AMBER: Amber8 parallel compilation problems on an OSCAR Cluster
On our system the serial version of amber8 compiles without error but
the parallel version does not compile. I've looked but cannot find the
missing libraries. I get many messages of the form:
egb.o(.text+0x1eeb): In function `genborn_mp_egb_':
: undefined reference to `mpi_allreduce_'
sander.o(.text+0x28): In function `MAIN__':
: undefined reference to `mpi_init_'sander.o(.text+0xa17): more
undefined references to `mpi_bcast_' follow
: undefined reference to `mpi_comm_free_'
sander.o(.text+0x3bdf): In function `sander_':
: undefined reference to `mpi_bcast_'
runmd.o(.text+0x8a5): In function `runmd_':
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x52): In function `startup_':
: undefined reference to `mpi_bcast_'
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x1348): In function `fsum_':
: undefined reference to `mpi_sendrecv_'
ew_force.o(.text+0x34): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0x336): In function `ewald_force_':
: undefined reference to `mpi_barrier_'
ew_force.o(.text+0x16a2): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_fft.o(.text+0xd87): In function `xy_zx_transpose_.':
: undefined reference to `mpi_recv_'
debug.o(.text+0x74a): In function `debug_frc_':
: undefined reference to `mpi_barrier_'
The following variables were set:
AMBERHOME
MKL_HOME
LAM_HOME
Fortran Compiler ==> The Intel Fortran Compiler 9.0 for Linux
MKL ==> Math Kernel Library 8.0.1
I configured with both .configure -lam ifort and .configure -lam -static
ifort
Any suggestions would be appreciated.
Best regards,
Aaron
David A. Case wrote:
> On Thu, Feb 02, 2006, HL Eastwood wrote:
>
>> I have been trying to compile the parallel version of amber but nothing
>> I do seems to work. Here is how I configured it:
>>
>>
>> /opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0xa0): In function
>> `malloc_atfork':
>> : undefined reference to `pthread_getspecific'
>>
>
> LAM requires pthreads, but its "showme" option (which is supposed to list
> its dependencies) does not.
>
> Try this: edit your config.h file and add "-lpthread" to the end of the
> LOADLIB variable.
>
> Generically, when you have a "undefined reference", you need to figure out
> which library is missing, and add that to loadlib.
>
> (caveat: I haven't run LAM in a while, having moved over to its successor,
> openMPI. But this advice or something like it should be in the right
> direction.)
>
> ...good luck...dac
>
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Received on Fri Feb 03 2006 - 06:10:09 PST
