Hi All,
Is anybody testing / using PIMD? It seems to be irreparably broken in
parallel. This is for both amber10 and amber11.
I found this out by trying to test NEB:
export DO_PARALLEL='mpirun -np 8'
cd $AMBERHOME/test/neb/neb_gb/
./Run.neb_classical
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[cli_4]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
[cli_5]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5
[cli_6]: program error.
found in all output files:
Parameters:
number of beads = 8
number of classical atoms = 22
temperature (Kelvin) = 300.00
ASSERTion 'ierr.eq.0' failed in pimd_init.f at line 320.
(same error for both amber10 and amber11)
Looking at pimd_init.f line 320 it is
allocate( nrg_all(nbead), stat=ierr )
REQUIRE(ierr.eq.0)
So only trying to allocate nrg_all to be size 8 and nbead is set correct on
all nodes so I can't understand why this is broken - maybe memory corruption
elsewhere.
BTW, pimd_init.f is also pretty dangerous - e.g. just below the allocation
above we have:
allocate( springforce(3*natomCL) )
allocate( tangents(3*natomCL) )
allocate( fitgroup(natomCL) )
allocate( rmsgroup(natomCL) )
so 4 allocate statements where NO return value is checked.
It is not just NEB which is broken though. If I try to run PIMD itself:
export DO_PARALLEL='mpirun -np 8'
cd $AMBERHOME/test/
make test.sander.PIMD.MPI.partial
These all pass.
make test.sander.PIMD.MPI.full
Everything fails with invalid communicators etc. E.g.
cd PIMD/full_cmd_water/equilib && ./Run.full_cmd
Testing Centroid MD
[cli_3]: aborting job:
Fatal error in MPI_Reduce: Invalid communicator, error stack:
MPI_Reduce(843): MPI_Reduce(sbuf=0x1614130, rbuf=0x60b2330, count=28,
MPI_DOUBLE_PRECISION, MPI_SUM, root=0, MPI_COMM_NULL) failed
MPI_Reduce(714): Null communicator
[cli_1]: aborting job:
Fatal error in MPI_Reduce: Invalid communicator, error stack:
MPI_Reduce(843): MPI_Reduce(sbuf=0x1614130, rbuf=0x60b2330, count=28,
MPI_DOUBLE_PRECISION, MPI_SUM, root=0, MPI_COMM_NULL) failed
MPI_Reduce(714): Null communicator
[cli_7]: aborting job:
Fatal error in MPI_Reduce: Invalid communicator, error stack:
MPI_Reduce(843): MPI_Reduce(sbuf=0x1614130, rbuf=0x60b2330, count=28,
MPI_DOUBLE_PRECISION, MPI_SUM, root=0, MPI_COMM_NULL) failed
MPI_Reduce(714): Null communicator
[cli_5]: aborting job:
Fatal error in MPI_Reduce: Invalid communicator, error stack:
MPI_Reduce(843): MPI_Reduce(sbuf=0x1614130, rbuf=0x60b2330, count=28,
MPI_DOUBLE_PRECISION, MPI_SUM, root=0, MPI_COMM_NULL) failed
MPI_Reduce(714): Null communicator
[cli_0]: aborting job:
Fatal error in MPI_Allreduce: Other MPI error, error stack:
MPI_Allreduce(696)........................: MPI_Allreduce(sbuf=0x1717c68,
rbuf=0x1717c88, count=4, MPI_DOUBLE_PRECISION, MPI_SUM, MPI_COMM_WORLD)
failed
MPIR_Allreduce(285).......................:
MPIC_Sendrecv(161)........................:
MPIC_Wait(321)............................:
MPIDI_CH3_Progress_wait(198)..............: an error occurred while handling
an event returned by MPIDU_Sock_Wait()
MPIDI_CH3I_Progress_handle_sock_event(422):
MPIDU_Socki_handle_read(649)..............: connection failure
(set=0,sock=3,errno=104:(strerror() not found))
program error.
So it looks like it is completely broken here.
Interesting with 4cpus these test cases pass. So something is very wrong
when you use something other than 4 cpus. Additionally of course the NEB
code which used PIMD does not work.
Any suggestions? Who is maintaining the PIMD code these days and wants to
fix it and release some bugfixes?
All the best
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Sep 07 2008 - 06:07:55 PDT
