July 2015 - discuss - mailman3.cels.anl.gov

mpich hangs in MPI_Send() - multi threaded environment
by Nenad Vukicevic 17 Jul '15

17 Jul '15

I am having a problem where the system locks up inside the MPI_Send() routine. In my test, each MPI rank has an additional pthread and system locks up when: - main thread does MPI_Recv from ANY rank - pthread does MPI_Send to another rank I verified with MPI_Init_thread() that I can run MPI_THREAD_MULTIPLE environment. The same thing happened on MPICH with Fedora 20 (3.0.4) and the one build from 3.2b3 sources. When building from sources I provided '--enable-threads=multiple' option. I also tried to play with '--enable-thread-cs' option but got build failure when 'per-object' was selected. Is this supposed to work? Thanks, Nenad I am attaching traces form GDB for the rank that locks up. (gdb) info thread Id Target Id Frame 2 Thread 0x7ffff6a5a700 (LWP 29570) "barrier_test" 0x0000003ef040bca0 in pthread_cond_wait@@GLIBC_2.3.2 () from /usr/lib64/libpthread.so.0 * 1 Thread 0x7ffff7a64b80 (LWP 29568) "barrier_test" 0x00007ffff7c58717 in MPIU_Thread_CS_yield_lockname_recursive_impl_ ( lockname=0x7ffff7cdc8b1 "global_mutex", mutex=<optimized out>, kind=MPIU_Nest_global_mutex) at ../src/src/include/mpiimplthreadpost.h:190 (gdb) where #0 0x00007ffff7c58717 in MPIU_Thread_CS_yield_lockname_recursive_impl_ (lockname=0x7ffff7cdc8b1 "global_mutex", mutex=<optimized out>, kind=MPIU_Nest_global_mutex) at ../src/src/include/mpiimplthreadpost.h:190 #1 0x00007ffff7c5db42 in MPIDI_CH3I_Progress (progress_state=progress_state@entry=0x7fffffffd2c0, is_blocking=is_blocking@entry=1) at ../src/src/mpid/ch3/channels/nemesis/src/ch3_progress.c:507 #2 0x00007ffff7b5e795 in PMPI_Recv (buf=0x7fffffffd61c, count=1, datatype=1275069445, source=-2, tag=299, comm=1140850688, status=0x7fffffffd620) at ../src/src/mpi/pt2pt/recv.c:157 #3 0x0000000000401732 in receive_int () at comm.c:52 #4 0x0000000000400bf2 in main (argc=1, argv=0x7fffffffd758) at barrier_test.c:39 (gdb) thread 2 [Switching to thread 2 (Thread 0x7ffff6a5a700 (LWP 29570))] #0 0x0000003ef040bca0 in pthread_cond_wait@@GLIBC_2.3.2 () from /usr/lib64/libpthread.so.0 (gdb) where #0 0x0000003ef040bca0 in pthread_cond_wait@@GLIBC_2.3.2 () from /usr/lib64/libpthread.so.0 #1 0x00007ffff7c5d614 in MPIDI_CH3I_Progress_delay (completion_count=<optimized out>) at ../src/src/mpid/ch3/channels/nemesis/src/ch3_progress.c:566 #2 MPIDI_CH3I_Progress (progress_state=progress_state@entry=0x7ffff6a59710, is_blocking=is_blocking@entry=1) at ../src/src/mpid/ch3/channels/nemesis/src/ch3_progress.c:347 #3 0x00007ffff7b632ec in PMPI_Send (buf=0x7ffff6a5985c, count=1, datatype=1275069445, dest=0, tag=199, comm=1140850688) at ../src/src/mpi/pt2pt/send.c:145 #4 0x0000000000400e42 in barrier_thread_release (id=0) at barrier.c:115 #5 0x0000000000401098 in barrier_helper (arg=0x0) at barrier.c:186 #6 0x0000003ef0407ee5 in start_thread () from /usr/lib64/libpthread.so.0 #7 0x0000003eef8f4d1d in clone () from /usr/lib64/libc.so.6 _______________________________________________ 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] mpich-3.1.4: 'make testing' fails
by Junchao Zhang 13 Jul '15

13 Jul '15

Perhaps the time limit set by the test script is too low. On my machine `mpiexec -n 4 ./getfence1` finishes in 3+ minutes. You can manually test it to see if will complete successfully. --Junchao Zhang On Sun, Jul 12, 2015 at 2:17 AM, arindam ghosh <arindamgr(a)gmail.com> wrote: > Thanks. > Adding -lpthread to the LDFLAGS solves my problem. > > only one problem left: > > not ok 333 - ./rma/getfence1 4 > --- > Directory: ./rma > File: getfence1 > Num-procs: 4 > Date: "Sun Jul 12 12:28:19 2015" > ... > ## Test output (expected 'No Errors'): > ## /usr/local/bin/mpiexec -n 4 ./getfence1 > ## > ## > =================================================================================== > ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > ## = PID 18069 RUNNING AT localhost.localdomain > ## = EXIT CODE: 9 > ## = CLEANING UP REMAINING PROCESSES > ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > ## > =================================================================================== > ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) > ## This typically refers to a problem with your application. > ## Please see the FAQ page for debugging suggestions > > > please tell me how t fix this error. > > Thanking you, > > Regards, > Arindam > > > > On Thu, Jul 9, 2015 at 9:12 AM, Junchao Zhang <jczhang(a)mcs.anl.gov> wrote: > >> Not sure if this is the reason, >> http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missi… >> You can go to one failure directory, e.g., test/mpi/threads/pt2pt, and >> type "make V=1 threads", and find out what is the actual link command line. >> >> --Junchao Zhang >> >> On Wed, Jul 8, 2015 at 12:00 AM, arindam ghosh <arindamgr(a)gmail.com> >> wrote: >> >>> Dear All, >>> >>> I'm trying to install mpich-3.1.4 in my desktop: >>> >>> CC=gcc CXX=g++ FC=gfortran F77=gfortran ./configure --prefix=/usr/local >>> --enable-fortran --enable-cxx 2>&1 | tee c.txt >>> make 2>&1 | tee m.txt >>> make install 2>&1 | tee mi.txt >>> >>> I'm using gcc/gfortran/g++ version 4.9.2-6. As such there is no error, >>> but while doing 'make testing', it shows following errors (taken from file >>> ./test/mpi/summary.tap), please see below: >>> >>> not ok 297 - ./pt2pt/sendflood 8 >>> --- >>> Directory: ./pt2pt >>> File: sendflood >>> Num-procs: 8 >>> Date: "Wed Jul 8 00:01:41 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## [mpiexec(a)localhost.localdomain] APPLICATION TIMED OUT >>> >>> not ok 333 - ./rma/getfence1 4 >>> --- >>> Directory: ./rma >>> File: getfence1 >>> Num-procs: 4 >>> Date: "Wed Jul 8 00:06:49 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## >>> ## >>> =================================================================================== >>> ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >>> ## = PID 12669 RUNNING AT localhost.localdomain >>> ## = EXIT CODE: 9 >>> ## = CLEANING UP REMAINING PROCESSES >>> ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >>> ## >>> =================================================================================== >>> ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) >>> ## This typically refers to a problem with your application. >>> ## Please see the FAQ page for debugging suggestions >>> >>> not ok 836 - ./threads/pt2pt/threads >>> --- >>> Directory: ./threads/pt2pt >>> File: threads >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build threads; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC threads.o >>> ## (cd ../../threads/util && make mtestthread.o) >>> ## make[4]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' >>> ## CC mtestthread.o >>> ## make[4]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' >>> ## CCLD threads >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:522: recipe for target 'threads' failed >>> ## make[3]: *** [threads] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 837 - ./threads/pt2pt/threaded_sr >>> --- >>> Directory: ./threads/pt2pt >>> File: threaded_sr >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build threaded_sr; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC threaded_sr.o >>> ## CCLD threaded_sr >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:518: recipe for target 'threaded_sr' failed >>> ## make[3]: *** [threaded_sr] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 838 - ./threads/pt2pt/alltoall >>> --- >>> Directory: ./threads/pt2pt >>> File: alltoall >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build alltoall; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC alltoall.o >>> ## CCLD alltoall >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:482: recipe for target 'alltoall' failed >>> ## make[3]: *** [alltoall] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 839 - ./threads/pt2pt/sendselfth >>> --- >>> Directory: ./threads/pt2pt >>> File: sendselfth >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build sendselfth; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC sendselfth.o >>> ## CCLD sendselfth >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:514: recipe for target 'sendselfth' failed >>> ## make[3]: *** [sendselfth] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 840 - ./threads/pt2pt/multisend >>> --- >>> Directory: ./threads/pt2pt >>> File: multisend >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multisend; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC multisend.o >>> ## CCLD multisend >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:498: recipe for target 'multisend' failed >>> ## make[3]: *** [multisend] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 841 - ./threads/pt2pt/multisend2 >>> --- >>> Directory: ./threads/pt2pt >>> File: multisend2 >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multisend2; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC multisend2.o >>> ## CCLD multisend2 >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:502: recipe for target 'multisend2' failed >>> ## make[3]: *** [multisend2] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 842 - ./threads/pt2pt/multisend3 >>> --- >>> Directory: ./threads/pt2pt >>> File: multisend3 >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multisend3; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC multisend3.o >>> ## CCLD multisend3 >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:506: recipe for target 'multisend3' failed >>> ## make[3]: *** [multisend3] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 843 - ./threads/pt2pt/multisend4 >>> --- >>> Directory: ./threads/pt2pt >>> File: multisend4 >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multisend4; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC multisend4.o >>> ## CCLD multisend4 >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:510: recipe for target 'multisend4' failed >>> ## make[3]: *** [multisend4] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 844 - ./threads/pt2pt/greq_wait >>> --- >>> Directory: ./threads/pt2pt >>> File: greq_wait >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build greq_wait; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC greq_wait.o >>> ## CCLD greq_wait >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:490: recipe for target 'greq_wait' failed >>> ## make[3]: *** [greq_wait] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 845 - ./threads/pt2pt/greq_test >>> --- >>> Directory: ./threads/pt2pt >>> File: greq_test >>> Num-procs: >>> Date: "Wed Jul 8 00:11:54 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build greq_test; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC greq_test.o >>> ## CCLD greq_test >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:486: recipe for target 'greq_test' failed >>> ## make[3]: *** [greq_test] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 846 - ./threads/pt2pt/ibsend >>> --- >>> Directory: ./threads/pt2pt >>> File: ibsend >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build ibsend; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> ## CC ibsend.o >>> ## CCLD ibsend >>> ## /usr/bin/ld: ibsend.o: undefined reference to symbol 'pthread_create@ >>> @GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:494: recipe for target 'ibsend' failed >>> ## make[3]: *** [ibsend] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >>> not ok 847 - ./threads/comm/ctxdup >>> --- >>> Directory: ./threads/comm >>> File: ctxdup >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build ctxdup; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ## CC ctxdup.o >>> ## CCLD ctxdup >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:471: recipe for target 'ctxdup' failed >>> ## make[3]: *** [ctxdup] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> not ok 848 - ./threads/comm/dup_leak_test >>> --- >>> Directory: ./threads/comm >>> File: dup_leak_test >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build dup_leak_test; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ## CC dup_leak_test.o >>> ## CCLD dup_leak_test >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:479: recipe for target 'dup_leak_test' failed >>> ## make[3]: *** [dup_leak_test] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> not ok 849 - ./threads/comm/comm_dup_deadlock >>> --- >>> Directory: ./threads/comm >>> File: comm_dup_deadlock >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build comm_dup_deadlock; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ## CC comm_dup_deadlock.o >>> ## CCLD comm_dup_deadlock >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:463: recipe for target 'comm_dup_deadlock' failed >>> ## make[3]: *** [comm_dup_deadlock] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> not ok 850 - ./threads/comm/comm_create_threads >>> --- >>> Directory: ./threads/comm >>> File: comm_create_threads >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build comm_create_threads; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ## CC comm_create_threads.o >>> ## CCLD comm_create_threads >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:459: recipe for target 'comm_create_threads' failed >>> ## make[3]: *** [comm_create_threads] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> not ok 851 - ./threads/comm/comm_create_group_threads >>> --- >>> Directory: ./threads/comm >>> File: comm_create_group_threads >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build comm_create_group_threads; make[3]: Entering >>> directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ## CC comm_create_group_threads.o >>> ## CCLD comm_create_group_threads >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:455: recipe for target 'comm_create_group_threads' failed >>> ## make[3]: *** [comm_create_group_threads] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >>> ok 859 - ./threads/comm/comm_idup 4 # SKIP xfail tests disabled >>> ok 860 - ./threads/comm/ctxidup 4 # SKIP xfail tests disabled >>> not ok 852 - ./threads/init/initth >>> --- >>> Directory: ./threads/init >>> File: initth >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build initth; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >>> ## CC initth.o >>> ## CCLD initth >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:405: recipe for target 'initth' failed >>> ## make[3]: *** [initth] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >>> not ok 853 - ./threads/init/initth >>> --- >>> Directory: ./threads/init >>> File: initth >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build initth; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >>> ## CC initth.o >>> ## CCLD initth >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:405: recipe for target 'initth' failed >>> ## make[3]: *** [initth] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >>> not ok 854 - ./threads/mpi_t/mpit_threading >>> --- >>> Directory: ./threads/mpi_t >>> File: mpit_threading >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build mpit_threading; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' >>> ## CC mpit_threading.o >>> ## CCLD mpit_threading >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:405: recipe for target 'mpit_threading' failed >>> ## make[3]: *** [mpit_threading] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' >>> not ok 855 - ./threads/spawn/multispawn >>> --- >>> Directory: ./threads/spawn >>> File: multispawn >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multispawn; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >>> ## CC multispawn.o >>> ## CCLD multispawn >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:412: recipe for target 'multispawn' failed >>> ## make[3]: *** [multispawn] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >>> not ok 856 - ./threads/spawn/th_taskmaster >>> --- >>> Directory: ./threads/spawn >>> File: th_taskmaster >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build th_taskmaster; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >>> ## CC th_taskmaster.o >>> ## CCLD th_taskmaster >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:416: recipe for target 'th_taskmaster' failed >>> ## make[3]: *** [th_taskmaster] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >>> not ok 857 - ./threads/rma/multirma >>> --- >>> Directory: ./threads/rma >>> File: multirma >>> Num-procs: >>> Date: "Wed Jul 8 00:11:55 2015" >>> ... >>> ## Test output (expected 'No Errors'): >>> ## Failed to build multirma; make[3]: Entering directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' >>> ## CC multirma.o >>> ## CCLD multirma >>> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >>> symbol 'pthread_create@@GLIBC_2.2.5' >>> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from >>> command line >>> ## collect2: error: ld returned 1 exit status >>> ## Makefile:416: recipe for target 'multirma' failed >>> ## make[3]: *** [multirma] Error 1 >>> ## make[3]: Leaving directory >>> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' >>> ok 867 - ./threads/rma/multiget 2 # SKIP xfail tests disabled >>> ok 858 - ./impls/mpich/mpi_t/collparmt 16 >>> >>> Please tell me how to fix these errors. >>> >>> Thanking you, >>> >>> Regards, >>> >>> Arindam >>> >>> >>> _______________________________________________ >>> 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 > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPI_Comm_idup hang with multiple nodes
by Huiwei Lu 13 Jul '15

13 Jul '15

Hi Daniel, The ticket has been fixed in the latest MPICH master (or you can check out the nightly tarballs). Please let me know if it fixes your issues. Thanks, -- Huiwei Lu Postdoc Appointee Mathematics and Computer Science Division Argonne National Laboratory http://www.mcs.anl.gov/~huiweilu/ On Tue, Jun 2, 2015 at 5:04 PM, Huiwei Lu <huiweilu(a)mcs.anl.gov> wrote: > Hi Daniel, > > Thanks for reporting the bug. I can reproduce it on my desktop. I will > work on a fix. You can track the progress here. > > http://trac.mpich.org/projects/mpich/ticket/2269 > > -- > Huiwei Lu > Postdoc Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > http://www.mcs.anl.gov/~huiweilu/ > > On Tue, Jun 2, 2015 at 4:32 PM, Daniel Pou <daniel.pou(a)gmail.com> wrote: > >> Starting with the test comm_idup_mul.c, and increasing the value of >> NUM_ITER 10, I am seeing a >> fairly regular hang with a build from latest master (commit 25204 5/31). >> >> I am running with 2 ranks (1 per node) from SLURM (v2.6.5). I was able to >> see the behavior with >> >> srun -N 2 -n 2 ./comm_idup_mul >> (linking against SLURM PMI) and >> >> salloc -N 2 -n 2 mpiexec ./comm_idup_mul. >> >> I witnessed this with both the MXM and TCP netmods. I don't see any >> issues on single node runs. >> >> Thank you, >> -Dan >> >> For reference: >> Modified code from http://trac.mpich.org/projects/mpich/ticket/1935 >> >> >> /* -*- Mode: C; c-basic-offset:4 ; indent-tabs-mode:nil ; -*- */ >> /* >> * * (C) 2012 by Argonne National Laboratory. >> * * See COPYRIGHT in top-level directory. >> * */ >> >> /* >> * * Test creating multiple communicators with MPI_Comm_idup. >> * */ >> >> #include <stdio.h> >> #include <mpi.h> >> >> #define NUM_ITER 10 >> >> int main(int argc, char **argv) >> { >> int i, rank; >> MPI_Comm comms[NUM_ITER]; >> MPI_Request req[NUM_ITER]; >> >> MPI_Init(&argc, &argv); >> MPI_Comm_rank(MPI_COMM_WORLD, &rank); >> >> for (i = 0; i < NUM_ITER; i++) >> MPI_Comm_idup(MPI_COMM_WORLD, &comms[i], &req[i]); >> >> MPI_Waitall(NUM_ITER, req, MPI_STATUSES_IGNORE); >> >> for (i = 0; i < NUM_ITER; i++) >> MPI_Comm_free(&comms[i]); >> >> if (rank == 0) >> printf(" No Errors\n"); >> >> MPI_Finalize(); >> >> return 0; >> } >> >> _______________________________________________ >> 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

1 0

Re: [mpich-discuss] mpich-3.1.4: 'make testing' fails
by arindam ghosh 12 Jul '15

12 Jul '15

Thanks. Adding -lpthread to the LDFLAGS solves my problem. only one problem left: not ok 333 - ./rma/getfence1 4 --- Directory: ./rma File: getfence1 Num-procs: 4 Date: "Sun Jul 12 12:28:19 2015" ... ## Test output (expected 'No Errors'): ## /usr/local/bin/mpiexec -n 4 ./getfence1 ## ## =================================================================================== ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES ## = PID 18069 RUNNING AT localhost.localdomain ## = EXIT CODE: 9 ## = CLEANING UP REMAINING PROCESSES ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES ## =================================================================================== ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) ## This typically refers to a problem with your application. ## Please see the FAQ page for debugging suggestions please tell me how t fix this error. Thanking you, Regards, Arindam On Thu, Jul 9, 2015 at 9:12 AM, Junchao Zhang <jczhang(a)mcs.anl.gov> wrote: > Not sure if this is the reason, > http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missi… > You can go to one failure directory, e.g., test/mpi/threads/pt2pt, and > type "make V=1 threads", and find out what is the actual link command line. > > --Junchao Zhang > > On Wed, Jul 8, 2015 at 12:00 AM, arindam ghosh <arindamgr(a)gmail.com> > wrote: > >> Dear All, >> >> I'm trying to install mpich-3.1.4 in my desktop: >> >> CC=gcc CXX=g++ FC=gfortran F77=gfortran ./configure --prefix=/usr/local >> --enable-fortran --enable-cxx 2>&1 | tee c.txt >> make 2>&1 | tee m.txt >> make install 2>&1 | tee mi.txt >> >> I'm using gcc/gfortran/g++ version 4.9.2-6. As such there is no error, >> but while doing 'make testing', it shows following errors (taken from file >> ./test/mpi/summary.tap), please see below: >> >> not ok 297 - ./pt2pt/sendflood 8 >> --- >> Directory: ./pt2pt >> File: sendflood >> Num-procs: 8 >> Date: "Wed Jul 8 00:01:41 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## [mpiexec(a)localhost.localdomain] APPLICATION TIMED OUT >> >> not ok 333 - ./rma/getfence1 4 >> --- >> Directory: ./rma >> File: getfence1 >> Num-procs: 4 >> Date: "Wed Jul 8 00:06:49 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## >> ## >> =================================================================================== >> ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >> ## = PID 12669 RUNNING AT localhost.localdomain >> ## = EXIT CODE: 9 >> ## = CLEANING UP REMAINING PROCESSES >> ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >> ## >> =================================================================================== >> ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) >> ## This typically refers to a problem with your application. >> ## Please see the FAQ page for debugging suggestions >> >> not ok 836 - ./threads/pt2pt/threads >> --- >> Directory: ./threads/pt2pt >> File: threads >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build threads; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC threads.o >> ## (cd ../../threads/util && make mtestthread.o) >> ## make[4]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' >> ## CC mtestthread.o >> ## make[4]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' >> ## CCLD threads >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:522: recipe for target 'threads' failed >> ## make[3]: *** [threads] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 837 - ./threads/pt2pt/threaded_sr >> --- >> Directory: ./threads/pt2pt >> File: threaded_sr >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build threaded_sr; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC threaded_sr.o >> ## CCLD threaded_sr >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:518: recipe for target 'threaded_sr' failed >> ## make[3]: *** [threaded_sr] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 838 - ./threads/pt2pt/alltoall >> --- >> Directory: ./threads/pt2pt >> File: alltoall >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build alltoall; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC alltoall.o >> ## CCLD alltoall >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:482: recipe for target 'alltoall' failed >> ## make[3]: *** [alltoall] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 839 - ./threads/pt2pt/sendselfth >> --- >> Directory: ./threads/pt2pt >> File: sendselfth >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build sendselfth; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC sendselfth.o >> ## CCLD sendselfth >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:514: recipe for target 'sendselfth' failed >> ## make[3]: *** [sendselfth] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 840 - ./threads/pt2pt/multisend >> --- >> Directory: ./threads/pt2pt >> File: multisend >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multisend; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC multisend.o >> ## CCLD multisend >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:498: recipe for target 'multisend' failed >> ## make[3]: *** [multisend] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 841 - ./threads/pt2pt/multisend2 >> --- >> Directory: ./threads/pt2pt >> File: multisend2 >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multisend2; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC multisend2.o >> ## CCLD multisend2 >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:502: recipe for target 'multisend2' failed >> ## make[3]: *** [multisend2] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 842 - ./threads/pt2pt/multisend3 >> --- >> Directory: ./threads/pt2pt >> File: multisend3 >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multisend3; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC multisend3.o >> ## CCLD multisend3 >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:506: recipe for target 'multisend3' failed >> ## make[3]: *** [multisend3] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 843 - ./threads/pt2pt/multisend4 >> --- >> Directory: ./threads/pt2pt >> File: multisend4 >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multisend4; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC multisend4.o >> ## CCLD multisend4 >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:510: recipe for target 'multisend4' failed >> ## make[3]: *** [multisend4] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 844 - ./threads/pt2pt/greq_wait >> --- >> Directory: ./threads/pt2pt >> File: greq_wait >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build greq_wait; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC greq_wait.o >> ## CCLD greq_wait >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:490: recipe for target 'greq_wait' failed >> ## make[3]: *** [greq_wait] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 845 - ./threads/pt2pt/greq_test >> --- >> Directory: ./threads/pt2pt >> File: greq_test >> Num-procs: >> Date: "Wed Jul 8 00:11:54 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build greq_test; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC greq_test.o >> ## CCLD greq_test >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:486: recipe for target 'greq_test' failed >> ## make[3]: *** [greq_test] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 846 - ./threads/pt2pt/ibsend >> --- >> Directory: ./threads/pt2pt >> File: ibsend >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build ibsend; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> ## CC ibsend.o >> ## CCLD ibsend >> ## /usr/bin/ld: ibsend.o: undefined reference to symbol 'pthread_create@ >> @GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:494: recipe for target 'ibsend' failed >> ## make[3]: *** [ibsend] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' >> not ok 847 - ./threads/comm/ctxdup >> --- >> Directory: ./threads/comm >> File: ctxdup >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build ctxdup; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ## CC ctxdup.o >> ## CCLD ctxdup >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:471: recipe for target 'ctxdup' failed >> ## make[3]: *** [ctxdup] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> not ok 848 - ./threads/comm/dup_leak_test >> --- >> Directory: ./threads/comm >> File: dup_leak_test >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build dup_leak_test; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ## CC dup_leak_test.o >> ## CCLD dup_leak_test >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:479: recipe for target 'dup_leak_test' failed >> ## make[3]: *** [dup_leak_test] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> not ok 849 - ./threads/comm/comm_dup_deadlock >> --- >> Directory: ./threads/comm >> File: comm_dup_deadlock >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build comm_dup_deadlock; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ## CC comm_dup_deadlock.o >> ## CCLD comm_dup_deadlock >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:463: recipe for target 'comm_dup_deadlock' failed >> ## make[3]: *** [comm_dup_deadlock] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> not ok 850 - ./threads/comm/comm_create_threads >> --- >> Directory: ./threads/comm >> File: comm_create_threads >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build comm_create_threads; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ## CC comm_create_threads.o >> ## CCLD comm_create_threads >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:459: recipe for target 'comm_create_threads' failed >> ## make[3]: *** [comm_create_threads] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> not ok 851 - ./threads/comm/comm_create_group_threads >> --- >> Directory: ./threads/comm >> File: comm_create_group_threads >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build comm_create_group_threads; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ## CC comm_create_group_threads.o >> ## CCLD comm_create_group_threads >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:455: recipe for target 'comm_create_group_threads' failed >> ## make[3]: *** [comm_create_group_threads] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' >> ok 859 - ./threads/comm/comm_idup 4 # SKIP xfail tests disabled >> ok 860 - ./threads/comm/ctxidup 4 # SKIP xfail tests disabled >> not ok 852 - ./threads/init/initth >> --- >> Directory: ./threads/init >> File: initth >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build initth; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >> ## CC initth.o >> ## CCLD initth >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:405: recipe for target 'initth' failed >> ## make[3]: *** [initth] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >> not ok 853 - ./threads/init/initth >> --- >> Directory: ./threads/init >> File: initth >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build initth; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >> ## CC initth.o >> ## CCLD initth >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:405: recipe for target 'initth' failed >> ## make[3]: *** [initth] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' >> not ok 854 - ./threads/mpi_t/mpit_threading >> --- >> Directory: ./threads/mpi_t >> File: mpit_threading >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build mpit_threading; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' >> ## CC mpit_threading.o >> ## CCLD mpit_threading >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:405: recipe for target 'mpit_threading' failed >> ## make[3]: *** [mpit_threading] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' >> not ok 855 - ./threads/spawn/multispawn >> --- >> Directory: ./threads/spawn >> File: multispawn >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multispawn; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >> ## CC multispawn.o >> ## CCLD multispawn >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:412: recipe for target 'multispawn' failed >> ## make[3]: *** [multispawn] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >> not ok 856 - ./threads/spawn/th_taskmaster >> --- >> Directory: ./threads/spawn >> File: th_taskmaster >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build th_taskmaster; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >> ## CC th_taskmaster.o >> ## CCLD th_taskmaster >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:416: recipe for target 'th_taskmaster' failed >> ## make[3]: *** [th_taskmaster] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' >> not ok 857 - ./threads/rma/multirma >> --- >> Directory: ./threads/rma >> File: multirma >> Num-procs: >> Date: "Wed Jul 8 00:11:55 2015" >> ... >> ## Test output (expected 'No Errors'): >> ## Failed to build multirma; make[3]: Entering directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' >> ## CC multirma.o >> ## CCLD multirma >> ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to >> symbol 'pthread_create@@GLIBC_2.2.5' >> ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command >> line >> ## collect2: error: ld returned 1 exit status >> ## Makefile:416: recipe for target 'multirma' failed >> ## make[3]: *** [multirma] Error 1 >> ## make[3]: Leaving directory >> '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' >> ok 867 - ./threads/rma/multiget 2 # SKIP xfail tests disabled >> ok 858 - ./impls/mpich/mpi_t/collparmt 16 >> >> Please tell me how to fix these errors. >> >> Thanking you, >> >> Regards, >> >> Arindam >> >> >> _______________________________________________ >> 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

1 0

Re: [mpich-discuss] mpich-3.1.4: 'make testing' fails
by Junchao Zhang 08 Jul '15

08 Jul '15

Not sure if this is the reason, http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missi… You can go to one failure directory, e.g., test/mpi/threads/pt2pt, and type "make V=1 threads", and find out what is the actual link command line. --Junchao Zhang On Wed, Jul 8, 2015 at 12:00 AM, arindam ghosh <arindamgr(a)gmail.com> wrote: > Dear All, > > I'm trying to install mpich-3.1.4 in my desktop: > > CC=gcc CXX=g++ FC=gfortran F77=gfortran ./configure --prefix=/usr/local > --enable-fortran --enable-cxx 2>&1 | tee c.txt > make 2>&1 | tee m.txt > make install 2>&1 | tee mi.txt > > I'm using gcc/gfortran/g++ version 4.9.2-6. As such there is no error, but > while doing 'make testing', it shows following errors (taken from file > ./test/mpi/summary.tap), please see below: > > not ok 297 - ./pt2pt/sendflood 8 > --- > Directory: ./pt2pt > File: sendflood > Num-procs: 8 > Date: "Wed Jul 8 00:01:41 2015" > ... > ## Test output (expected 'No Errors'): > ## [mpiexec(a)localhost.localdomain] APPLICATION TIMED OUT > > not ok 333 - ./rma/getfence1 4 > --- > Directory: ./rma > File: getfence1 > Num-procs: 4 > Date: "Wed Jul 8 00:06:49 2015" > ... > ## Test output (expected 'No Errors'): > ## > ## > =================================================================================== > ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > ## = PID 12669 RUNNING AT localhost.localdomain > ## = EXIT CODE: 9 > ## = CLEANING UP REMAINING PROCESSES > ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > ## > =================================================================================== > ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) > ## This typically refers to a problem with your application. > ## Please see the FAQ page for debugging suggestions > > not ok 836 - ./threads/pt2pt/threads > --- > Directory: ./threads/pt2pt > File: threads > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build threads; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC threads.o > ## (cd ../../threads/util && make mtestthread.o) > ## make[4]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' > ## CC mtestthread.o > ## make[4]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' > ## CCLD threads > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:522: recipe for target 'threads' failed > ## make[3]: *** [threads] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 837 - ./threads/pt2pt/threaded_sr > --- > Directory: ./threads/pt2pt > File: threaded_sr > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build threaded_sr; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC threaded_sr.o > ## CCLD threaded_sr > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:518: recipe for target 'threaded_sr' failed > ## make[3]: *** [threaded_sr] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 838 - ./threads/pt2pt/alltoall > --- > Directory: ./threads/pt2pt > File: alltoall > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build alltoall; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC alltoall.o > ## CCLD alltoall > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:482: recipe for target 'alltoall' failed > ## make[3]: *** [alltoall] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 839 - ./threads/pt2pt/sendselfth > --- > Directory: ./threads/pt2pt > File: sendselfth > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build sendselfth; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC sendselfth.o > ## CCLD sendselfth > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:514: recipe for target 'sendselfth' failed > ## make[3]: *** [sendselfth] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 840 - ./threads/pt2pt/multisend > --- > Directory: ./threads/pt2pt > File: multisend > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multisend; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC multisend.o > ## CCLD multisend > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:498: recipe for target 'multisend' failed > ## make[3]: *** [multisend] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 841 - ./threads/pt2pt/multisend2 > --- > Directory: ./threads/pt2pt > File: multisend2 > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multisend2; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC multisend2.o > ## CCLD multisend2 > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:502: recipe for target 'multisend2' failed > ## make[3]: *** [multisend2] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 842 - ./threads/pt2pt/multisend3 > --- > Directory: ./threads/pt2pt > File: multisend3 > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multisend3; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC multisend3.o > ## CCLD multisend3 > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:506: recipe for target 'multisend3' failed > ## make[3]: *** [multisend3] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 843 - ./threads/pt2pt/multisend4 > --- > Directory: ./threads/pt2pt > File: multisend4 > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multisend4; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC multisend4.o > ## CCLD multisend4 > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:510: recipe for target 'multisend4' failed > ## make[3]: *** [multisend4] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 844 - ./threads/pt2pt/greq_wait > --- > Directory: ./threads/pt2pt > File: greq_wait > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build greq_wait; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC greq_wait.o > ## CCLD greq_wait > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:490: recipe for target 'greq_wait' failed > ## make[3]: *** [greq_wait] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 845 - ./threads/pt2pt/greq_test > --- > Directory: ./threads/pt2pt > File: greq_test > Num-procs: > Date: "Wed Jul 8 00:11:54 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build greq_test; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC greq_test.o > ## CCLD greq_test > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:486: recipe for target 'greq_test' failed > ## make[3]: *** [greq_test] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 846 - ./threads/pt2pt/ibsend > --- > Directory: ./threads/pt2pt > File: ibsend > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build ibsend; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > ## CC ibsend.o > ## CCLD ibsend > ## /usr/bin/ld: ibsend.o: undefined reference to symbol 'pthread_create@ > @GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:494: recipe for target 'ibsend' failed > ## make[3]: *** [ibsend] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' > not ok 847 - ./threads/comm/ctxdup > --- > Directory: ./threads/comm > File: ctxdup > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build ctxdup; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ## CC ctxdup.o > ## CCLD ctxdup > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:471: recipe for target 'ctxdup' failed > ## make[3]: *** [ctxdup] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > not ok 848 - ./threads/comm/dup_leak_test > --- > Directory: ./threads/comm > File: dup_leak_test > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build dup_leak_test; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ## CC dup_leak_test.o > ## CCLD dup_leak_test > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:479: recipe for target 'dup_leak_test' failed > ## make[3]: *** [dup_leak_test] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > not ok 849 - ./threads/comm/comm_dup_deadlock > --- > Directory: ./threads/comm > File: comm_dup_deadlock > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build comm_dup_deadlock; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ## CC comm_dup_deadlock.o > ## CCLD comm_dup_deadlock > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:463: recipe for target 'comm_dup_deadlock' failed > ## make[3]: *** [comm_dup_deadlock] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > not ok 850 - ./threads/comm/comm_create_threads > --- > Directory: ./threads/comm > File: comm_create_threads > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build comm_create_threads; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ## CC comm_create_threads.o > ## CCLD comm_create_threads > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:459: recipe for target 'comm_create_threads' failed > ## make[3]: *** [comm_create_threads] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > not ok 851 - ./threads/comm/comm_create_group_threads > --- > Directory: ./threads/comm > File: comm_create_group_threads > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build comm_create_group_threads; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ## CC comm_create_group_threads.o > ## CCLD comm_create_group_threads > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:455: recipe for target 'comm_create_group_threads' failed > ## make[3]: *** [comm_create_group_threads] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' > ok 859 - ./threads/comm/comm_idup 4 # SKIP xfail tests disabled > ok 860 - ./threads/comm/ctxidup 4 # SKIP xfail tests disabled > not ok 852 - ./threads/init/initth > --- > Directory: ./threads/init > File: initth > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build initth; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' > ## CC initth.o > ## CCLD initth > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:405: recipe for target 'initth' failed > ## make[3]: *** [initth] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' > not ok 853 - ./threads/init/initth > --- > Directory: ./threads/init > File: initth > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build initth; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' > ## CC initth.o > ## CCLD initth > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:405: recipe for target 'initth' failed > ## make[3]: *** [initth] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' > not ok 854 - ./threads/mpi_t/mpit_threading > --- > Directory: ./threads/mpi_t > File: mpit_threading > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build mpit_threading; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' > ## CC mpit_threading.o > ## CCLD mpit_threading > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:405: recipe for target 'mpit_threading' failed > ## make[3]: *** [mpit_threading] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' > not ok 855 - ./threads/spawn/multispawn > --- > Directory: ./threads/spawn > File: multispawn > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multispawn; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' > ## CC multispawn.o > ## CCLD multispawn > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:412: recipe for target 'multispawn' failed > ## make[3]: *** [multispawn] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' > not ok 856 - ./threads/spawn/th_taskmaster > --- > Directory: ./threads/spawn > File: th_taskmaster > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build th_taskmaster; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' > ## CC th_taskmaster.o > ## CCLD th_taskmaster > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:416: recipe for target 'th_taskmaster' failed > ## make[3]: *** [th_taskmaster] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' > not ok 857 - ./threads/rma/multirma > --- > Directory: ./threads/rma > File: multirma > Num-procs: > Date: "Wed Jul 8 00:11:55 2015" > ... > ## Test output (expected 'No Errors'): > ## Failed to build multirma; make[3]: Entering directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' > ## CC multirma.o > ## CCLD multirma > ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to > symbol 'pthread_create@@GLIBC_2.2.5' > ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command > line > ## collect2: error: ld returned 1 exit status > ## Makefile:416: recipe for target 'multirma' failed > ## make[3]: *** [multirma] Error 1 > ## make[3]: Leaving directory > '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' > ok 867 - ./threads/rma/multiget 2 # SKIP xfail tests disabled > ok 858 - ./impls/mpich/mpi_t/collparmt 16 > > Please tell me how to fix these errors. > > Thanking you, > > Regards, > > Arindam > > > _______________________________________________ > 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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mpich-3.1.4: 'make testing' fails
by arindam ghosh 08 Jul '15

08 Jul '15

Dear All, I'm trying to install mpich-3.1.4 in my desktop: CC=gcc CXX=g++ FC=gfortran F77=gfortran ./configure --prefix=/usr/local --enable-fortran --enable-cxx 2>&1 | tee c.txt make 2>&1 | tee m.txt make install 2>&1 | tee mi.txt I'm using gcc/gfortran/g++ version 4.9.2-6. As such there is no error, but while doing 'make testing', it shows following errors (taken from file ./test/mpi/summary.tap), please see below: not ok 297 - ./pt2pt/sendflood 8 --- Directory: ./pt2pt File: sendflood Num-procs: 8 Date: "Wed Jul 8 00:01:41 2015" ... ## Test output (expected 'No Errors'): ## [mpiexec(a)localhost.localdomain] APPLICATION TIMED OUT not ok 333 - ./rma/getfence1 4 --- Directory: ./rma File: getfence1 Num-procs: 4 Date: "Wed Jul 8 00:06:49 2015" ... ## Test output (expected 'No Errors'): ## ## =================================================================================== ## = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES ## = PID 12669 RUNNING AT localhost.localdomain ## = EXIT CODE: 9 ## = CLEANING UP REMAINING PROCESSES ## = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES ## =================================================================================== ## YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9) ## This typically refers to a problem with your application. ## Please see the FAQ page for debugging suggestions not ok 836 - ./threads/pt2pt/threads --- Directory: ./threads/pt2pt File: threads Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build threads; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC threads.o ## (cd ../../threads/util && make mtestthread.o) ## make[4]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' ## CC mtestthread.o ## make[4]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/util' ## CCLD threads ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:522: recipe for target 'threads' failed ## make[3]: *** [threads] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 837 - ./threads/pt2pt/threaded_sr --- Directory: ./threads/pt2pt File: threaded_sr Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build threaded_sr; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC threaded_sr.o ## CCLD threaded_sr ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:518: recipe for target 'threaded_sr' failed ## make[3]: *** [threaded_sr] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 838 - ./threads/pt2pt/alltoall --- Directory: ./threads/pt2pt File: alltoall Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build alltoall; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC alltoall.o ## CCLD alltoall ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:482: recipe for target 'alltoall' failed ## make[3]: *** [alltoall] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 839 - ./threads/pt2pt/sendselfth --- Directory: ./threads/pt2pt File: sendselfth Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build sendselfth; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC sendselfth.o ## CCLD sendselfth ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:514: recipe for target 'sendselfth' failed ## make[3]: *** [sendselfth] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 840 - ./threads/pt2pt/multisend --- Directory: ./threads/pt2pt File: multisend Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multisend; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC multisend.o ## CCLD multisend ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:498: recipe for target 'multisend' failed ## make[3]: *** [multisend] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 841 - ./threads/pt2pt/multisend2 --- Directory: ./threads/pt2pt File: multisend2 Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multisend2; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC multisend2.o ## CCLD multisend2 ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:502: recipe for target 'multisend2' failed ## make[3]: *** [multisend2] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 842 - ./threads/pt2pt/multisend3 --- Directory: ./threads/pt2pt File: multisend3 Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multisend3; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC multisend3.o ## CCLD multisend3 ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:506: recipe for target 'multisend3' failed ## make[3]: *** [multisend3] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 843 - ./threads/pt2pt/multisend4 --- Directory: ./threads/pt2pt File: multisend4 Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multisend4; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC multisend4.o ## CCLD multisend4 ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:510: recipe for target 'multisend4' failed ## make[3]: *** [multisend4] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 844 - ./threads/pt2pt/greq_wait --- Directory: ./threads/pt2pt File: greq_wait Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build greq_wait; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC greq_wait.o ## CCLD greq_wait ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:490: recipe for target 'greq_wait' failed ## make[3]: *** [greq_wait] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 845 - ./threads/pt2pt/greq_test --- Directory: ./threads/pt2pt File: greq_test Num-procs: Date: "Wed Jul 8 00:11:54 2015" ... ## Test output (expected 'No Errors'): ## Failed to build greq_test; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC greq_test.o ## CCLD greq_test ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:486: recipe for target 'greq_test' failed ## make[3]: *** [greq_test] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 846 - ./threads/pt2pt/ibsend --- Directory: ./threads/pt2pt File: ibsend Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build ibsend; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' ## CC ibsend.o ## CCLD ibsend ## /usr/bin/ld: ibsend.o: undefined reference to symbol 'pthread_create@ @GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:494: recipe for target 'ibsend' failed ## make[3]: *** [ibsend] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/pt2pt' not ok 847 - ./threads/comm/ctxdup --- Directory: ./threads/comm File: ctxdup Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build ctxdup; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ## CC ctxdup.o ## CCLD ctxdup ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:471: recipe for target 'ctxdup' failed ## make[3]: *** [ctxdup] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' not ok 848 - ./threads/comm/dup_leak_test --- Directory: ./threads/comm File: dup_leak_test Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build dup_leak_test; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ## CC dup_leak_test.o ## CCLD dup_leak_test ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:479: recipe for target 'dup_leak_test' failed ## make[3]: *** [dup_leak_test] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' not ok 849 - ./threads/comm/comm_dup_deadlock --- Directory: ./threads/comm File: comm_dup_deadlock Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build comm_dup_deadlock; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ## CC comm_dup_deadlock.o ## CCLD comm_dup_deadlock ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:463: recipe for target 'comm_dup_deadlock' failed ## make[3]: *** [comm_dup_deadlock] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' not ok 850 - ./threads/comm/comm_create_threads --- Directory: ./threads/comm File: comm_create_threads Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build comm_create_threads; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ## CC comm_create_threads.o ## CCLD comm_create_threads ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:459: recipe for target 'comm_create_threads' failed ## make[3]: *** [comm_create_threads] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' not ok 851 - ./threads/comm/comm_create_group_threads --- Directory: ./threads/comm File: comm_create_group_threads Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build comm_create_group_threads; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ## CC comm_create_group_threads.o ## CCLD comm_create_group_threads ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:455: recipe for target 'comm_create_group_threads' failed ## make[3]: *** [comm_create_group_threads] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/comm' ok 859 - ./threads/comm/comm_idup 4 # SKIP xfail tests disabled ok 860 - ./threads/comm/ctxidup 4 # SKIP xfail tests disabled not ok 852 - ./threads/init/initth --- Directory: ./threads/init File: initth Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build initth; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' ## CC initth.o ## CCLD initth ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:405: recipe for target 'initth' failed ## make[3]: *** [initth] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' not ok 853 - ./threads/init/initth --- Directory: ./threads/init File: initth Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build initth; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' ## CC initth.o ## CCLD initth ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:405: recipe for target 'initth' failed ## make[3]: *** [initth] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/init' not ok 854 - ./threads/mpi_t/mpit_threading --- Directory: ./threads/mpi_t File: mpit_threading Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build mpit_threading; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' ## CC mpit_threading.o ## CCLD mpit_threading ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:405: recipe for target 'mpit_threading' failed ## make[3]: *** [mpit_threading] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/mpi_t' not ok 855 - ./threads/spawn/multispawn --- Directory: ./threads/spawn File: multispawn Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multispawn; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' ## CC multispawn.o ## CCLD multispawn ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:412: recipe for target 'multispawn' failed ## make[3]: *** [multispawn] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' not ok 856 - ./threads/spawn/th_taskmaster --- Directory: ./threads/spawn File: th_taskmaster Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build th_taskmaster; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' ## CC th_taskmaster.o ## CCLD th_taskmaster ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:416: recipe for target 'th_taskmaster' failed ## make[3]: *** [th_taskmaster] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/spawn' not ok 857 - ./threads/rma/multirma --- Directory: ./threads/rma File: multirma Num-procs: Date: "Wed Jul 8 00:11:55 2015" ... ## Test output (expected 'No Errors'): ## Failed to build multirma; make[3]: Entering directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' ## CC multirma.o ## CCLD multirma ## /usr/bin/ld: ../../threads/util/mtestthread.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5' ## /lib64/libpthread.so.0: error adding symbols: DSO missing from command line ## collect2: error: ld returned 1 exit status ## Makefile:416: recipe for target 'multirma' failed ## make[3]: *** [multirma] Error 1 ## make[3]: Leaving directory '/home/arindam/software/mpich-3.1.4/test/mpi/threads/rma' ok 867 - ./threads/rma/multiget 2 # SKIP xfail tests disabled ok 858 - ./impls/mpich/mpi_t/collparmt 16 Please tell me how to fix these errors. Thanking you, Regards, Arindam _______________________________________________ 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] channel initialization failed
by Balaji, Pavan 05 Jul '15

05 Jul '15

Can you try these suggestions: https://wiki.mpich.org/mpich/index.php/Frequently_Asked_Questions#Q:_My_MPI… On 7/5/15, 10:53 PM, "Victor Rodriguez" <vm.rod25(a)gmail.com> wrote: >Hi > >I am facing the following issue on my MPICH build from source code: > >(the only change in config was disable fortran ) > >Any help is more than welcome > > >root@intel-corei7-64:~/test# mpirun -n 2 ./mpi_hello >Fatal error in MPI_Init: Other MPI error, error stack: >MPIR_Init_thread(498)..............: >MPID_Init(187).....................: channel initialization failed >MPIDI_CH3_Init(89).................: >MPID_nem_init(320).................: >MPID_nem_tcp_init(171).............: >MPID_nem_tcp_get_business_card(418): >MPID_nem_tcp_init(377).............: gethostbyname failed, >intel-corei7-64 (errno 1) > >=================================================================================== >= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES >= PID 483 RUNNING AT intel-corei7-64 >= EXIT CODE: 1 >= CLEANING UP REMAINING PROCESSES >= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES >=================================================================================== > >Source code : >https://github.com/VictorRodriguez/parallel/blob/master/mpi/hello.c > >All help is more than welcome > >Best Regards > >Victor Rodriguez >_______________________________________________ >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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channel initialization failed
by Victor Rodriguez 05 Jul '15

05 Jul '15

Hi I am facing the following issue on my MPICH build from source code: (the only change in config was disable fortran ) Any help is more than welcome root@intel-corei7-64:~/test# mpirun -n 2 ./mpi_hello Fatal error in MPI_Init: Other MPI error, error stack: MPIR_Init_thread(498)..............: MPID_Init(187).....................: channel initialization failed MPIDI_CH3_Init(89).................: MPID_nem_init(320).................: MPID_nem_tcp_init(171).............: MPID_nem_tcp_get_business_card(418): MPID_nem_tcp_init(377).............: gethostbyname failed, intel-corei7-64 (errno 1) =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 483 RUNNING AT intel-corei7-64 = EXIT CODE: 1 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== Source code : https://github.com/VictorRodriguez/parallel/blob/master/mpi/hello.c All help is more than welcome Best Regards Victor Rodriguez _______________________________________________ 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] MPI_Allreduce over multiple machines
by Gordon Reid 02 Jul '15

02 Jul '15

Hello, Yes, it fails at even 1 iteration. It also fails with separate send/recv buffers. Each Pi is able to talk to each other (ssh without password). Thanks for your replies,Gordon _______________________________________________ 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] Failed to allocate memory for an unexpected message
by Halim Amer 02 Jul '15

02 Jul '15

Hi Luiz, Please use the latest MPICH. The one you are using it very old. --Halim Abdelhalim Amer (Halim) Postdoctoral Appointee MCS Division Argonne National Laboratory On 7/2/15 1:22 PM, Luiz Carlos da Costa Junior wrote: > Hello all, > > In 2013 I had problems regarding the allocation of unexpected messages > in MPI. > After your kind assistance, I implemented a "buffer" matrix in the > receiver process, using MPI_IRECV, MPI_WAITANY and MPI_TESTANY functions > (the code snippet is attached). > > It has been working nicely since than until recently, when I faced the > same problems again: > > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186)......................: MPI_Recv(buf=0x7fffe8dd5974, > count=1, MPI_INTEGER, src=0, tag=MPI_ANY_TAG, MPI_COMM_WORLD, > status=0xd213d0) failed > MPIDI_CH3I_Progress(402)...........: > MPID_nem_mpich2_blocking_recv(905).: > MPID_nem_tcp_connpoll(1838)........: > state_commrdy_handler(1676)........: > MPID_nem_tcp_recv_handler(1564)....: > MPID_nem_handle_pkt(636)...........: > MPIDI_CH3_PktHandler_EagerSend(606): Failed to allocate memory for > an unexpected message. 261895 unexpected messages queued. > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186).............: MPI_Recv(buf=0x7fffd052b9f4, count=1, > MPI_INTEGER, src=0, tag=MPI_ANY_TAG, MPI_COMM_WORLD, > status=0xd213d0) failed > dequeue_and_set_error(596): Communication error with rank 0 > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186).............: MPI_Recv(buf=0x7fff58fe5b74, count=1, > MPI_INTEGER, src=0, tag=MPI_ANY_TAG, MPI_COMM_WORLD, > status=0xd213d0) failed > dequeue_and_set_error(596): Communication error with rank 0 > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186).............: MPI_Recv(buf=0x7fff6fae19f4, count=1, > MPI_INTEGER, src=0, tag=MPI_ANY_TAG, MPI_COMM_WORLD, > status=0xd213d0) failed > dequeue_and_set_error(596): Communication error with rank 0 > Fatal error in MPI_Recv: Other MPI error, error stack: > MPI_Recv(186).............: MPI_Recv(buf=0x7fff55bc8e74, count=1, > MPI_INTEGER, src=0, tag=MPI_ANY_TAG, MPI_COMM_WORLD, > status=0xd213d0) failed > dequeue_and_set_error(596): Communication error with rank 0 > > > I'm using the MPICH2 1.4.1p1 on a Linux x64 machine (AWS EC2 instance). > The last execution with this error had 63 working processes sending all > the output to just one receiver/writer process. > > The program and number of messages sent/received are pretty much the > same. The only thing I can imagine is that, probably, the processor is > proportionally faster than the network/IO speed today when compared to > 2013 AWS EC2 instance. In this way, probably the writer process gets > "flooded" with messages earlier. Does it make sense? > > Could you please give some advice on how to solve this issue? > > Best regards, > Luiz > > On 13 March 2014 at 16:01, Luiz Carlos da Costa Junior <lcjunior(a)ufrj.br > <mailto:[email protected]>> wrote: > > Thanks again Kenneth, I could solve using MPI_TESTANY. > Regards, Luiz > > > On 13 March 2014 15:35, Kenneth Raffenetti <raffenet(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > On 03/13/2014 12:35 PM, Luiz Carlos da Costa Junior wrote: > > Does anyone have any clue about this? > > Thanks in advance. > > > On 12 March 2014 14:40, Luiz Carlos da Costa Junior > <lcjunior(a)ufrj.br <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Dear Kenneth, > > Thanks for your quick reply. > I tested your suggestion and, unfortunately, this > approach didn't work. > > Question: when I call MPI_IPROBE it accounts also for > the messages > that were already received asynchronously? > > > That should not be the case. If a message has been matched by a > recv/irecv, MPI_Probe should not match it again. > > > > Is there any way to know, for my list of mpi_requests > (from my > MPI_IRECV's), which ones are "opened" and which ones > have messages? > > > MPI_Test will take a request as an argument and tell you whether > or not that requested operation has been completed. > > Ken > > _________________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/__mailman/listinfo/discuss > <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

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