Volodymyr,
I have the most updated version of runmin.f file. The .diff file you sent
me has only one change in it; committed by Case.
You said that you produced the same error, right? Are you sure that we can
use more than 2 CPUs in the amber9 minimization? Thanks.
On Tue, 11 Nov 2008, Volodymyr Babin wrote:
> Ilyas,
>
> this has been fixed in newer versions by the following commits:
>
> revision 9.3
> date: 2006/08/17 23:10:58; author: case; state: Exp; lines: +1 -0
> initialize gmin to 1 to avoid divide by zero
>
> ----------------------------
> revision 9.8
> date: 2007/10/24 22:46:00; author: steinbrt; state: Exp; lines: +19 -33
> TBS: Extended and cleaned up Softcore potentials for TI
>
> Please find the .diff attached (I did not test it throughly though).
>
> Have a great night,
> Volodymyr
>
> On Tue, November 11, 2008 14:38, Ilyas Yildirim wrote:
> > 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/ =
> > ---------------------------------------------------------------
> >
> >
>
--
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 - 14:32:19 PST
