try it single processor first, it is better for getting error
messages to the output file.
is the md input file the exact same as another one that
ran fine?
wendy wrote:
> I have run the tests successfully by use the DNA structure in Amber
> Tutoral 1. So I think it is not the problem of the batch system. I
> suspect the Pt Atom I added is doing something wrong.
>
> I use the real filename instead of ***. I am sorry for the confusing
> character. :)
>
> I do not have licence to run Amber on my own computer. I am using
> cluster which is using LoadLeveler V3.2 for submitting jobs. My batch
> file is listed below.
>
> Thank you very much!
>
>
> #!/bin/csh
> # . job_type = parallel
> # . node = 1
> # . tasks_per_node = 4
> # . class = q1n4g
> # . node_usage = not_shared
> # queue the program
> # . queue
> setenv hostlist hostlistfile
> setenv K5MUTE 1
> rm -f $hostlist
> echo $LOADL_PROCESSOR_LIST > templist
> awk '{gsub (/.itsc.cuhk.edu.hk/,"");print $1}' templist | tr " " "\n"
> > $hostlist
> /usr/local/bin/wipe $hostlist
> /usr/local/bin/lamboot $hostlist
> /usr/local/bin/mpirun -np 4 sander -O -i 1AIO-1D4-min.in -o
> 1AIO-1D4-min.out -c 1AIO-1D4.inpcrd -p 1AIO-1D4.prmtop -r
> 1AIO-1D4-min.rst < /dev
> /null
> /usr/local/bin/wipe $hostlist
>
>
>
>
>
>
>
> ----- Original Message ----- From: "Carlos Simmerling"
> <carlos.ilion.bio.sunysb.edu>
> To: <amber.scripps.edu>
> Sent: Monday, June 06, 2005 7:24 PM
> Subject: Re: AMBER: fail of minimization in sander
>
>
>> did you runn the tests successfully?
>>
>> did you use real filenames, or did they really say "***" in the file
>> name?
>>
>> try running locally instead of using the batch system.it may
>> be easier to see the error message.
>> have you run any other jobs successfully on the batch system?
>>
>> wendy wrote:
>>
>>> I start sander -O -i ***.in -o ***.out -c ***.inpcrd -p
>>> ***.prmtop -r ***.rst". I have try to use my ".in" input file tlike
>>> this "sander o minimize
>>> the DNA structure in tutorial 1 and get normal output file.
>>>
>>> By the way, I run sander in remote computer by sending the jobs by
>>> remote
>>> logon. And I didn't find out batch output file.
>>>
>>> Thank you !
>>>
>>>
>>>
>>> ----- Original Message ----- From: "wendy" <chenchengwen.gmail.com>
>>> To: <amber.scripps.edu>
>>> Sent: Monday, June 06, 2005 12:59 PM
>>> Subject: Re: AMBER: fail of minimization in sander
>>>
>>>
>>>> I start sander like this "sander -O -i ***.in -o ***.out -c
>>>> ***.inpcrd -p ***.prmtop -r ***.rst". I have try to use my ".in"
>>>> input file to minimize the DNA structure in tutorial 1 and get normal
>>>> output file.
>>>>
>>>> By the way, I run sander in remote computer by sending the jobs by
>>>> remote logon. And I didn't find out batch output file.
>>>>
>>>> Thank you !
>>>>
>>>>
>>>> ----- Original Message ----- From: "Bill Ross" <ross.cgl.ucsf.edu>
>>>> To: <amber.scripps.edu>
>>>> Sent: Monday, June 06, 2005 11:50 AM
>>>> Subject: Re: AMBER: fail of minimization in sander
>>>>
>>>>
>>>>>> when I begin minimization with sander, =
>>>>>> the output file contain nothing.
>>>>>
>>>>>
>>>>>
>>>>> How do you start sander? Is there any output to the screen
>>>>> or batch output file or -?
>>>>>
>>>>> Bill
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>> The AMBER Mail Reflector
>>>>> To post, send mail to amber.scripps.edu
>>>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>>>
>>>>
>>>>
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>>
>>
>>
>> --
>> ===================================================================
>> Carlos L. Simmerling, Ph.D.
>> Associate Professor Phone: (631) 632-1336
>> Center for Structural Biology Fax: (631) 632-1555
>> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
>> ===================================================================
>>
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
--
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jun 06 2005 - 17:53:00 PDT
