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 <[email protected]> wrote:
Not sure if this is the reason, http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missin... 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 <[email protected]> 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'): ## [[email protected]] 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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