Re: amber-developers: Extra Points Calculation

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Tue, 11 Nov 2008 14:38:26 -0500 (EST)

The test script is as follows:

--------- runsim -------------
#!/bin/csh -f

set sander = $AMBERHOME/exe/sander.MPI

/bin/rm -f min

cat > min <<EOF
Initial Minimization of solvent + ions
 &cntrl
  imin = 1,
  maxcyc = 10,
  ncyc = 5,
  ntb = 1,
  ntr = 0,
  cut = 8.0,
  ntpr = 1, ntx = 1,
  icfe=1,klambda=6,clambda=0.5
 /
EOF

cat > groups_md <<EOF
-O -i min -p prmtop1 -c inpcrd -o min.out.p1 -r min.rst.p1 -x
mdcrd_02.traj.p1
-O -i min -p prmtop2 -c inpcrd -o min.out.p2 -r min.rst.p2 -x
mdcrd_02.traj.p2
EOF

mpiexec -np 4 $sander -ng 2 -groupfile groups_md < /dev/null || goto error
------------------------------------

The error message is as follows: 

----
[yildirim.malatya02 ~/l_0.5]# runsim
  Running multisander version of sander amber9
     Total processors =            4
     Number of groups =            2
     Looping over processors:
        WorldRank is the global PE rank
        NodeID is the local PE rank in current group
        Group     =            0
        WorldRank =            0
        NodeID    =            0
        Group     =            1
        WorldRank =            2
        NodeID    =            0
        WorldRank =            1
        NodeID    =            1
        WorldRank =            3
        NodeID    =            1
[cli_1]: [cli_3]: aborting job:
Fatal error in MPI_Bcast: Message truncated, error stack:
MPI_Bcast(784).........................: MPI_Bcast(buf=0xe63888, count=1,
MPI_INTEGER, root=0, comm=0x84000000) f
ailed
MPIR_Bcast(198)........................:
MPIDI_CH3U_Post_data_receive_found(163): Message from rank 0 and tag 2
truncated; 144408 bytes received but buffe
r size is 4
aborting job:
Fatal error in MPI_Bcast: Message truncated, error stack:
MPI_Bcast(784).........................: MPI_Bcast(buf=0xe63888, count=1,
MPI_INTEGER, root=0, comm=0x84000000) f
ailed
MPIR_Bcast(198)........................:
MPIDI_CH3U_Post_data_receive_found(163): Message from rank 0 and tag 2
truncated; 144408 bytes received but buffe
r size is 4
rank 3 in job 1  malatya02_48011   caused collective abort of all ranks
  exit status of rank 3: return code 1
rank 1 in job 1  malatya02_48011   caused collective abort of all ranks
  exit status of rank 1: return code 1
error: label not found.
--------------
mpich2version is
[yildirim.malatya02 ~/l_0.5]# mpich2version
Version:           1.0.5
Device:            ch3:sock
Configure Options: '--prefix=/programs/mpich2'
'CC=/opt/intel/cce/10.0.026/bin/icc'
'CXX=/opt/intel/cce/10.0.026/bin/icpc'
CC:  /opt/intel/cce/10.0.026/bin/icc
CXX: /opt/intel/cce/10.0.026/bin/icpc
F77: /opt/intel/fce/10.0.026/bin/ifort
F90: ifort
---------------
Thanks.
On Tue, 11 Nov 2008, Volodymyr Babin wrote:
> On Tue, November 11, 2008 14:18, Ilyas Yildirim wrote:
> > While the subject has minimization in it, I have a quick question: Is it
> > possible to use more than 2 CPUs in Thermodynamic Integration
> > minimization? I could never use 4 CPUs when I wanted to do minimization
> > with icfe set to either 1 or 2. Everything works fine with 2 CPUs, but not
> > with 4 CPUs in the minimization process. I use mpich2 and amber9.
>
> Could you provide more details on what happens with > 2 cpus?
> An easily runnable test-case that shows the problem would also be
> very helpful.
>
> Have a great day,
>   Volodymyr
>
>
-- 
  Ilyas Yildirim, Ph.D.
  ---------------------------------------------------------------
  = Hutchison Hall B#10          - Department of Chemistry      =
  =                              - University of Rochester      =
  = 585-275-6766 (office)        -                              =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------
Received on Fri Dec 05 2008 - 14:29:25 PST
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