Bob,
Thanks for this explanation. Its hard to think that MPICH
developers would not have come across this problem. Surely there
are other people in the world who use Windows and data on network
drives for parallel processing problems?
Have you been in touch with MPICH to see if they are aware of the
problem and perhaps might have a work around?
It is just the pnm file that needs to be somewhere on the local
drive?
Nick
On 16/06/2011 3:53 p.m., Bauer, Robert wrote:
Nick and Andreas:
I do not have an
appropriate windows network drive available for testing, but
I think I know what is going on. On Windows, when mpiexec
is loaded and begins executing through the call to
nmmpi.bat, which is right after the statement
> Starting MPI version of nonmem
execution ...
mpiexec takes control of all ports, including
those established for WIndows network drives. Therefore
during that time, the host computer cannot communicate with
the file system on remote systems.
This does not happen
with Linux NFS file systems. Unfortunately this is a
limitation of MPICH2 itself. The manager computer must
therefore foot-print itself on a local drive. Once mpiexec
exits, then network file systems are re-established.
Nick,
I am having exactly the same
problem that you describe. Have you already found a solution?
Regards, Andreas.
 |
| Dr. Andreas Lindauer
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and in vivo ADME |
| Dept. of Pharmacokinetics
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Internacional S.A. |
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Barcelona |
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On 2/06/2011 5:03 a.m., Nick Holford wrote:
>
> Hi,
>
> I can use nmfe72 to perform an MPI run when executed from
the host
> local C: drive but when I use exactly the same files
(control stream
> file, data file, parafile) copied to a network drive I
get an error
> about the parafile being missing.
>
> I'm using NM7.2.0 on WinSrvEnt2003. I get the same error
with Intel
> 11.1 or gfortran compiled versions. Hard coding the run
directory in
> the parafile instead of using %cd% has the same error.
> nmfe72 without a parafile option works OK with the
network drive run
> directory.
>
> Has anyone else had success in getting mpi to execute
with a Windows
> network drive as the run directory?
>
> nmfe72 theopd.ctl theopd.lst "-parafile=mpi2.pnm"
> [...]
>
> USING PARALLEL PROFILE mpi2.pnm
>
> MPI TRANSFER TYPE SELECTED
>
> Starting MPI version of nonmem execution ...
>
> PARAFILE NOT FOUND: mpi2.pnm
>
>
> ============= mpi2.pnm ========================
> $DEFAULTS
> [nodes]=2
> $GENERAL
> NODES=[nodes] PARSE_TYPE=2 PARSE_NUM=200 TIMEOUTI=600
TIMEOUT=1000
> PARAPRINT=0 TRANSFER_TYPE=1
> $COMMANDS
> 1:mpiexec -wdir "%cd%" -hosts 1 localhost 1
<<nmexec>> %*
> 2-[nodes]:-wdir "%cd%\worker{#-1}" -hosts 1 localhost 1
<<nmexec>>
> $DIRECTORIES
> 1:NONE ; FIRST DIRECTORY IS THE COMMON DIRECTORY
> 2-[nodes]:worker{#-1} ; NEXT SET ARE THE WORKER
directories
>
> ============= nmmpi.bat created by nmfe72
========================
> mpiexec -wdir "%cd%" -hosts 1 localhost 1 nonmem.exe %*
: ^
> -wdir "%cd%\worker1" -hosts 1 localhost 1 nonmem.exe
>
>
>
>
>
>
> --
> Nick Holford, Professor Clinical Pharmacology
> Dept Pharmacology& Clinical Pharmacology
> University of Auckland,85 Park Rd,Private Bag
92019,Auckland,New Zealand
> tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23
53
> email:[email protected]
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology& Clinical Pharmacology
University of Auckland,85 Park Rd,Private Bag
92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
email:[email protected]
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
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Nick Holford, Professor Clinical Pharmacology
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University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New Zealand
tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53
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