Hi,
after using Amber 9 in serial mode, recently the wish to use it in
parallel mode has come up. Our cluster is running PBS with integrated
LAM/MPI on CentOS 4.6.
When compiling Amber 9 for parallel execution, I get the following error
messages:
# make clean
# setenv MPI_HOME /usr
# setenv LD_LIBRARY_PATH /usr/lib64:/usr/lib
# ./configure -lam gfortran
[...]
# make parallel
[.. output truncated ..]
spatial_fft.o(.text+0x2187): In function `__fft__transpose':
: undefined reference to `mpi_waitall_'
spatial_fft.o(.text+0x2199): In function `__fft__transpose':
: undefined reference to `mpi_type_free_'
spatial_fft.o(.text+0x23e2): In function `__fft__ftranspose':
: undefined reference to `mpi_type_contiguous_'
spatial_fft.o(.text+0x23f4): In function `__fft__ftranspose':
: undefined reference to `mpi_type_commit_'
spatial_fft.o(.text+0x26dc): In function `__fft__ftranspose':
: undefined reference to `mpi_irecv_'
spatial_fft.o(.text+0x2977): In function `__fft__ftranspose':
: undefined reference to `mpi_isend_'
spatial_fft.o(.text+0x2bde): In function `__fft__ftranspose':
: undefined reference to `mpi_waitany_'
spatial_fft.o(.text+0x2d7b): In function `__fft__ftranspose':
: undefined reference to `mpi_waitall_'
spatial_fft.o(.text+0x2da7): In function `__fft__ftranspose':
: undefined reference to `mpi_type_free_'
qm_ewald.o(.text+0x4b10): In function `qm_ewald_setup_':
: undefined reference to `mpi_gather_'
qm2_load_params_and_allocate.o(.text+0x1ac8a): In function
`qm2_load_params_and_allocate_':
: undefined reference to `mpi_allgather_'
qm2_scf.o(.text+0x25a6): In function `qm2_scf_':
: undefined reference to `mpi_allreduce_'
qm2_scf.o(.text+0x286e): In function `qm2_scf_':
: undefined reference to `mpi_reduce_'
qm2_scf.o(.text+0x298b): In function `qm2_scf_':
: undefined reference to `mpi_bcast_'
force.o(.text+0x1469): In function `force_':
: undefined reference to `mpi_bcast_'
force.o(.text+0x1b68): In function `force_':
: undefined reference to `mpi_bcast_'
force.o(.text+0x1ba4): In function `force_':
: undefined reference to `mpi_bcast_'
force.o(.text+0x1bc6): In function `force_':
: undefined reference to `mpi_bcast_'
force.o(.text+0x1beb): more undefined references to `mpi_bcast_' follow
force.o(.text+0x23d7): In function `force_':
: undefined reference to `mpi_allgather_'
force.o(.text+0x2405): In function `force_':
: undefined reference to `mpi_allgather_'
collect2: ld returned 1 exit status
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/struct/software/linux/amber-9/src/sander'
make: *** [parallel] Error 2
#
(the full output can be seen on
http://pastebin.com/smHiJa6f. This is
the output of a repeated `make parallel`, not of the initial one).
From older postings on this list I understand, that this is due to a
compiler mismatch between MPI and Amber. BUT: Our MPI installation has
been compiled using g77 and there is no way to change that. On the
other hand, Amber 9 doesn't seem to offer a configuration to use g77 as
compiler.
Does anyone know a workaround for that or did anyone ever compile Amber
9 with g77? I could use any hint possible.
Thanks in advance
frank
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Received on Wed Sep 08 2010 - 06:00:03 PDT
