Dear Ross.
I am sorry for the early reply. I have checked it again but it 's still
found the problem but not the localhost problem any more. Here is the error
i found when i uses make test.parallel
[root.chemoinfo test]# make test.parallel
export TESTsander=/usr/local/src/amber9/exe/sander.MPI; make
test.sander.BASIC
make[1]: Entering directory `/usr/local/src/amber9/test'
cd dmp; ./Run.dmp
/usr/local/src/amber9/exe/sander.MPI: error while loading shared libraries:
liborte.so.0: cannot open shared object file: No such file or directory
./Run.dmp: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/usr/local/src/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2
To solve with this problem is difficult for me since I am new for unix
installation and I need some learning. So, if anyone can give me some advice
in practical way. It would help me very much.
Thanks.
Jitrayut
2008/5/6, jitrayut jitonnom <jitrayut.018.gmail.com>:
>
> Dear Ross Walker,
>
> Thank you for you suggestion. As you mention, I forgot to add the line
> 127.0.0.1 localhost at /etc/host so that why i got error. Besides, when
> i try sander.MPI it show a missing library file liborte.so.0 as follow:
>
> sander.MPI: error while loading shared libraries: liborte.so.0: cannot
> open shared object file: No such file or directory
>
> how can I remove this error ?
>
> Thanks.
>
> Jitrayut
>
>
> 2008/5/6, Ross Walker <ross.rosswalker.co.uk>:
> >
> > Hi Jitrayut,
> >
> >
> >
> > This is a problem with your MPI implementation. You should check the
> > documentation for the version of MPI you are using. If someone manages your
> > machine or queuing system then check with them to see what specific
> > requirements there are for running parallel jobs on your system.
> >
> >
> >
> > You should also try some of the simple mpi examples that came with the
> > mpi implementation you are using since if you can't get these to run there
> > will be no chance of getting amber to run in parallel.
> >
> >
> >
> > Note from the error message you may need to check that the line:
> >
> >
> >
> > 127.0.0.1 localhost.localdomain localhost
> >
> >
> >
> > Exists in /etc/hosts
> >
> >
> >
> > Although you should also carefully check the mpi documentation to make
> > sure there is nothing else you need to add.
> >
> >
> >
> > Good luck,
> >
> > Ross
> >
> >
> >
> > *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> > Behalf Of *jitrayut jitonnom
> > *Sent:* Monday, May 05, 2008 11:38 AM
> > *To:* amber.scripps.edu
> > *Subject:* AMBER: AMBER Parallel test error
> >
> >
> >
> > Dear Amber users,
> >
> >
> >
> > I can't complete the parallel test with the command and errors belows,
> > So, what is my problem and how to solve this problem ?
> >
> >
> >
> >
> > [root.chemoinfo test]# make test.parallel
> > export TESTsander=/usr/local/src/amber9/exe/sander.MPI; make
> > test.sander.BASIC
> > make[1]: Entering directory `/usr/local/src/amber9/test'
> > cd dmp; ./Run.dmp
> > This test not set up for parallel
> > cannot run in parallel with #residues < #pes
> > cd adenine; ./Run.adenine
> > This test not set up for parallel
> > cannot run in parallel with #residues < #pes
> > ==============================================================
> > cd cytosine; ./Run.cytosine
> > ssh: localhost: Name or service not known
> > [chemoinfo.science.cmu.ac.th:13300] ERROR: A daemon on node localhost
> > failed to start as expected.
> > [chemoinfo.science.cmu.ac.th:13300] ERROR: There may be more information
> > available from
> > [chemoinfo.science.cmu.ac.th:13300] ERROR: the remote shell (see above).
> > [chemoinfo.science.cmu.ac.th:13300] ERROR: The daemon exited
> > unexpectedly with status 255.
> > ./Run.cytosine: Program error
> > make[1]: *** [test.sander.BASIC] Error 1
> >
> >
> > Jitrayut
> >
>
>
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Received on Wed May 07 2008 - 06:07:40 PDT
