[Dock-fans] failure on dock.mpi

Alessandro Nascimento al.s.nascimento at gmail.com
Tue Jul 10 12:51:32 PDT 2007


Hi Scottt and Dock-fans,

using the same mpich implementation I compiled pmemd (software of
particle mesh ewald implementation in amber 9). It is running okay in
my cluster now on the 5 nodes (6 processors).
However, neither dock parallel tests or my own dock run there....
Just to mention, my machines are Intel Xeon 64 (3.4Ghz), in a Gigabit
network (I don't know if hardware issue matter in this kind of
problems).
As was mentioned, it may be a mpi problem rather than dock problems. I
just would like to know if has anyone else seen the same problem....

Thanks in advance one more time!!!!!

-alessandro

Initializing MPI Routines...
Initializing MPI Routines...
Initializing MPI Routines...
Initializing MPI Routines...
tail -f rigid.out
cluster_rmsd_threshold                                       2.0
num_clusterheads_for_rescore                                 5
num_secondary_scored_conformers_written                      4
rank_primary_ligands                                         no
rank_secondary_ligands                                       no

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Grid Score Routines...
 Reading the energy grid from grid.nrg
[cli_1]: aborting job:
Fatal error in MPI_Recv: Other MPI error, error stack:
MPI_Recv(186).............................:
MPI_Recv(buf=0x7fffffc48f1c, count=2, MPI_INT, src=0, tag=100,
MPI_COMM_WORLD, status=0x7fffffc46620) failed
MPIDI_CH3_Progress_wait(212)..............: an error occurred while
handling an event returned by MPIDU_Sock_Wait()
MPIDI_CH3I_Progress_handle_sock_event(413):
MPIDU_Socki_handle_read(633)..............: connection failure
(set=0,sock=1,errno=104:Connection reset by peer)
rank 0 in job 6  ruska_34405   caused collective abort of all ranks
  exit status of rank 0: killed by signal 11

-----------------------------------
Molecule: ZINC00000012

 Anchors:               1
 Orientations:          120000
 Conformations:         2375

 Primary Score
[2]   Exit 11                 /home/apps/mpich2/bin/mpiexec -n 5
/home/apps/dock/dock6/bin/dock6.mpi -i rigid.in -o rigid.out
</dev/null


On 7/9/07, Alessandro Nascimento <al.s.nascimento at gmail.com> wrote:
> On 7/9/07, Scott Brozell <sbrozell at scripps.edu> wrote:
> > The error above is a generic one from MPI.
> > Did you look for clues in the dock output ?
>
> Yes, I did, but there is no information. The output file is truncated.
> One molecule was docked and the file finished without any
> information....
>
> > What happens with 1, 2, or 3 numbers of processors ?
> >
>
> With 3 and 2 processors the same error occurs at the same moment
> (first molecule being docked). In a single processor (mpirun -np1
> dock.mpi ) the job is running fine (at least until this moment)... 3
> molecules have already being docked
>
> > Did the dock6/install/test/mpi quality control regression test pass ?
> > Retry it:
> > cd dock6/install/test/mpi
> > make clean
> > make
>
> I did it again and pasted below the results. I failed, but without any
> mpi messages (to my best knowledge, at least ;) !!!! )
>
> >
> > Can you run other MPI programs ?
> >
> > Scott
> >
>
> I run amber over lam-mpi. I'm not experienced with mpich2. Maybe I
> might be doing something wrong!
>
> By this poor report, can you have any idea of what might be happening?
>
> Thanks a lot, one more time!
>
>
>
> make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi'
> cd ../grid_generation && make test
> make[2]: Entering directory `/home/apps/dock/dock6/install/test/grid_generation'
> # Construct box to enclose spheres
> ../../../bin/showbox < box.in > /dev/null
> ../dockdif box.pdb.save box.pdb
> diffing box.pdb.save with box.pdb
> PASSED
> ==============================================================
> # Compute scoring grids
> ../../../bin/grid -i grid.in -o grid.out
> ../dockdif grid.out.save grid.out
> diffing grid.out.save with grid.out
> PASSED
> ==============================================================
> make[2]: Leaving directory `/home/apps/dock/dock6/install/test/grid_generation'
> make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi'
> make[1]: Entering directory `/home/apps/dock/dock6/install/test/mpi'
>
> Processing test mpi
> /home/apps/mpich2/bin/mpirun -np 2 ../../../bin/dock6.mpi -i
> mpi.dockin -o mpi.dockmpiout
> Initializing MPI Routines...
> Initializing MPI Routines...
> ../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout
> diffing mpi.dockmpiout.save with mpi.dockmpiout
> possible FAILURE:  check mpi.dockmpiout.dif
> ==============================================================
> diffing mpi_ranked.mol2.save with mpi_ranked.mol2
> possible FAILURE:  check mpi_ranked.mol2.dif
> ==============================================================
> make[1]: Leaving directory `/home/apps/dock/dock6/install/test/mpi'
>
>
> more mpi.dockmpiout.dif :
>
>
> 106c106
> <  Conformations:               3
> ---
> >  Conformations:               4
> 110a111,118
> > Molecule: ZINC01555236
> >  Anchors:             1
> >  Orientations:                50
> >  Conformations:               18
> >     Grid Score:    501606144.
> >            vdw:    501606144.
> >             es:          -10.
> > -----------------------------------
> 114,117c122,125
> <  Conformations:               6
> <     Grid Score:           21.
> <            vdw:           19.
> <             es:            1.
> ---
> >  Conformations:               7
> >     Grid Score:          -12.
> >            vdw:          -12.
> >             es:           -0.
> 123,125c131,133
> <     Grid Score:           19.
> <            vdw:           20.
> <             es:           -1.
> ---
> >     Grid Score:           30.
> >            vdw:           32.
> >             es:           -2.
> 130,133c138,141
> <  Conformations:               48
> <     Grid Score:          -15.
> <            vdw:          -13.
> <             es:           -1.
> ---
> >  Conformations:               44
> >     Grid Score:          -12.
> >            vdw:          -12.
> >             es:           -0.
> 138c146
> <  Conformations:               12
> ---
> >  Conformations:               16
> 146,148c154,156
> <  Conformations:               6
> <     Grid Score:       145519.
> <            vdw:       145519.
> ---
> >  Conformations:               2
> >     Grid Score:       168506.
> >            vdw:       168506.
> 154c162
> <  Conformations:               28
> ---
> >  Conformations:               29
>
>
>
> --
> [ ]s
>
> --alessandro
>


-- 
[ ]s

--alessandro


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