/Makefile
config.status: creating f77/topo/Makefile
config.status: creating f77/init/Makefile
config.status: creating f77/rma/addsize.h
config.status: creating f77/pt2pt/Makefile
config.status: creating f77/info/Makefile
config.status: creating f77/spawn/Makefile
config.status: creating f77/spawn/testlist
config.status: creating f77/spawn/type1aint.h
config.status: creating f77/rma/Makefile
config.status: creating f77/ext/Makefile
config.status: creating f77/ext/testlist
config.status: creating f77/io/Makefile
config.status: creating f77/io/iooffset.h
config.status: creating f77/io/iodisp.h
config.status: creating f77/io/ioaint.h
config.status: creating f77/io/testlist
config.status: creating f77/profile/Makefile
config.status: creating f90/Makefile
config.status: creating f90/attr/Makefile
config.status: creating f90/datatype/Makefile
config.status: creating f90/f90types/Makefile
config.status: creating f90/util/Makefile
config.status: creating f90/coll/Makefile
config.status: creating f90/comm/Makefile
config.status: creating f90/topo/Makefile
config.status: creating f90/init/Makefile
config.status: creating f90/pt2pt/Makefile
config.status: creating f90/rma/Makefile
config.status: creating f90/info/Makefile
config.status: creating f90/spawn/Makefile
config.status: creating f90/spawn/testlist
config.status: creating f90/timer/Makefile
config.status: creating f90/ext/Makefile
config.status: creating f90/ext/testlist
config.status: creating f90/io/Makefile
config.status: creating f90/io/testlist
config.status: creating f90/misc/Makefile
config.status: creating f90/profile/Makefile
config.status: creating f08/Makefile
config.status: creating f08/attr/Makefile
config.status: creating f08/datatype/Makefile
config.status: creating f08/util/Makefile
config.status: creating f08/coll/Makefile
config.status: creating f08/comm/Makefile
config.status: creating f08/pt2pt/Makefile
config.status: creating f08/rma/Makefile
config.status: creating f08/subarray/Makefile
config.status: creating f08/topo/Makefile
config.status: creating f08/io/Makefile
config.status: creating f08/io/testlist
config.status: creating f08/init/Makefile
config.status: creating f08/info/Makefile
config.status: creating f08/spawn/Makefile
config.status: creating f08/spawn/testlist
config.status: creating f08/timer/Makefile
config.status: creating f08/ext/Makefile
config.status: creating f08/misc/Makefile
config.status: creating f08/profile/Makefile
config.status: creating cxx/Makefile
config.status: creating cxx/util/Makefile
config.status: creating cxx/attr/Makefile
config.status: creating cxx/pt2pt/Makefile
config.status: creating cxx/comm/Makefile
config.status: creating cxx/coll/Makefile
config.status: creating cxx/errhan/Makefile
config.status: creating cxx/info/Makefile
config.status: creating cxx/datatype/Makefile
config.status: creating cxx/io/Makefile
config.status: creating cxx/init/Makefile
config.status: creating cxx/rma/Makefile
config.status: creating cxx/spawn/Makefile
config.status: creating cxx/spawn/testlist
config.status: creating cxx/topo/Makefile
config.status: creating threads/Makefile
config.status: creating threads/pt2pt/Makefile
config.status: creating threads/util/Makefile
config.status: creating threads/comm/Makefile
config.status: creating threads/comm/testlist
config.status: creating threads/init/Makefile
config.status: creating threads/mpi_t/Makefile
config.status: creating threads/spawn/Makefile
config.status: creating threads/rma/Makefile
config.status: creating threads/coll/Makefile
config.status: creating threads/coll/testlist
config.status: creating errors/Makefile
config.status: creating errors/attr/Makefile
config.status: creating errors/basic/Makefile
config.status: creating errors/coll/Makefile
config.status: creating errors/comm/Makefile
config.status: creating errors/datatype/Makefile
config.status: creating errors/faults/Makefile
config.status: creating errors/group/Makefile
config.status: creating errors/pt2pt/Makefile
config.status: creating errors/rma/Makefile
config.status: creating errors/spawn/Makefile
config.status: creating errors/spawn/testlist
config.status: creating errors/topo/Makefile
config.status: creating errors/io/Makefile
config.status: creating errors/cxx/Makefile
config.status: creating errors/cxx/errhan/Makefile
config.status: creating errors/cxx/io/Makefile
config.status: creating errors/f77/Makefile
config.status: creating errors/f77/io/Makefile
config.status: creating errors/f77/io/addsize.h
config.status: creating errors/f77/io/iooffset.h
config.status: creating errors/f90/Makefile
config.status: creating errors/f90/io/Makefile
config.status: creating errors/f08/Makefile
config.status: creating errors/f08/io/Makefile
config.status: creating ckpoint/Makefile
config.status: creating ft/Makefile
config.status: creating manual/Makefile
config.status: creating manual/manyconnect
config.status: creating manual/mpi_t/Makefile
config.status: creating perf/Makefile
config.status: creating testlist
config.status: creating cxx/testlist
config.status: creating cxx/topo/testlist
config.status: creating f77/testlist
config.status: creating f90/testlist
config.status: creating threads/testlist
config.status: creating errors/testlist
config.status: creating errors/cxx/testlist
config.status: creating errors/f77/testlist
config.status: creating errors/f90/testlist
config.status: creating impls/testlist
config.status: creating f77/rma/testlist
config.status: creating f90/rma/testlist
config.status: creating f08/rma/testlist
config.status: creating impls/Makefile
config.status: creating impls/hydra/Makefile
config.status: creating impls/hydra/proc_binding.sh
config.status: creating impls/mpich/Makefile
config.status: creating impls/mpich/testlist
config.status: creating impls/mpich/mpi_t/Makefile
config.status: creating include/mpitestconf.h
config.status: executing depfiles commands
config.status: executing default-1 commands
config.status: executing default-2 commands
config.status: executing default-3 commands
config.status: executing default-4 commands
=== configuring in contrib/hwloc (/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/contrib/hwloc)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/opt/mvapich2/2.3.1/pgi/18.5'  '--enable-fortran=yes' '--enable-cxx' '--with-pmi=pmi2' '--with-pm=slurm' '--with-slurm=/apps/slurm/default' '-
-with-device=ch3:psm' '--enable-romio' 'CC=pgcc' 'CXX=pgc++' 'FC=pgfortran' 'F77=pgfortran' --cache-file=/dev/null --srcdir=.

###
### Configuring hwloc distribution tarball
### Startup tests
###
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '3441' is supported by ustar format... yes
checking whether GID '18001' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for style of include used by make... GNU
checking for gcc... pgcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ISO C89... none needed
checking whether pgcc understands -c and -o together... yes
checking dependency style of pgcc... pgcc
checking how to run the C preprocessor... pgcc -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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... (cached) pgcc
checking whether we are using the GNU C compiler... (cached) no
checking whether pgcc accepts -g... (cached) yes
checking for pgcc option to accept ISO C89... (cached) none needed
checking whether pgcc understands -c and -o together... (cached) yes
checking dependency style of pgcc... (cached) pgcc
checking whether we are using the GNU C++ compiler... yes
checking whether pgc++ accepts -g... yes
checking dependency style of pgc++... none
checking the archiver (ar) interface... ar
checking for pkg-config... /bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking how to run the C++ preprocessor... pgc++ -E
checking for X... libraries , headers 

###
### Configuring hwloc core
###
checking hwloc building mode... embedded
configure: hwloc builddir: /scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/contrib/hwloc
configure: hwloc srcdir: /scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/contrib/hwloc
checking for hwloc version... 1.11.11rc3-git
checking if want hwloc maintainer support... disabled (embedded mode)
checking for hwloc directory prefix... (none)
checking for hwloc symbol prefix... hwloc_
checking size of void *... 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... portland group
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)... no
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)... no
checking for __attribute__(noreturn)... yes
checking for __attribute__(packed)... yes
checking for __attribute__(pure)... yes
checking for __attribute__(sentinel)... no
checking for __attribute__(unused)... yes
checking for __attribute__(warn_unused_result)... no
checking for __attribute__(weak_alias)... yes
checking if pgcc supports -fvisibility=hidden... no
checking whether to enable symbol visibility... no (unsupported)
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 dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... 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 strncasecmp is declared... yes
checking whether function strncasecmp has a complete prototype... yes
checking for strftime... yes
checking for setlocale... yes
checking for stdint.h... (cached) yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... 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 for PostQuitMessage in -luser32... 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 whether modff is declared... yes
checking for modff 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 sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking for sys/sysctl.h... yes
checking whether CTL_HW is declared... no
checking whether HW_NCPU is declared... no
checking whether strtoull is declared... yes
checking for ssize_t... yes
checking whether snprintf is declared... yes
checking whether strcasecmp is declared... yes
checking whether _strdup is declared... no
checking whether _putenv is declared... no
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 sched_getcpu is declared... yes
checking whether sched_setaffinity is declared... yes
checking whether function sched_setaffinity has a complete prototype... 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 ffs is declared... yes
checking whether function ffs has a complete prototype... yes
checking for ffsl... yes
checking whether ffsl is declared... yes
checking whether function ffsl has a complete prototype... yes
checking for fls... no
checking for flsl... no
checking for clz... no
checking for clzl... no
checking for openat... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for getpagesize... yes
checking for memalign... yes
checking for posix_memalign... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... 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 for move_pages in -lnuma... yes
checking libudev.h usability... yes
checking libudev.h presence... yes
checking for libudev.h... yes
checking for udev_device_new_from_subsystem_sysname in -ludev... yes
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 LIBXML2... yes
checking libxml/parser.h usability... yes
checking libxml/parser.h presence... yes
checking for libxml/parser.h... yes
checking for xmlNewDoc... yes
checking for final LIBXML2 support... yes
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 xml_libxml x86
checking components to build as plugins... 
checking for a sed that does not truncate output... /bin/sed

###
### Performing final hwloc configuration
###
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for GNU ld... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld -m elf_x86_64 option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from pgcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking for pgcc option to produce PIC... -fpic -DPIC
checking if pgcc PIC flag -fpic -DPIC works... yes
checking if pgcc static flag -Bstatic works... no
checking if pgcc supports -c -o file.o... yes
checking if pgcc supports -c -o file.o... (cached) yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... pgc++ -E
checking for ld used by pgc++... /usr/bin/ld -m elf_x86_64 -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) is GNU ld... yes
pgc++-Error-Unknown switch: -print-prog-name=ld
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking for pgc++ option to produce PIC... -fPIC -DPIC
checking if pgc++ PIC flag -fPIC -DPIC works... yes
checking if pgc++ static flag -static works... no
checking if pgc++ supports -c -o file.o... yes
checking if pgc++ supports -c -o file.o... (cached) yes
checking whether the pgc++ linker (/usr/bin/ld -m elf_x86_64 -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating include/Makefile
config.status: creating src/Makefile
config.status: creating include/private/autogen/config.h
config.status: creating include/hwloc/autogen/config.h
config.status: executing depfiles commands
config.status: executing libtool commands

-----------------------------------------------------------------------------
Hwloc optional build support status (more details can be found above):

Probe / display I/O devices: PCI(linux)
Graphical output (Cairo):    
XML input / output:          full
libnuma memory support:      yes
Plugin support:              no
-----------------------------------------------------------------------------

Configuration completed.



> On May 4, 2019, at 8:59 AM, Christopher Harrop - NOAA Affiliate <christopher.w.harrop at noaa.gov> wrote:
> 
> Hi,
> 
> I am triying to build mvapich2 2.3.1 for Intel TrueScale IB with PGI 18.5.
> 
> I am doing this for setting variables and configure:
> 
> export CC=pgcc
> export CXX=pgc++
> export F77=pgf77
> export FC=pgfortran
> unset F90
> export CPP=cpp  # Leaving this out causes the configure to fail
> 
> ./configure --prefix=${INSTALLDIR}/${path} --enable-fortran=yes --enable-cxx --with-pmi=pmi2 --with-pm=slurm --with-slurm=/apps/slurm/default \
> --with-device=ch3:psm --enable-romio
> 
> The configure and build succeeds until the very end, when it is linking libmpi.  At that point, for reasons I have been unable to figure out, it inserts an illegal compiler flag “-pthread”
> 
> …...
> id/common/datatype/.libs/lib_libmpi_la-mpid_type_struct.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpid_type_vector.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpid_type_zerolen.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpir_type_flatten.o src/mpid/common/sched/.libs/lib_libmpi_la-mpid_sched.o src/mpi_t/.libs/lib_libmpi_la-mpit.o src/mpi_t/.libs/lib_libmpi_la-mv2_mpit.o src/nameserv/pmi/.libs/lib_libmpi_la-pmi_nameserv.o src/pmi/upmi/.libs/lib_libmpi_la-upmi.o  -Wl,--whole-archive,src/mpl/.libs/libmpl.a,/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/openpa/src/.libs/libopa.a,src/mpi/romio/.libs/libromio.a,./.libs/libch3affinity.a,contrib/hwloc/src/.libs/libhwloc_embedded.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/apps/slurm/18.08.7.p1-2/lib -Wl,-rpath -Wl,/apps/slurm/18.08.7.p1-2/lib -L/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/mpl -L/apps/slurm/default/lib -L/usr/lib64 -L/usr/lib -lrt -lm -lnuma -ludev -lxml2 -libverbs -lpsm_infinipath /apps/slurm/18.08.7.p1-2/lib/libpmi2.so -lpthread    -pthread -Wl,-soname -Wl,libmpi.so.12 -o lib/.libs/libmpi.so.12.1.1
> pgf77-Error-Unknown switch: -pthread
> make[3]: *** [lib/libmpi.la] Error 1
> 
> I have tried many things, including adding the following:
> 
>         export lt_cv_sys_lib_search_path_spec="/lib64 /usr/lib64 /usr/local/lib64"
>         export lt_cv_sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/local/lib64"
>         export CPPFLAGS="-D__x86_64”
> 
> Nothing works to get rid of that erroneous -pthread.  
> 
> Has anyone else run into this or have ideas about how to fix it?  (I can provide the full config.log, but thought I’d start here since that is enormous).
> 
> Chris

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