[Dock-fans] failure on dock.mpi

Alessandro Nascimento al.s.nascimento at gmail.com
Mon Jul 9 15:32:42 PDT 2007


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


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