AMBER Archive (2009)

Subject: RE: [AMBER] mairun

From: wl2290_at_columbia.edu
Date: Thu Jan 08 2009 - 17:11:56 CST

Thank you so much Ross! - it works now!

I make a writing permission to /test/cytosine.

Wen

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> 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
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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