Commenting out the -pthread flag in /usr/lib/libpmi.la allows it to compile OK. But while 'srun' successfully runs mpi jobs on one 64-core node, the following error appears when trying to run on 2 nodes, and the job hangs: srun: error: slurm_send_recv_rc_msg_only_one: Connection timed out No help from google... Thanks, Jim On Jul 9, 2014, at 3:37 PM, Kenneth Raffenetti wrote:
Libtool is adding the -pthread flag because it exists in the "inherited_linker_flags" in libpmi.la. However, PGI clearly doesn't understand it. The libtool devs called this issue a bug when it was reported here:
http://lists.gnu.org/archive/html/libtool/2010-11/msg00034.html
You could either remove the flag from the /usr/lib/libpmi.la file, or use the workaround suggested by Gus Correa to finish your build.
Ken
On 07/09/2014 05:56 PM, Gus Correa wrote:
Hi James
Adding '-noswitcherror' to the CFLAGS, FFLAGS, FCFLAGS, may be a workaround to this problem.
My two cents, Gus Correa
On 07/09/2014 05:55 PM, James Long wrote:
I need to use srun to launch mpi jobs under slurm, so configured mpich-3.1.1 with
$ env CC=pgcc FC=pgf90 CXX=pgCC CPPFLAGS="-DNDEBUG -DpgiFortran" CFLAGS="-O2" FFLAGS="-O2 -w" ./configure --prefix=/opt/mpich-slurm --with-pmi=slurm --with-pm=no --with-slurm-include=/usr/include/slurm --with-slurm-lib=/usr/lib/slurm --enable-fortran=yes
The following error occurs when compiling:
CC src/mpid/common/datatype/lib_libmpi_la-mpir_type_flatten.lo CC src/mpid/common/sched/lib_libmpi_la-mpid_sched.lo CC src/mpid/common/thread/lib_libmpi_la-mpid_thread.lo CC src/mpi_t/lib_libmpi_la-mpit.lo CC src/nameserv/pmi/lib_libmpi_la-pmi_nameserv.lo GEN lib/libmpi.la pgf90-Error-Unknown switch: -pthread make[2]: *** [lib/libmpi.la] Error 1 make[2]: Leaving directory `/home/boss/mpich-3.1.1' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/boss/mpich-3.1.1' make: *** [all] Error 2
config.log is at http://pastebin.com/aB8CZsr0
Jim --
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% James Long International Arctic Research Center University of Alaska Fairbanks jlong|at|alaska.edu (907) 474-2440 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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-- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% James Long International Arctic Research Center University of Alaska Fairbanks jlong|at|alaska.edu (907) 474-2440 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%