AMBER Archive (2006)

Subject: AMBER: RE: Intel Compiler.

From: Priti Hansia (priti_at_mbu.iisc.ernet.in)
Date: Tue May 09 2006 - 12:12:18 CDT

Yes, it was a typo and stupidly I didnt even check it before posting the
error !

I have corrected it:

echo $AMBERHOME gives /software/amber9

However, after doing this I ran the test again and got the following:

export TESTsander=/software/amber9/exe/sander.MPI; make test.sander.BASIC
make[1]: Entering directory `/software/amber9/test'
cd dmp; ./Run.dmp
mpirun must be used to launch all MPI applications
  ./Run.dmp: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/software/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2

Can someone tell me how to launch mpirun ?

Thanks,
-Priti

> Dear Priti
>
>>export TESTsander=/software/amebr9/exe/sander.MPI; make test.sander.BASIC
>
> Is the amebr9 in the error message here a typo in the email or the real
> message? I suspect that you may have a typo in your definition of
> AMBERHOME.
> Try:
>
> echo $AMBERHOME
>
> Does it show /software/amebr9 or /software/amber9
>
> If it points to the wrong path correct it, then logout and try logging
> back
> in and running the test again.
>
> Alternatively if it was simply a typo in the email then the error may be
> due
> to the fact that some nodes can't see the executable. When running in
> parallel 'ALL' nodes need to be able to see the executable in the 'SAME'
> place. I.e. you will likely have to make sure that the executable
> directory
> is on an NFS path that is mounted by all nodes.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | 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 |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>> -----Original Message-----
>> From: Priti Hansia [mailto:priti_at_mbu.iisc.ernet.in]
>> Sent: Tuesday, May 09, 2006 08:57
>> To: Ross Walker
>> Subject: RE: Intel Compiler.
>>
>>
>> Thanks Ross. I would do that.
>>
>> Following is the error I got while testing parallel version:
>>
>> [root_at_genomics test]# make test.parallel
>> export TESTsander=/software/amebr9/exe/sander.MPI; make
>> test.sander.BASIC
>> make[1]: Entering directory `/software/amber9/test'
>> cd dmp; ./Run.dmp
>> /software/amebr9/exe/sander.MPI: Command not found.
>> ./Run.dmp: Program error
>> make[1]: *** [test.sander.BASIC] Error 1
>> make[1]: Leaving directory `/software/amber9/test'
>> make: *** [test.sander.BASIC.MPI] Error 2
>>
>> I have checked that 'sander.MPI' IS there in
>> /software/amber9/exe path.
>> But I dont know why it says '/software/amebr9/exe/sander.MPI:
>> Command not
>> found' !
>>
>> Regards,
>> -Priti
>>
>>
>>
>> > Hi Priti,
>> >
>> > What was the error you saw? I haven't seen the message turn
>> up yet on the
>> > mailing list. I am glad you got it working in serial though.
>> >
>> > This is fine, don't worry about that. I just didn't want it
>> getting around
>> > that I used my premier account to give you the file since I have a
>> > developers account with Intel and they wouldn't be very
>> happy. But yes
>> > feel free to hand that file around and just tell people you
>> logged into
>> > premier.intel.com to get it.
>> >
>> > All the best
>> > Ross
>> >
>> > /\
>> > \/
>> > |\oss Walker
>> >
>> > | HPC Consultant and Staff Scientist |
>> > | 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 |
>> >
>> > Note: Electronic Mail is not secure, has no guarantee of
>> delivery, may not
>> > be read every day, and should not be used for urgent or
>> sensitive issues.
>> >
>> >
>> >
>>
>>
>
>
>

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