at first glance, you are building OpenMPI with a gcc you compiled by yourself, and that appears busted
for example, gnu_dev_major is an extern symbol, so the linker should not complain about it being multiply defined (!) can you simply preprocess a file and post the output, for example cd opal rm class/opal_bitmap.lo make V=1 class/opal_bitmap.lo look at the end how gcc is invoked, and then replace '-c' with '-E' and run the command manually the preprocessed file is in class/.libs/opal_bitmap.o Cheers, Gilles On Fri, Feb 26, 2016 at 11:39 AM, Tang Cheng Yee <lsit...@nus.edu.sg> wrote: > Attached are the log file for ./configure and make all install. I am using > the openmpi-1.10.2 > > Thanks > > -----Original Message----- > From: users [mailto:users-boun...@open-mpi.org] On Behalf Of Jeff Squyres > (jsquyres) > Sent: Friday, 26 February, 2016 10:13 AM > To: Open MPI User's List > Subject: Re: [OMPI users] Problem when installing OpenMPI during make all > install > > Can you send all the information listed here: > > https://www.open-mpi.org/community/help/ > > >> On Feb 25, 2016, at 9:09 PM, Tang Cheng Yee <lsit...@nus.edu.sg> wrote: >> >> Hi all, >> >> I am new to the bioinformatics world. When I was trying to install OpenMPI, >> I encountered the following error during ‘make all install’: >> >> >> class/.libs/opal_bitmap.o:opal_bitmap.c:(.text+0x200): first defined >> here >> mca/timer/linux/.libs/libmca_timer_linux.a(timer_linux_component.o): In >> function `pthread_equal': >> timer_linux_component.c:(.text+0x8d0): multiple definition of `pthread_equal' >> class/.libs/opal_free_list.o:opal_free_list.c:(.text+0x590): first >> defined here >> collect2: error: ld returned 1 exit status >> make[2]: *** [libopen-pal.la] Error 1 >> make[2]: Leaving directory `/data/chengyee/software/openmpi-1.10.2/opal' >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory `/data/chengyee/software/openmpi-1.10.2/opal' >> make: *** [all-recursive] Error 1 >> >> I can’t find solution on the internet, please help. >> My configuration command was: ./configure --prefix=/local/bin/ >> --disable-mpi-fortran >> >> Part of my configuration log that I suspect might be helpful to track my >> error (but I do not understand): >> config.status: creating opal/include/opal_config.h >> config.status: opal/include/opal_config.h is unchanged >> config.status: creating orte/include/orte_config.h >> config.status: orte/include/orte_config.h is unchanged >> config.status: creating ompi/include/mpi.h >> config.status: ompi/include/mpi.h is unchanged >> config.status: creating oshmem/include/shmem.h >> config.status: oshmem/include/shmem.h is unchanged >> config.status: creating >> opal/mca/hwloc/hwloc191/hwloc/include/private/autogen/config.h >> config.status: >> opal/mca/hwloc/hwloc191/hwloc/include/private/autogen/config.h is >> unchanged >> config.status: creating >> opal/mca/hwloc/hwloc191/hwloc/include/hwloc/autogen/config.h >> config.status: >> opal/mca/hwloc/hwloc191/hwloc/include/hwloc/autogen/config.h is >> unchanged >> config.status: executing depfiles commands >> config.status: executing >> opal/mca/event/libevent2021/libevent/include/event2/event-config.h >> commands >> opal/mca/event/libevent2021/libevent/include/event2/event-config.h is >> unchanged >> config.status: executing libtool commands >> >> Appreciate anyone who helps. Thanks. >> >> With regards, >> CY >> >> >> Important: This email is confidential and may be privileged. If you are not >> the intended recipient, please delete it and notify us immediately; you >> should not copy or use it for any purpose, nor disclose its contents to any >> other person. Thank you. >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/02/28580.php > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/02/28581.php > > ________________________________ > > Important: This email is confidential and may be privileged. If you are not > the intended recipient, please delete it and notify us immediately; you > should not copy or use it for any purpose, nor disclose its contents to any > other person. Thank you. > > _______________________________________________ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/02/28582.php
