[mpich-discuss] mpich-3.1.4: 'make testing' fails
Junchao Zhang
jczhang at mcs.anl.gov
Wed Jul 8 22:42:41 CDT 2015
Not sure if this is the reason,
http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missing-from-command-line
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 at 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 at 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
>
>
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