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Hi
I am trying to install Meep on a Linux
cluster with Itanium-2
processors.
Since I don't have root privilege, I installed the
libraries in non-standard directories (e.g. all user libraries are installed
into .home/../meeplibs/).
I am using the following sub-program
versions:
harminv-1.3
guile-1.6.7
libctl-3.0
libtool-1.5.22
hdf5-1.6.5
szip-2.0
zlib-1.2.1
The Lapack and Blas libraries were already
installed on the cluster...
I was not able to compile the parallel version of
hdf5-1.6.5 only the serial one. However the manual mentions that there is a hack
in the parallel version of meep that makes it work with the serial
hdf5.
I was able to compile successfully configure and
compile meep. However when I run ./make check, the following error
occurs. Din anyone have a similar experience?
Does anybody has an idea how I could localize the
error? It seems to occur in some mathematical operation...
Thanks in advance for your help !!!
David Leuenberger
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% make
check Making check in src make[1]: Entering directory `/home/eecs/dleuen/software/meep-0.9/src' make check-am make[2]: Entering directory `/home/eecs/dleuen/software/meep-0.9/src' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/src' make[1]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/src' Making check in libctl make[1]: Entering directory `/home/eecs/dleuen/software/meep-0.9/libctl' make check-am make[2]: Entering directory `/home/eecs/dleuen/software/meep-0.9/libctl' make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/libctl' make[1]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/libctl' Making check in tests make[1]: Entering directory `/home/eecs/dleuen/software/meep-0.9/tests' make check-local make[2]: Entering directory `/home/eecs/dleuen/software/meep-0.9/tests' /bin/sh ../libtool --tag=CXX --mode=link mpiCC -O2 -L/home/eecs/dleuen/software/meeplibs/lib -o bench.dac bench.o ../src/libmeep_mpi.la -lhdf5 -lz -lgsl -lharminv -llapack -lcblas -lf77blas -latlas -lfftw3 -lm -L/home/eecs/dleuen/software/meeplibs/lib -L/usr/lib/gcc-lib/ia64-linux/3.3.5 -L/usr/lib/gcc-lib/ia64-linux/3.3.5/../../.. -lfftw3 -lfrtbegin -lg2c -lm -lgcc_s -lunwind libtool: link: warning: library `/home/eecs/dleuen/software/meeplibs/lib/libharminv.la' was moved. libtool: link: warning: library `/home/eecs/dleuen/software/meeplibs/lib/libharminv.la' was moved. mpiCC -O2 -o bench.dac bench.o -L/home/eecs/dleuen/software/meeplibs/lib ../src/.libs/libmeep_mpi.a /home/eecs/dleuen/software/meeplibs/lib/libhdf5.so -lz -lgsl /home/eecs/dleuen/software/meeplibs/lib/libharminv.a -L/usr/lib/gcc-lib/ia64-linux/3.3.5 -L/usr/lib/gcc-lib/ia64-linux/3.3.5/../../.. -llapack -lcblas -lf77blas -latlas /usr/lib/libfftw3.so -lfrtbegin /usr/lib/libg2c.so -lm -lgcc_s -lunwind -Wl,--rpath -Wl,/home/eecs/dleuen/software/meeplibs/lib -Wl,--rpath -Wl,/home/eecs/dleuen/software/meeplibs/lib mpirun -np 2 ./bench.dac Using MPI version 1.2, 2 processes Benchmarking with 2 processors... bench:, test, total time (s), normalized time (s/Mgs) bench:, Periodic 6x4 , 1.05078, 0.469099 bench:, Periodic 12x1, 1.28516, 0.606206 bench:, Periodic 1x12, 1.29297, 0.609891 bench:, Periodic 12x0, 6.20703, 3.08501 bench:, Periodic 12x12, 1.38281, 0.40198 p1_13870: p4_error: interrupt SIGSEGV: 11 rm_l_1_13877: (11.261719) net_send: could not write to fd=5, errno = 32 p1_13870: (11.261719) net_send: could not write to fd=5, errno = 32 touch bench.done if mpiCC -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/home/eecs/dleuen/software/meeplibs/include -O2 -MT bragg_transmission.o -MD -MP -MF ".deps/bragg_transmission.Tpo" -c -o bragg_transmission.o bragg_transmission.cpp; \ then mv -f ".deps/bragg_transmission.Tpo" ".deps/bragg_transmission.Po"; else rm -f ".deps/bragg_transmission.Tpo"; exit 1; fi /tmp/cc8IcpiQ.s: Assembler messages: /tmp/cc8IcpiQ.s:904: Warning: Additional NOP may be necessary to workaround Itanium processor A/B step errata /bin/sh ../libtool --tag=CXX --mode=link mpiCC -O2 -L/home/eecs/dleuen/software/meeplibs/lib -o bragg_transmission.dac bragg_transmission.o ../src/libmeep_mpi.la -lhdf5 -lz -lgsl -lharminv -llapack -lcblas -lf77blas -latlas -lfftw3 -lm -L/home/eecs/dleuen/software/meeplibs/lib -L/usr/lib/gcc-lib/ia64-linux/3.3.5 -L/usr/lib/gcc-lib/ia64-linux/3.3.5/../../.. -lfftw3 -lfrtbegin -lg2c -lm -lgcc_s -lunwind libtool: link: warning: library `/home/eecs/dleuen/software/meeplibs/lib/libharminv.la' was moved. libtool: link: warning: library `/home/eecs/dleuen/software/meeplibs/lib/libharminv.la' was moved. mpiCC -O2 -o bragg_transmission.dac bragg_transmission.o -L/home/eecs/dleuen/software/meeplibs/lib ../src/.libs/libmeep_mpi.a /home/eecs/dleuen/software/meeplibs/lib/libhdf5.so -lz -lgsl /home/eecs/dleuen/software/meeplibs/lib/libharminv.a -L/usr/lib/gcc-lib/ia64-linux/3.3.5 -L/usr/lib/gcc-lib/ia64-linux/3.3.5/../../.. -llapack -lcblas -lf77blas -latlas /usr/lib/libfftw3.so -lfrtbegin /usr/lib/libg2c.so -lm -lgcc_s -lunwind -Wl,--rpath -Wl,/home/eecs/dleuen/software/meeplibs/lib -Wl,--rpath -Wl,/home/eecs/dleuen/software/meeplibs/lib mpirun -np 2 ./bragg_transmission.dac Using MPI version 1.2, 2 processes meep: large error inf at freq = 0.1: T = nan instead of 0.704209 [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_22184: p4_error: : 1 make[2]: *** [bragg_transmission.done] Error 1 rm bragg_transmission.o make[2]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/tests' make[1]: *** [check-am] Error 2 make[1]: Leaving directory `/home/eecs/dleuen/software/meep-0.9/tests' make: *** [check-recursive] Error 1 |
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