When I run make check, on the test "h5test", one of the processes shuts
down, consistently.
I have an ubuntu package install of lam-mpi as well as h5utils, and am
compiling meep-mpi 0.20.3 manually. The repository packages installed
are libhdf5-lam-1.6.5-0, libhdf5-lam-dev, liblam4, and lam4-dev.
config.log doesn't show any clues.
the configure command I used was
./configure CXX=mpic++ --prefix=/home/matthewm/usr --with-mpi
--with-libctl=/home/matthewm/usr/share/libctl
--with-blas=/usr/lib/libblas.so.3
--with-lapack=/usr/lib/liblapack.so.3
LDFLAGS="-L/usr/local/lib -L/home/matthewm/usr/lib"
CPPFLAGS="-I/usr/include -I/usr/include/mpi
-I/home/matthewm/usr/include"
LD_LIBRARY_PATH="/usr/lib:/home/matthewm/usr/lib"
make check output:
mpic++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -I/usr/include/mpi
-I/home/matthewm/usr/include -O2 -MT h5test.o -MD -MP -MF .deps/h5test.Tpo
-c -o h5test.o h5test.cpp
mv -f .deps/h5test.Tpo .deps/h5test.Po
/bin/bash ../libtool --tag=CXX --mode=link mpic++ -O2 -L/usr/local/lib
-L/home/matthewm/usr/lib -o h5test.dac h5test.o ../src/libmeep_mpi.la -lhdf5
-lz -lgsl -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3
-L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../../../lib64 -L/lib/../lib64
-L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../.. -lharminv
-llapack -lblas -lgfortranbegin -lgfortran -lm -lgcc_s -lfftw3 -lm
mpic++ -O2 -o h5test.dac h5test.o -L/usr/local/lib -L/home/matthewm/usr/lib
../src/.libs/libmeep_mpi.a -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3
-L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../../../lib64 -L/lib/../lib64
-L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../..
-L/usr/lib/gcc/x86_64-linux-gnu/3.4.6
-L/usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib
-L/usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../.. /usr/lib/libhdf5.so -lpthread
-lz -lgsl /home/matthewm/usr/lib/libharminv.a -L/lib/../lib -L/usr/lib/../lib
-lfrtbegin /usr/lib/libg2c.so -llapack -lblas -lgfortranbegin -lgfortran
-lgcc_s /usr/lib/libfftw3.so -lm
mpirun -np 4 ./h5test.dac
Using MPI version 1.2, 4 processes
Checking check_2d_tm_identity_0_plane_eps_r...
MPI_File_set_size: size argument must be the same on all processes
MPI_File_set_size: size argument must be the same on all processes
MPI_File_set_size: size argument must be the same on all processes
HDF5: infinite loop closing library
D,G,S,T,G,F,F,AC,FD,P,D,F,FD,P,FD,P,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 18986 failed on node n0 (127.0.0.1) with exit status 1.
-----------------------------------------------------------------------------
HDF5: infinite loop closing library
D,G,S,T,G,F,F,AC,FD,P,D,F,FD,P,FD,P,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD
HDF5: infinite loop closing library
D,G,S,T,G,F,F,AC,FD,P,D,F,FD,P,FD,P,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD
HDF5: infinite loop closing library
D,G,S,T,G,F,F,AC,FD,P,D,F,FD,P,FD,P,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD,FD
make[2]: *** [h5test.done] Error 1
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