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Problems running upcxx application on Edison

Issue #172 resolved
Alexander Pöppl created an issue

I am having some issues running my actor-based shallow water code on Edison. I tried building the code using the intel environment and the new upcxx release. I loaded the following modules:

gcc/7.3.0 upcxx/2018.9.0-6.0.4-intel-18.0.1.163 cray-netcdf-hdf5parallel cmake/3.8.1

I grab the needed PPFLAGS, LDFLAGS and LIBS from the upcxx-meta script and use cmake to generate a Makefile:

CC=cc CXX=CC cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_RELEASE=1 -DNOWRITE=1 -DNETCDF_INCLUDE_DIR=$CRAY_NETCDF_DIR/intel/16.0/include/ -DNETCDF_LIBRARY=$CRAY_NETCDF_DIR/intel/16.0/lib/libnetcdf.a <path/to/CMakeFile>

resulting in the following compiler call:

/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/ActorGraph.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/ActorGraph.cpp

this yields an executable, but running it fails with 

apoeppl@nid00079:~/actor-upcxx/build> GASNET_BACKTRACE=1 upcxx-run -np 1 square_root_example 3
*** FATAL ERROR: Failed to mmap 528 KB for intra-node shared memory communication, errno=Bad file descriptor(9)
NOTICE: We recommend linking the debug version of GASNet to assist you in resolving this application issue.
[0] Invoking GDB for backtrace...
[0] /usr/bin/gdb -nx -batch -x /tmp/gasnet_WapRCU '/global/u1/a/apoeppl/actor-upcxx/build/square_root_example' 46802
[0] [Thread debugging using libthread_db enabled]
[0] Using host libthread_db library "/lib64/libthread_db.so.1".
[0] 0x00000000005b8e2a in __waitpid (pid=46803, stat_loc=stat_loc@entry=0x7fffffff3920, options=options@entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
[0] #0  0x00000000005b8e2a in __waitpid (pid=46803, stat_loc=stat_loc@entry=0x7fffffff3920, options=options@entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
[0] #1  0x000000000086125d in do_system (line=0xc98340 <cmd.1882.0> "/usr/bin/gdb -nx -batch -x /tmp/gasnet_WapRCU '/global/u1/a/apoeppl/actor-upcxx/build/square_root_example' 46802") at ../sysdeps/posix/system.c:148
[0] #2  0x00000000004759b7 in gasneti_bt_gdb ()
[0] #3  0x000000000047c6fa in _gasneti_print_backtrace_ifenabled ()
[0] #4  0x000000000047f180 in gasneti_fatalerror ()
[0] #5  0x000000000048b77f in gasneti_pshm_init ()
[0] #6  0x000000000044cb9b in gex_Client_Init_GASNET_201890SEQpshmFASTnodebugnotracenostatsnodebugmallocnosrclines ()
[0] #7  0x0000000000438087 in upcxx::init() ()
[0] #8  0x0000000000417d86 in main ()
srun: error: nid00079: task 0: Aborted

the same code works in my development environment on kotten. I also get the same issue when running my sample applications. I realize this is probably something I am missing on my end, but I'm not exactly sure where to start looking.

My code is available at https://bitbucket.org/apoeppl/actor-upcxx

Comments (9)

  1. Dan Bonachea

    Hi Alexander -

    Edison is a cross-compilation environment, so the UPC++ executables should not be run directly from the frontend node - you need to run them inside a SLURM batch script or SLURM interactive batch session, to launch the job on reserved compute nodes. Are you doing this?

    You can find more information in the Edison user documentation

  2. Alexander Pöppl reporter

    Yes, I ran it in an interactive session on the debug queue (salloc -q debug -N 1). upcxx-run and srun yielded the same result.

  3. Paul Hargrove

    Alexander,

    I have just tried to reproduce on Edison with the hello-world application from example/prog-guide
    I don't see the problem, which is a failure at startup (and thus not likely relate to the application code).

    I may help if you can try again with UPCXX_CODEMODE=debug, which will provide more detail in the backtrace, as well as adding some assertions that may find issues like bad arguments.

    I am suspicious that cmake or some other aspect of your build might be a contributing factor, perhaps preventing linking of the proper Cray support libraries. You showed the compile line but not the link. I am not sure what I am looking for, but the complete build output might be helpful in sorting out what is happening.

    -Paul

  4. Alexander Pöppl reporter

    Here's the full output (long). I am also guessing that there's something going wrong during the build process. But I don't know how or where.

    apoeppl@edison05:~/actor-upcxx/build> make   
Scanning dependencies of target actorlib
[  2%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/AbstractInPort.cpp.o
[  5%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/AbstractOutPort.cpp.o
[  8%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/Actor.cpp.o
[ 11%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/ActorGraph.cpp.o
[ 14%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/ActorRegistration.cpp.o
[ 17%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/config.cpp.o
^Cmake[2]: *** wait: No child processes.  Stop.
make[2]: *** Waiting for unfinished jobs....
make[2]: *** wait: No child processes.  Stop.
CMakeFiles/Makefile2:141: recipe for target 'CMakeFiles/actorlib.dir/all' failed
make[1]: *** [CMakeFiles/actorlib.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Interrupt

apoeppl@edison05:~/actor-upcxx/build> make clean
apoeppl@edison05:~/actor-upcxx/build> make VERBOSE=1
/global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -H/global/homes/a/apoeppl/actor-upcxx -B/global/homes/a/apoeppl/actor-upcxx/build --check-build-system CMakeFiles/Makefile.cmake 0
/global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_progress_start /global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles /global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/global/u1/a/apoeppl/actor-upcxx/build'
make -f CMakeFiles/actorlib.dir/build.make CMakeFiles/actorlib.dir/depend
make[2]: Entering directory '/global/u1/a/apoeppl/actor-upcxx/build'
cd /global/homes/a/apoeppl/actor-upcxx/build && /global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_depends "Unix Makefiles" /global/homes/a/apoeppl/actor-upcxx /global/homes/a/apoeppl/actor-upcxx /global/homes/a/apoeppl/actor-upcxx/build /global/homes/a/apoeppl/actor-upcxx/build /global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/actorlib.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/global/u1/a/apoeppl/actor-upcxx/build'
make -f CMakeFiles/actorlib.dir/build.make CMakeFiles/actorlib.dir/build
make[2]: Entering directory '/global/u1/a/apoeppl/actor-upcxx/build'
[  2%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/AbstractInPort.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/AbstractInPort.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/AbstractInPort.cpp
[  5%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/AbstractOutPort.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/AbstractOutPort.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/AbstractOutPort.cpp
[  8%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/Actor.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/Actor.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/Actor.cpp
[ 11%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/ActorGraph.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/ActorGraph.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/ActorGraph.cpp
[ 14%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/ActorRegistration.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/ActorRegistration.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/ActorRegistration.cpp
[ 17%] Building CXX object CMakeFiles/actorlib.dir/src/actorlib/config.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DACTORLIB_UPCXX_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CODEMODE="" -DACTORLIB_UPCXX_GASNET_CONDUIT="" -DACTORLIB_UPCXX_INSTALLATION=/global/common/edison/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163 -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG -fPIC   -std=c++14 -o CMakeFiles/actorlib.dir/src/actorlib/config.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/actorlib/config.cpp
[ 20%] Linking CXX static library libactorlib.a
/global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -P CMakeFiles/actorlib.dir/cmake_clean_target.cmake
/global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_link_script CMakeFiles/actorlib.dir/link.txt --verbose=1
/usr/bin/ar qc libactorlib.a  CMakeFiles/actorlib.dir/src/actorlib/AbstractInPort.cpp.o CMakeFiles/actorlib.dir/src/actorlib/AbstractOutPort.cpp.o CMakeFiles/actorlib.dir/src/actorlib/Actor.cpp.o CMakeFiles/actorlib.dir/src/actorlib/ActorGraph.cpp.o CMakeFiles/actorlib.dir/src/actorlib/ActorRegistration.cpp.o CMakeFiles/actorlib.dir/src/actorlib/config.cpp.o
/usr/bin/ranlib libactorlib.a
make[2]: Leaving directory '/global/u1/a/apoeppl/actor-upcxx/build'
[ 20%] Built target actorlib
make -f CMakeFiles/square_root_example.dir/build.make CMakeFiles/square_root_example.dir/depend
make[2]: Entering directory '/global/u1/a/apoeppl/actor-upcxx/build'
cd /global/homes/a/apoeppl/actor-upcxx/build && /global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_depends "Unix Makefiles" /global/homes/a/apoeppl/actor-upcxx /global/homes/a/apoeppl/actor-upcxx /global/homes/a/apoeppl/actor-upcxx/build /global/homes/a/apoeppl/actor-upcxx/build /global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/square_root_example.dir/DependInfo.cmake --color=
Dependee "/global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/square_root_example.dir/DependInfo.cmake" is newer than depender "/global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/square_root_example.dir/depend.internal".
Dependee "/global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/global/homes/a/apoeppl/actor-upcxx/build/CMakeFiles/square_root_example.dir/depend.internal".
Scanning dependencies of target square_root_example
make[2]: Leaving directory '/global/u1/a/apoeppl/actor-upcxx/build'
make -f CMakeFiles/square_root_example.dir/build.make CMakeFiles/square_root_example.dir/build
make[2]: Entering directory '/global/u1/a/apoeppl/actor-upcxx/build'
[ 22%] Building CXX object CMakeFiles/square_root_example.dir/src/examples/square_root/SinkActor.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/square_root_example.dir/src/examples/square_root/SinkActor.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/examples/square_root/SinkActor.cpp
[ 25%] Building CXX object CMakeFiles/square_root_example.dir/src/examples/square_root/SourceActor.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/square_root_example.dir/src/examples/square_root/SourceActor.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/examples/square_root/SourceActor.cpp
[ 28%] Building CXX object CMakeFiles/square_root_example.dir/src/examples/square_root/SquareRootActor.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -std=c++14 -o CMakeFiles/square_root_example.dir/src/examples/square_root/SquareRootActor.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/examples/square_root/SquareRootActor.cpp
[ 31%] Building CXX object CMakeFiles/square_root_example.dir/src/examples/square_root/main.cpp.o
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/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(87): warning #3180: unrecognized OpenMP #pragma
  #pragma omp parallel
          ^

/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(93): warning #3180: unrecognized OpenMP #pragma
    #pragma omp for
            ^

/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(99): warning #3948: simd pragma has been deprecated, and will be removed in a future release.  Please refer to release notes for details and recommended alternatives
        #pragma simd
                ^

/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(133): warning #3180: unrecognized OpenMP #pragma
    #pragma omp for
            ^

/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(170): warning #3180: unrecognized OpenMP #pragma
    #pragma omp critical
            ^

/global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(204): warning #3180: unrecognized OpenMP #pragma
    #pragma omp parallel for
            ^

[ 65%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/main.cpp.o
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[ 68%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorDistributor.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DLOOP_OPENMP -DNDEBUG -DNOWRITE -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -DVECTORIZE -DWAVE_PROPAGATION_SOLVER=3 -DWRITENETCDF -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/global/homes/a/apoeppl/actor-upcxx/src/applications/pond -I/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.6/intel/16.0/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -fstrict-aliasing -fargument-noalias -O3 -march=native -std=c++14 -o CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorDistributor.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/orchestration/ActorDistributor.cpp
[ 71%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorOrchestrator.cpp.o
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[ 74%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/orchestration/SimpleActorDistributor.cpp.o
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[ 77%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/orchestration/dist.cpp.o
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[ 80%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfData.cpp.o
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[ 82%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfScenario.cpp.o
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[ 85%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/scenario/SimulationArea.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DLOOP_OPENMP -DNDEBUG -DNOWRITE -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -DVECTORIZE -DWAVE_PROPAGATION_SOLVER=3 -DWRITENETCDF -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/global/homes/a/apoeppl/actor-upcxx/src/applications/pond -I/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.6/intel/16.0/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -fstrict-aliasing -fargument-noalias -O3 -march=native -std=c++14 -o CMakeFiles/pond.dir/src/applications/pond/scenario/SimulationArea.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/scenario/SimulationArea.cpp
[ 88%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/util/Configuration.cpp.o
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[ 91%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/util/Logger.cpp.o
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[ 94%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/writer/NetCdfWriter.cpp.o
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[ 97%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/writer/VtkWriter.cpp.o
/opt/cray/pe/craype/2.5.14/bin/CC  -DGASNET_CONDUIT_ARIES -DGASNET_SEQ -DLOOP_OPENMP -DNDEBUG -DNOWRITE -DUPCXX_ASSERT_ENABLED=0 -DUPCXX_BACKEND=1 -DUPCXX_BACKEND_GASNET_SEQ=1 -DUPCXX_MPSC_QUEUE_ATOMIC=1 -DVECTORIZE -DWAVE_PROPAGATION_SOLVER=3 -DWRITENETCDF -D_GNU_SOURCE=1 -I/global/homes/a/apoeppl/actor-upcxx/src -I/global/homes/a/apoeppl/actor-upcxx/src/applications/pond -I/opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.6/intel/16.0/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/include/aries-conduit -I/usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/include  -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   -fstrict-aliasing -fargument-noalias -O3 -march=native -std=c++14 -o CMakeFiles/pond.dir/src/applications/pond/writer/VtkWriter.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/writer/VtkWriter.cpp
[100%] Linking CXX executable pond
/global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_link_script CMakeFiles/pond.dir/link.txt --verbose=1
/opt/cray/pe/craype/2.5.14/bin/CC   -O3 -wd177 -wd279 -wd1572 -O3 -DNDEBUG   CMakeFiles/pond.dir/src/applications/pond/actor/SimulationActor.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/BlockCommunicator.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/SWE_Block.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp.o CMakeFiles/pond.dir/src/applications/pond/main.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorDistributor.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorOrchestrator.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/SimpleActorDistributor.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/dist.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfData.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfScenario.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/SimulationArea.cpp.o CMakeFiles/pond.dir/src/applications/pond/util/Configuration.cpp.o CMakeFiles/pond.dir/src/applications/pond/util/Logger.cpp.o CMakeFiles/pond.dir/src/applications/pond/writer/NetCdfWriter.cpp.o CMakeFiles/pond.dir/src/applications/pond/writer/VtkWriter.cpp.o  -o pond /opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.6/intel/16.0/lib/libnetcdf.a libactorlib.a /usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/upcxx.O3.gasnet_seq.aries/lib/libupcxx.a /usr/common/ftg/upcxx/2018.9.0/ivb/intel/PrgEnv-intel-6.0.4-18.0.1.163/gasnet.opt/lib/libgasnet-aries-seq.a /opt/cray/pe/pmi/5.0.13/lib64/libpmi.a /opt/cray/ugni/6.0.14.0-6.0.7.0_23.1__gea11d3d.ari/lib64/libugni.a /opt/cray/udreg/2.3.2-6.0.7.0_33.18__g5196236.ari/lib64/libudreg.a /opt/cray/xpmem/2.2.15-6.0.7.1_5.8__g7549d06.ari/lib64/libxpmem.a /usr/lib64/libhugetlbfs.a /usr/lib64/libm.a 
/opt/cray/pe/hdf5-parallel/1.10.1.1/INTEL/16.0/lib/libhdf5_parallel.a(H5PL.o): In function `H5PL_load':
H5PL.c:(.text+0x612): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
make[2]: Leaving directory '/global/u1/a/apoeppl/actor-upcxx/build'
[100%] Built target pond
  5. Paul Hargrove

    Alexander,

    I have determined that the problem stems from the link step in the output you provided.
    A "normal" link line using the output of upcxx-meta LIBS contains pairs of -L[DIR] and -l[LIB] options which have apparently been transformed into full paths to the corresponding .a files. This is defeating some "magic" performed by Cray's CC compiler wrapper (with respect to the hugetlbfs library, IIRC).

    When I apply the same transformation to a build of the hello-world example, I get the same errors you have reported.

    -Paul

  6. Alexander Pöppl reporter

    Paul,

    It seems like the find_library functionality of CMake performs that transformation. So essentially the that feature of CMake has an issue/is incompatible with the Cray compiler wrapper. I initially tried adding the libraries manually within CMake, but that didn't really work.

    The only solution for me is to write a manual Makefile then, I guess?

  7. Dan Bonachea

    The only solution for me is to write a manual Makefile then, I guess?

    Alexander,

    Note the new release of upcxx has a upcxx compiler wrapper that can be used as the compiler and/or linker that automatically adds the include paths and system libraries required by GASNet and UPC++. Simple example from the programming guide:

    <upcxx-install-path>/bin/upcxx -O hello-world.cpp

    So for your code a command something like the following should work:

    upcxx   -O   CMakeFiles/pond.dir/src/applications/pond/actor/SimulationActor.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/BlockCommunicator.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/SWE_Block.cpp.o CMakeFiles/pond.dir/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp.o CMakeFiles/pond.dir/src/applications/pond/main.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorDistributor.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/ActorOrchestrator.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/SimpleActorDistributor.cpp.o CMakeFiles/pond.dir/src/applications/pond/orchestration/dist.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfData.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfScenario.cpp.o CMakeFiles/pond.dir/src/applications/pond/scenario/SimulationArea.cpp.o CMakeFiles/pond.dir/src/applications/pond/util/Configuration.cpp.o CMakeFiles/pond.dir/src/applications/pond/util/Logger.cpp.o CMakeFiles/pond.dir/src/applications/pond/writer/NetCdfWriter.cpp.o CMakeFiles/pond.dir/src/applications/pond/writer/VtkWriter.cpp.o  -o pond /opt/cray/pe/netcdf-hdf5parallel/4.4.1.1.6/intel/16.0/lib/libnetcdf.a libactorlib.a

    Hopefully this way CMake never needs to see the system libraries that it's botching.

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Assignee
–
Type
bug
Priority
major
Status
resolved
Component
Examples
Milestone
2019.03.31 release
Version
2018.9.0 release
Votes
0
Watchers
2
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