ahmadia
commented
11 years ago On Tue, Oct 8, 2013 at 1:12 PM, Chris Kees notifications@github.com wrote:
Writing /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py-3.4-py2.7.egg-info 0 [main] python2.7 1864 child_info_fork::abort: unable to remap cygopen-pal-5.dll to same address as parent (0xB30000) - try running rebaseall
The hint is here. Although they've significantly improved the DLLs in Cygwin, you still occasionally need to run rebaseall when you encounter these problems.
Instructions here: http://cygwin.wikia.com/wiki/Rebaseall
The good news is that this appeared to happened after you install OpenMPI, so maybe we should manually have the Cygwin user rebaseall after installation of the dependencies?
certik
cekees
Here's the build.log:
running ['bash', '../bash_script'] environment: {'ARTIFACT': '/home/Administrator/proteus/hashstack/opt/petsc4py/o7do', 'BUILD': '/home/Administrator/proteus/hashstack/bld/petsc4py-n-o7do', 'CYTHON': '/home/Administrator/proteus/hashstack/opt/cython/7jet', 'CYTHON_ID': 'cython/7jet5u55c354gkflnsevinyljxgy5pea', 'HDIST_CONFIG': '{"builder/build-temp":"/home/Administrator/proteus/hashstack/bld","sourcecache/sources":"/home/Administrator/proteus/hashstack/src","builder/artifacts":"/home/Administrator/proteus/hashstack/opt","global/cache":"/home/Administrator/proteus/hashstack/cache","builder/artifact-dir-pattern":"{name}/{shorthash}","global/db":"/home/Administrator/proteus/hashstack/db"}', 'HDIST_IMPORT': 'launcher/esqmcgomhx3s72wynnzkhlu3bdyo5mk7 python/iy6dwbrifbsqslph4s7spaf24icezkty cython/7jet5u55c354gkflnsevinyljxgy5pea lapack/pazegt5vmt47v6nrnffpgazebvsmol6y numpy/kjgrlkjjg56coeorm4bybg2mmeu7nmca openmpi/l2gwlizppqr5gnwu5nahregiwijgjnwl petsc/et3ziethn4h5ruihgzn3535quhvcwjx5', 'HDIST_IMPORT_PATHS': '/home/Administrator/proteus/hashstack/opt/launcher/esqm:/home/Administrator/proteus/hashstack/opt/python/iy6d:/home/Administrator/proteus/hashstack/opt/cython/7jet:/home/Administrator/proteus/hashstack/opt/lapack/paze:/home/Administrator/proteus/hashstack/opt/numpy/kjgr:/home/Administrator/proteus/hashstack/opt/openmpi/l2gw:/home/Administrator/proteus/hashstack/opt/petsc/et3z', 'HDIST_VIRTUALS': '', 'LAPACK': u'/usr', 'LAPACK_ID': 'lapack/pazegt5vmt47v6nrnffpgazebvsmol6y', 'LAUNCHER': '/home/Administrator/proteus/hashstack/opt/launcher/esqm', 'LAUNCHER_ID': 'launcher/esqmcgomhx3s72wynnzkhlu3bdyo5mk7', 'MPI': u'/usr', 'MPI_ID': 'openmpi/l2gwlizppqr5gnwu5nahregiwijgjnwl', 'NUMPY': '/home/Administrator/proteus/hashstack/opt/numpy/kjgr', 'NUMPY_ID': 'numpy/kjgrlkjjg56coeorm4bybg2mmeu7nmca', u'OPENMPI': u'/usr', 'PATH': '/usr/bin:/bin', 'PETSC': '/home/Administrator/proteus/hashstack/opt/petsc/et3z', 'PETSC_ID': 'petsc/et3ziethn4h5ruihgzn3535quhvcwjx5', 'PWD': '/home/Administrator/proteus/hashstack/bld/petsc4py-n-o7do/src', 'PYTHON': u'/usr', 'PYTHONHPC_PREFIX': '/home/Administrator/proteus/hashstack/opt/petsc4py/o7do', u'PYTHONPATH': u'/home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages:/home/Administrator/proteus/hashstack/opt/cython/7jet/lib/python2.7/site-packages', 'PYTHON_ID': 'python/iy6dwbrifbsqslph4s7spaf24icezkty', u'PYTHON_SITE_PACKAGES_REL': u'lib/python2.7/site-packages'} patching file src/libpetsc4py/libpetsc4py.h running build running build_src running build_py creating build creating build/lib.cygwin-1.7.25-x86_64-2.7 creating build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py copying src/help.py -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py copying src/PETSc.py -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py copying src/init.py -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py copying src/main.py -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py creating build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib copying src/lib/init.py -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib creating build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include creating build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/numpy.h -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.h -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc.h -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.PETSc_api.h -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/petsc4py.i -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/PETSc.pxd -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/init.pxd -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/include/petsc4py/init.pyx -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py copying src/lib/petsc.cfg -> build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib running build_ext PETSC_DIR: /home/Administrator/proteus/hashstack/opt/petsc/et3z PETSC_ARCH:
scalar-type: real precision: double language: CONLY compiler: /usr/bin/mpicc linker: /usr/bin/mpicc building 'PETSc' extension creating build/temp.cygwin-1.7.25-x86_64-2.7 creating build/temp.cygwin-1.7.25-x86_64-2.7/src /usr/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 -fno-strict-aliasing -ggdb -O2 -pipe -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/build=/usr/src/debug/python-2.7.5-3 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/src/Python-2.7.5=/usr/src/debug/python-2.7.5-3 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/Administrator/proteus/hashstack/opt/petsc/et3z -DINSDIR=petsc4py-3.4/ -I/home/Administrator/proteus/hashstack/opt/petsc/et3z/include -Isrc/include -I/home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c src/PETSc.c -o build/temp.cygwin-1.7.25-x86_64-2.7/src/PETSc.o In file included from /home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1728:0, from /home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15, from src/include/petsc4py/numpy.h:11, from src/petsc4py.PETSc.c:258, from src/PETSc.c:3: /home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^ /usr/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 -fno-strict-aliasing -ggdb -O2 -pipe -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/build=/usr/src/debug/python-2.7.5-3 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/src/Python-2.7.5=/usr/src/debug/python-2.7.5-3 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/home/Administrator/proteus/hashstack/opt/petsc/et3z -DINSDIR=petsc4py-3.4/ -I/home/Administrator/proteus/hashstack/opt/petsc/et3z/include -Isrc/include -I/home/Administrator/proteus/hashstack/opt/numpy/kjgr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c src/libpetsc4py.c -o build/temp.cygwin-1.7.25-x86_64-2.7/src/libpetsc4py.o /usr/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -fno-inline -O0 -shared -Wl,--enable-auto-image-base -fno-strict-aliasing -ggdb -O2 -pipe -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/build=/usr/src/debug/python-2.7.5-3 -fdebug-prefix-map=/usr/src/ports/python/python-2.7.5-3/src/Python-2.7.5=/usr/src/debug/python-2.7.5-3 -DNDEBUG -g -fwrapv -O3 -Wall -L. build/temp.cygwin-1.7.25-x86_64-2.7/src/PETSc.o build/temp.cygwin-1.7.25-x86_64-2.7/src/libpetsc4py.o -L/home/Administrator/proteus/hashstack/opt/petsc/et3z/lib -L/usr/lib/python2.7/config -Wl,-R/home/Administrator/proteus/hashstack/opt/petsc/et3z/lib -lpetsc -lpython2.7 -o build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/PETSc.dll -L/usr/lib -llapack -lblas -lX11 -Wl,-rpath,/home/Administrator/proteus/hashstack/opt/petsc/et3z/lib -L/home/Administrator/proteus/hashstack/opt/petsc/et3z/lib -lparmetis -lmetis -lpthread -Wl,-rpath,/usr/lib/gcc/x86_64-pc-cygwin/4.8.1 -L/usr/lib/gcc/x86_64-pc-cygwin/4.8.1 -Wl,-rpath,/usr/x86_64-pc-cygwin/lib -L/usr/x86_64-pc-cygwin/lib -lmpi_cxx -lstdc++ -lgdi32 -luser32 -ladvapi32 -lkernel32 -ldl -lmpi -lopen-rte -lopen-pal -lgcc_s -lshell32 writing build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/petsc.cfg running install running build running build_src running build_py running build_ext PETSC_DIR: /home/Administrator/proteus/hashstack/opt/petsc/et3z PETSC_ARCH:
scalar-type: real precision: double language: CONLY compiler: /usr/bin/mpicc linker: /usr/bin/mpicc writing build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/petsc.cfg running install_lib creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7 creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/help.py -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/numpy.h -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/PETSc.pxd -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/petsc4py.h -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/petsc4py.i -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/petsc4py.PETSc.h -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/petsc4py.PETSc_api.h -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/init.pxd -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/include/petsc4py/init.pyx -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/include/petsc4py creating /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/lib copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/petsc.cfg -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/lib copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/PETSc.dll -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/lib copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/lib/init.py -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/lib copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/PETSc.py -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/init.py -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py copying build/lib.cygwin-1.7.25-x86_64-2.7/petsc4py/main.py -> /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py byte-compiling /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/help.py to help.pyc byte-compiling /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/lib/init.py to init.pyc byte-compiling /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/PETSc.py to PETSc.pyc byte-compiling /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/init.py to init.pyc byte-compiling /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py/main.py to main.pyc writing byte-compilation script '/tmp/tmpdE4DDF.py' /usr/bin/python -O /tmp/tmpdE4DDF.py removing /tmp/tmpdE4DDF.py running install_egg_info Writing /home/Administrator/proteus/hashstack/opt/petsc4py/o7do/lib/python2.7/site-packages/petsc4py-3.4-py2.7.egg-info 0 [main] python2.7 1864 child_info_fork::abort: unable to remap cygopen-pal-5.dll to same address as parent (0xB30000) - try running rebaseall [CHLUSER1:04580] [[INVALID],INVALID] ORTE_ERROR_LOG: The system limit on number of children a process can have was reached in file /pub/devel/openmpi/openmpi-1.7.1-2/src/openmpi-1.7.1/orte/mca/ess/singleton/ess_singleton_module.c at line 360
[CHLUSER1:04580] [[INVALID],INVALID] ORTE_ERROR_LOG: The system limit on number of children a process can have was reached in file /pub/devel/openmpi/openmpi-1.7.1-2/src/openmpi-1.7.1/orte/mca/ess/singleton/ess_singleton_module.c at line 211
It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
orte_ess_init failed
--> Returned value The system limit on number of children a process can have was reached (-119) instead of ORTE_SUCCESS
It looks like MPI_INIT failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during MPI_INIT; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer):
ompi_mpi_init: orte_init failed
--> Returned "The system limit on number of children a process can have was reached" (-119) instead of "Success" (0)
[CHLUSER1:4580] * An error occurred in MPI_Init_thread [CHLUSER1:4580] * reported by process [8589934591,25769803775] [CHLUSER1:4580] * on a NULL communicator [CHLUSER1:4580] * Unknown error [CHLUSER1:4580] *\ MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[CHLUSER1:4580] *\ and potentially your MPI job)
An MPI process is aborting at a time when it cannot guarantee that all of its peer processes in the job will be killed properly. You should double check that everything has shut down cleanly.
Reason: Before MPI_INIT completed Local host: CHLUSER1
PID: 4580
Command '['bash', '../bash_script']' returned non-zero exit status 1 command failed (code=1); raising