[mvapich-discuss] Link error with PGI
Christopher W. Harrop
christopher.w.harrop at gmail.com
Wed May 8 11:01:32 EDT 2019
Dear Yussuf,
Thank you for this suggestion. It did indeed provide the key to solving my issue. When I initially tried creating the .my*rc files you suggested, it didn’t work for me. It’s possible I messed something up somewhere, or maybe it was because I was using pgfortran for the linker and I’m not sure what the name of the corresponding .my*rc file is for pgfortran.
In any case, the machine was down for maintenance all day yesterday, so I spent some time looking at that thread you provided (not sure why, but the second link you provided didn’t work for me). In that thread, they suggest that the problem of the erroneous -pthread option is coming from Slurm. And when I look at our Slurm install, I do see this:
$ grep '\-pthread' /apps/slurm/default/lib/*.la
/apps/slurm/default/lib/libpmi2.la:inherited_linker_flags=' -pthread'
/apps/slurm/default/lib/libpmi.la:inherited_linker_flags=' -pthread'
/apps/slurm/default/lib/libslurmdb.la:inherited_linker_flags=' -pthread'
/apps/slurm/default/lib/libslurm.la:inherited_linker_flags=' -pthread'
One suggestion in that thread is to create a “siterc” file in $HOME with these contents:
$ cat ~/siterc
switch -ffast-math is hide;
switch -pipe is hide;
switch -fexpensive-optimizations is hide;
switch -pthread is append(LDLIB1= -lpthread);
switch -qversion is early
help(Display compiler version)
helpgroup(overall)
set(VERSION=YES);
switch -Wno-deprecated-declarations is hide;
switch -flat_namespace is hide;
I tried that (after removing my .my*rc files that I created earlier), and it worked!
Thank you so much for providing the link to that thread. It gave me the information I needed. It will also help me when I try to build OpenMPI, which I am planning to do next.
Chris
> On May 6, 2019, at 6:40 PM, Yussuf Ali <yussuf.ali at jaea.go.jp> wrote:
>
> Hi,
>
> I don't know if this is related but we had had a similar problem but not with MVAPICH but OpenMPI. This thread is related to this problem:
>
> https://users.open-mpi.narkive.com/k79isVDd/ompi-users-compiler-error-with-pgi-pgcc-error-unknown-switch-pthread <https://users.open-mpi.narkive.com/k79isVDd/ompi-users-compiler-error-with-pgi-pgcc-error-unknown-switch-pthread>
> (This gives some more information: https://www.pgroup.com/userforum/viewtopic.php?p=21105#21105 <https://www.pgroup.com/userforum/viewtopic.php?p=21105#21105>)
>
> In the case of OpenMPI the configuration stage already failed because of the unknow pthread option.
>
> The PGI compiler does not know the "-pthread" option so it must be mapped to the corresponding PGI compiler option.
>
> The PGI compiler will read some custom configuration files from your home directory:
>
> 1. Create the following files inside your home directory (note the dot at the beginning):
>
> .mypg++rc
>
> .mypgccrc
>
> .mypgf77rc
>
> .mypgf90rc
>
> 2. Copy the following lines of code into the files:
>
> switch -ffast-math is hide;
> switch -pipe is hide;
> switch -fexpensive-optimizations is hide;
> switch -pthread is append(LDLIB1= -lpthread);
> switch -qversion is
> early
> help(Display compiler version)
> helpgroup(overall)
> set(VERSION=YES);
> switch -Wno-deprecated-declarations is hide;
> switch -flat_namespace is hide;
>
> 3. Re-configure and re-compile
>
> In our case it solved the problem for OpenMPI maybe it will also solve it for MVAPICH.
>
>
>
> Good luck!
>
>
>
> On 5/7/2019 05:37, Christopher W.Harrop wrote:
>> ===( By JAEA Mail System )=================
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>>
>>
>> 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
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>> 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
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>> checking valgrind/memcheck.h usability... no
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>> checking helgrind.h usability... no
>> checking helgrind.h presence... no
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>> 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 <mailto:christopher.w.harrop at noaa.gov>
>> mailto:christopher.w.harrop at noaa.gov <mailto: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
>> http*//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
>>
>>
>>
>>
>>
>> _______________________________________________
>> mvapich-discuss mailing list
>> mvapich-discuss at cse.ohio-state.edu <mailto:mvapich-discuss at cse.ohio-state.edu>
>> http*//mailman.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
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