Problems running upcxx application on Edison
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)
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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.
-
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
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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 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CMakeFiles/square_root_example.dir/src/examples/square_root/main.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/main.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/examples/square_root/main.cpp [ 34%] Linking CXX executable square_root_example /global/common/sw/cray/cnl6/ivybridge/cmake/3.8.1/gcc/6.3.0/wlv4jle/bin/cmake -E cmake_link_script CMakeFiles/square_root_example.dir/link.txt 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-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/block/SWE_WaveAccumulationBlock.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/block/SWE_WaveAccumulationBlock.cpp(87): warning #3180: unrecognized OpenMP #pragma #pragma omp parallel ^ 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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 /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/main.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/main.cpp [ 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 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-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/dist.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/orchestration/dist.cpp [ 80%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfData.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/NetCdfData.cpp.o -c /global/homes/a/apoeppl/actor-upcxx/src/applications/pond/scenario/NetCdfData.cpp [ 82%] Building CXX object CMakeFiles/pond.dir/src/applications/pond/scenario/NetCdfScenario.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 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-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
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Alexander,
I have determined that the problem stems from the link step in the output you provided.
A "normal" link line using the output ofupcxx-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'sCC
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
-
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?
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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.
-
reporter that solution did it, yes. Thank you for both of your help. :)
Best, Alex
-
reporter - changed status to resolved
see above
- Log in to comment
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