Hi Wen,
> Thanks for your email help. I have made sure that the PATH is set such
> that lamboot can be executed in any directories now:
>
> echo $PATH
> --> /usr/bin:/bin:...:/opt/amber10/bin:/opt/amber10/exe
No no... The amber10/bin has to come at the beginning of your path since otherwise you run the risk of running a centrally installed copy of lamboot, say in /usr/bin instead of the copy that was used to build AMBER. Also you only need one of the amber10/bin or exe directories, they are the same thing.
> then, /test/make test.parallel.MM < /dev/null --> error below:
> export TESTsander=/exe/sander.MPI; make test.sander.BASIC
> make[1]: Entering directory `/usr/opt/amber10/test'
> cd cytosine && ./Run.cytosine
> in.md: Permission denied.
> mpirun: cannot start /exe/sander.MPI on n0 (o): No such file or directory
You probably don't have AMBERHOME set correctly - you also don't state what you set DO_PARALLEL to. In your case this should probably be set to 'mpirun -np 4'
So to run the parallel test cases you would have:
export AMBERHOME=/opt/amber10/
export PATH=$AMBERHOME/exe/:$PATH
export MPI_HOME=$AMBERHOME
export DO_PARALLEL='mpirun -np 4'
cd $AMBERHOME/test/
lamhalt (just in case any are running)
lamboot
make clean
make test.parallel
> I also tried in test/cytosine:
>
> mpirun -np 4 sander.MPI -O -i in.md -c crd.md.23 -o cytosine.out (no
> any output files were generated)
>
> Unit 6 Error on OPEN: cytosine.out
Do you have write permission to the $AMBERHOME/test/ directory? You need this in order to be able to run the tests.
All the best
Ross
/\
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
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Received on Fri Jan 09 2009 - 01:23:38 PST
