July 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] MPICH 3.1.1 on NI MyRIO, error at ar interface
by "Antonio J. Peña" 12 Jul '14

12 Jul '14

Thank you very much for this information. Antonio On 07/11/2014 11:44 PM, Kyle Hartley wrote: > > Hey Antonio, > I figured it out with the help of another colleague. I needed to also > install binutils-symlinks and the configure ran without issue after > that. Mpiexec worked but the c example failed. I'm remaking to be > sure. I've documented everything over at our website for those > curious. Google Ni.com mpi myrio should get you there > > Thanks > Kyle Hartley > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Re: [mpich-discuss] MPICH 3.1.1 on NI MyRIO, error at ar interface
by Kyle Hartley 11 Jul '14

11 Jul '14

Hey Antonio, I figured it out with the help of another colleague. I needed to also install binutils-symlinks and the configure ran without issue after that. Mpiexec worked but the c example failed. I'm remaking to be sure. I've documented everything over at our website for those curious. Google Ni.com mpi myrio should get you there Thanks Kyle Hartley

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Fatal error in PMPI_Bcast
by James Long 11 Jul '14

11 Jul '14

Compiled as shown in thread below for use with slurm (config.log at http://pastebin.com/aB8CZsr0) I get the following error: $ srun -n 64 -l ./mpi_wrapper -dl cfile 00: Fatal error in PMPI_Bcast: Other MPI error, error stack: 00: PMPI_Bcast(1607)......: MPI_Bcast(buf=0x6104e0, count=1, MPI_INT, root=0, MPI_COMM_WORLD) failed 00: MPIR_Bcast_impl(1459).: 00: MPIR_Bcast(1483)......: 00: MPIR_Bcast_intra(1254): 00: MPIR_SMP_Bcast(1168)..: Failure during collective . . . run: error: 10_4_5_11: tasks 0-31: Exited with exit code 1 where the fatal error is the same for tasks 0-31 on the first node (10_4_5_11), and no error for tasks 32-63 on the second node. The code runs fine if I only use one node for srun (-n 32), and works fine across two nodes if I compile mpich without the slurm flags (PGI compiler in all cases) and use mpirun. openmpi works OK across the two nodes when compiled with slurm support, so is the problem something to do with the slurm pmi library and mpich? I'm using slurm 2.6.7-1 and libpmi0 2.6.7-1 under debian. Jim On Jul 9, 2014, at 4:39 PM, James Long wrote: > 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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Re: [mpich-discuss] pgf90-Error-Unknown switch: -pthread
by James Long 11 Jul '14

11 Jul '14

Hi Gus, CC=gcc and F77=FC=pgf90 (with FFLAGS=FCFLAGS=noswitcherror) also fails. Removing the flag from the /usr/lib/libpmi.la lets it compile, so am testing that now. The "srun: error: slurm_send_recv_rc_msg_only_one: Connection timed out" was a firewall issue. Thanks, Jim On Jul 10, 2014, at 7:25 AM, Gus Correa wrote: > Hi Jim > > Hmmm ... the noswitcherror used to be OK, > dodging the PGI compilers default, > and ignoring the -pthread flag added by libtool. > > Have you tried CC=gcc and F77=FC=pgf90 > (with FFLAGS=FCFLAGS=noswitcherror)? > I have some functional hybrid (gcc+pgf90) builds of various MPIs. > > > I hope this helps, > Gus Correa > > On 07/09/2014 08:39 PM, James Long wrote: >> 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 >>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> discuss mailing list discuss(a)mpich.org >>>>> To manage subscription options or unsubscribe: >>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> -- >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> James Long >> International Arctic Research Center >> University of Alaska Fairbanks >> jlong|at|alaska.edu >> (907) 474-2440 >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% James Long International Arctic Research Center University of Alaska Fairbanks jlong|at|alaska.edu (907) 474-2440 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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Re: [mpich-discuss] MPICH 3.1.1 on NI MyRIO, error at ar interface
by "Antonio J. Peña" 11 Jul '14

11 Jul '14

Hi Kyle, Unfortunately that archiver seems to lack the functionality needed to compile MPICH with our current build interface. I've been trying to play around that issue but so far I haven't been able to find a good solution without the "r" flag. However, to the best of my knowledge we have positive reports of people compiling MPICH in busy box. Maybe someone else in this list can give you a hint on that. Antonio On 07/10/2014 10:45 PM, Kyle Hartley wrote: > Hey All, > > I'm trying to install MPICH on a set of National Instruments myRIOs. > They run the angstrom kernel. Currently when I run the configuration > for the build it errors at the AR interface because the ar function is > missing -r for replacement in archives. This is a busy box > implementation of ar. It doesn't look like busy box has a new > implementation. So i'm looking at two options avoiding the archiver if > that is an option or download a new ar function. The myRIO uses a > armv7a processor. > > Can I get by with disabling the archiver interface? skiming readme > looks like no option to do so > Can I disable the check on the archiver interface with --disable-ar > interface? > Another ar function? > Snippet of config.log below > > configure:6603: checking whether to enable maintainer-specific > portions of Makefiles > configure:6612: result: yes > configure:6676: checking for ar > configure:6692: found /usr/bin/ar > configure:6703: result: ar > configure:6729: checking the archiver (ar) interface > configure:6745: gcc -c conftest.c >&5 > configure:6745: $? = 0 > configure:6747: ar cru libconftest.a conftest.o >&5 > ar: invalid option -- 'r' > BusyBox v1.19.4 (2013-06-20 07:58:10 CDT) multi-call binary. > > Usage: ar [-o] [-v] [-p] [-t] [-x] ARCHIVE FILES > > configure:6750: $? = 1 > configure:6756: ar -NOLOGO -OUT:conftest.lib conftest.o >&5 > ar: invalid option -- 'N' > BusyBox v1.19.4 (2013-06-20 07:58:10 CDT) multi-call binary. > > Usage: ar [-o] [-v] [-p] [-t] [-x] ARCHIVE FILES > > configure:6759: $? = 1 > configure:6778: result: unknown > configure:6794: error: could not determine ar interface > > ## ---------------- ## > ## Cache variables. ## > ## ---------------- ## > > ac_cv_c_compiler_gnu=yes > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peï¿½a Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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MPICH 3.1.1 on NI MyRIO, error at ar interface
by Kyle Hartley 10 Jul '14

10 Jul '14

Hey All, I'm trying to install MPICH on a set of National Instruments myRIOs. They run the angstrom kernel. Currently when I run the configuration for the build it errors at the AR interface because the ar function is missing -r for replacement in archives. This is a busy box implementation of ar. It doesn't look like busy box has a new implementation. So i'm looking at two options avoiding the archiver if that is an option or download a new ar function. The myRIO uses a armv7a processor. Can I get by with disabling the archiver interface? skiming readme looks like no option to do so Can I disable the check on the archiver interface with --disable-ar interface? Another ar function? Snippet of config.log below configure:6603: checking whether to enable maintainer-specific portions of Makefiles configure:6612: result: yes configure:6676: checking for ar configure:6692: found /usr/bin/ar configure:6703: result: ar configure:6729: checking the archiver (ar) interface configure:6745: gcc -c conftest.c >&5 configure:6745: $? = 0 configure:6747: ar cru libconftest.a conftest.o >&5 ar: invalid option -- 'r' BusyBox v1.19.4 (2013-06-20 07:58:10 CDT) multi-call binary. Usage: ar [-o] [-v] [-p] [-t] [-x] ARCHIVE FILES configure:6750: $? = 1 configure:6756: ar -NOLOGO -OUT:conftest.lib conftest.o >&5 ar: invalid option -- 'N' BusyBox v1.19.4 (2013-06-20 07:58:10 CDT) multi-call binary. Usage: ar [-o] [-v] [-p] [-t] [-x] ARCHIVE FILES configure:6759: $? = 1 configure:6778: result: unknown configure:6794: error: could not determine ar interface ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_c_compiler_gnu=yes

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Re: [mpich-discuss] pgf90-Error-Unknown switch: -pthread
by Gus Correa 10 Jul '14

10 Jul '14

Hi Jim Hmmm ... the noswitcherror used to be OK, dodging the PGI compilers default, and ignoring the -pthread flag added by libtool. Have you tried CC=gcc and F77=FC=pgf90 (with FFLAGS=FCFLAGS=noswitcherror)? I have some functional hybrid (gcc+pgf90) builds of various MPIs. I hope this helps, Gus Correa On 07/09/2014 08:39 PM, James Long wrote: > 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 >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > -- > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > James Long > International Arctic Research Center > University of Alaska Fairbanks > jlong|at|alaska.edu > (907) 474-2440 > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] pgf90-Error-Unknown switch: -pthread
by James Long 09 Jul '14

09 Jul '14

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 >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> >>> >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >>> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% James Long International Arctic Research Center University of Alaska Fairbanks jlong|at|alaska.edu (907) 474-2440 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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Re: [mpich-discuss] pgf90-Error-Unknown switch: -pthread
by James Long 09 Jul '14

09 Jul '14

$ env CC=pgcc FC=pgf90 CXX=pgCC CPPFLAGS="-DNDEBUG -DpgiFortran" CFLAGS="-O2 -noswitcherror" FFLAGS="-O2 -w -noswitcherror" FCFLAGS="-noswitcherror" ./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 results in the same make error... Jim On Jul 9, 2014, at 2:56 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 >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% James Long International Arctic Research Center University of Alaska Fairbanks jlong|at|alaska.edu (907) 474-2440 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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Re: [mpich-discuss] pgf90-Error-Unknown switch: -pthread
by Kenneth Raffenetti 09 Jul '14

09 Jul '14

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 >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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