AMBER Archive (2006)

Subject: Re: AMBER: Parallel version of Amber: error message

From: Lihua Wang (lhw_at_broyde.nyu.edu)
Date: Mon Feb 06 2006 - 14:27:40 CST

this has to do with your mpich setup.

usually mpich uses rsh but rsh is not avaible on a lot of systems for
security reasons. as an alternative, mpich can use ssh for automatic log
in. you have to generate key pairs to enable that.

On Mon, 6 Feb 2006, snoze pa wrote:

> Date: Mon, 6 Feb 2006 15:19:15 -0500
> From: snoze pa <snoze.pa_at_gmail.com>
> To: Lihua Wang <lhw_at_broyde.nyu.edu>
> Subject: Re: AMBER: Parallel version of Amber: error message
>
> Thanks Mr Wang for your help. Now the problem is gone but now another
> problem with rsh.
>
> make test.sander | tee test.sander.parallel.out
> 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
> connect to address XXX.XXX.. port 544: Connection refused
> Trying krb4 rsh...
> connect to address XXX.XXX.. port 544: Connection refused
> trying normal rsh (/usr/bin/rsh)
> curie.utmb.edu: Connection refused
> p0_16668: p4_error: Child process exited while making connection to remote
> process on curie.utmb.edu: 0
> forrtl: error (69): process interrupted (SIGINT)
> p0_16668: (33.104658) net_send: could not write to fd=4, errno = 32
> ./Run.cytosine: Program error
> make: *** [test.sander.no_lmod] Error 1
>
> any help in this regards
> snoze
>
>
> when I use all three intel links together then again I am getting following
> error message as shown b4.
> /home/amber8/test/cytosine/../../exe/sander: error while loading shared
> libraries: libvml.so: cannot open shared object file: No such file or
> directory
>
> On 2/6/06, Lihua Wang <lhw_at_broyde.nyu.edu> wrote:
>>
>> maybe try add the library path of icc and ifort to the LD_LIBRARY_PATH
>> variable: sth like:
>>
>> export
>>
>> LD_LIBRARY_PATH='/opt/intel/mkl721/lib/64:/opt/intel_cc_80/lib:/opt/intel_fc_80/lib'
>>
>>
>>
>>
>>
>>
>>>>> but when I use
>>>>>
>>>>> export LD_LIBRARY_PATH='/usr/intel/mkl/8.0.1/lib/32:'
>>>>> then it is giving me following error message
>>>>> cd cytosine; ./Run.cytosine
>>>>> /home/amber8/test/cytosine/../../exe/sander: error while loading
>>>>> shared libraries: libimf.so: cannot open shared object file: No such
>>>>> file or directory
>>>>> ./Run.cytosine: Program error
>>>>> make: *** [test.sander.no_lmod] Error 1
>>>>>
>>>>>
>>>>> How to compile amber in parrallel using mpich, any help will be highly
>>>>> appreciated. LAM is not working in my case so I am using mpich.
>>>>> thanks in advance
>>>>> snoze
>>>>
>>>>
>>>> -----------------------------------------------------------------------
>>>> The AMBER Mail Reflector
>>>> To post, send mail to amber_at_scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>>
>>>
>>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu