[mvapich-discuss] Link error with PGI

[Christopher Harrop - NOAA Affiliate]

Hi,

I am triying to build mvapich2 2.3.1 for Intel TrueScale IB with PGI 18.5.

I am doing this for setting variables and configure:

export CC=pgcc
export CXX=pgc++
export F77=pgf77
export FC=pgfortran
unset F90
export CPP=cpp  # Leaving this out causes the configure to fail

./configure --prefix=${INSTALLDIR}/${path} --enable-fortran=yes --enable-cxx --with-pmi=pmi2 --with-pm=slurm --with-slurm=/apps/slurm/default \
--with-device=ch3:psm --enable-romio

The configure and build succeeds until the very end, when it is linking libmpi.  At that point, for reasons I have been unable to figure out, it inserts an illegal compiler flag “-pthread”

…...
id/common/datatype/.libs/lib_libmpi_la-mpid_type_struct.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpid_type_vector.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpid_type_zerolen.o src/mpid/common/datatype/.libs/lib_libmpi_la-mpir_type_flatten.o src/mpid/common/sched/.libs/lib_libmpi_la-mpid_sched.o src/mpi_t/.libs/lib_libmpi_la-mpit.o src/mpi_t/.libs/lib_libmpi_la-mv2_mpit.o src/nameserv/pmi/.libs/lib_libmpi_la-pmi_nameserv.o src/pmi/upmi/.libs/lib_libmpi_la-upmi.o  -Wl,--whole-archive,src/mpl/.libs/libmpl.a,/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/openpa/src/.libs/libopa.a,src/mpi/romio/.libs/libromio.a,./.libs/libch3affinity.a,contrib/hwloc/src/.libs/libhwloc_embedded.a -Wl,--no-whole-archive  -Wl,-rpath -Wl,/apps/slurm/18.08.7.p1-2/lib -Wl,-rpath -Wl,/apps/slurm/18.08.7.p1-2/lib -L/scratch4/BMC/gsd-hpcs/Christopher.W.Harrop/bass-develop/build/mvapich2/2.3.1/pgi/18.5/src/mpl -L/apps/slurm/default/lib -L/usr/lib64 -L/usr/lib -lrt -lm -lnuma -ludev -lxml2 -libverbs -lpsm_infinipath /apps/slurm/18.08.7.p1-2/lib/libpmi2.so -lpthread    -pthread -Wl,-soname -Wl,libmpi.so.12 -o lib/.libs/libmpi.so.12.1.1
pgf77-Error-Unknown switch: -pthread
make[3]: *** [lib/libmpi.la] Error 1

I have tried many things, including adding the following:

        export lt_cv_sys_lib_search_path_spec="/lib64 /usr/lib64 /usr/local/lib64"
        export lt_cv_sys_lib_dlsearch_path_spec="/lib64 /usr/lib64 /usr/local/lib64"
        export CPPFLAGS="-D__x86_64”

Nothing works to get rid of that erroneous -pthread.  

Has anyone else run into this or have ideas about how to fix it?  (I can provide the full config.log, but thought I’d start here since that is enormous).

Chris
-----------------------------------------------------------------------------------------------------------
Christopher W. Harrop                               email: christopher.w.harrop at noaa.gov <mailto:christopher.w.harrop at noaa.gov>
Global Systems Division                                                          voice: (303) 497-6808 <tel:%28303%29%20497-6808>
NOAA Earth System Research Laboratory                               fax: (303) 497-7259 <tel:%28303%29%20497-7259>
325 Broadway R/GSD2
Boulder, CO 80303



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