Look at the last line of min.out file, for info what happend.
It seems you have a space between & and cntrl keyword, which is incorrect.
Best,
Maciej
On 20.03.2018 11:13, malkeet singh Bahia wrote:
> Hi !
>
> I got it but following is also not running
>
> /private/gnss/AMBER_instal_files_malkeet/amber14/bin/pmemd.cuda -O -i min.in -o
> min.out -p pro.top -c pro.crd -r min.rst -inf min.mdinfo > resulted in STOP
> PMEMD Terminated Abnormally!
>
> min.in file contains
>
> Minimize
> & cntrl
> imin=1,
> ntx=1,
> irest=0,
> maxcyc=2000,
> ncyc=1000,
> ntpr=100,
> ntwx=0,
> cut=8.0,
> /
>
> On Tue, 20 Mar 2018 at 09:13 Luka Bilić <Luka.Bilic.irb.hr> wrote:
>
>> It might be that your input is not correct for the job setup.
>> If your pmemd and sander worked fine with some inputs, but are
>> suddenly failing with another inputs that means that you need to go
>> keyword by keyword and check it with amber manual (
>> http://ambermd.org/doc12/Amber16.pdf ).
>>
>> Somewhere there might be some keyword that either has wrong value,
>> calls for something that cannot be done or may even be completely
>> missing but is required for your type of MD/min job.
>>
>> Take some time with it.
>> It's a lot of data to process but after several weeks you'll be
>> running simulations and robbing your colleagues of "dem free gpu
>> slots" like a cowboy outlaw in the wild west.
>>
>> But first you need careful input revision and many trial and errors :)
>>
>> If your jobs fail on everything! Even on checked and prepared inputs
>> from Amber Tutorials... then there might be something else that's
>> happening. (But you said it worked on some things so I think it's just
>> your input setup)
>>
>> Yours,
>> Luka
>>
>>
>>
>> Citiram malkeet singh Bahia <msbahia17.gmail.com>:
>>
>>> ---------- Forwarded message ---------
>>> From: malkeet singh Bahia <msbahia17.gmail.com>
>>> Date: Mon, 19 Mar 2018, 20:17
>>> Subject: Re: [AMBER] error while installing AMBER for GPU
>>> To: <david.case.rutgers.edu>, AMBER Mailing List <amber.ambermd.org>
>>>
>>>
>>> Hello!
>>>
>>> I am getting the following problems while using
>>>
>>> mpirun -np 2
>>> /private/gnss/AMBER_instal_files_malkeet/amber14/bin/pmemd.cuda.MPI -O -i
>>> min.in -o min.out -p pro.top -c pro.crd -r min.rst -inf min.mdinfo >
>>> resulted in "application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0"
>>> while
>>> and /private/gnss/AMBER_instal_files_malkeet/amber14/bin/pmemd.cuda -O -i
>>> min.in -o min.out -p pro.top -c pro.crd -r min.rst -inf min.mdinfo >
>>> resulted in STOP PMEMD Terminated Abnormally!
>>>
>>> min.in file contains
>>>
>>> Minimize
>>> & cntrl
>>> imin=1,
>>> ntx=1,
>>> irest=0,
>>> maxcyc=2000,
>>> ncyc=1000,
>>> ntpr=100,
>>> ntwx=0,
>>> cut=8.0,
>>> /
>>>
>>>
>>> Could you please suggest the reasons and solutions?
>>>
>>> Thanks!
>>> MAlkeet
>>>
>>>
>>>
>>>
>>> On Wed, 14 Mar 2018 at 22:07 David A Case <david.case.rutgers.edu>
>> wrote:
>>>> On Wed, Mar 14, 2018, malkeet singh Bahia wrote:
>>>>> I didn't find any *.dif file. Below are make test results
>>>>>
>>>>> 62 file comparisons passed
>>>>> 35 file comparisons failed
>>>>> 0 tests experienced errors
>>>> Right below this output, there should be pointers to where all the logs
>>>> are: they will be under $AMBERHOME/logs, and labelled by the type of
>>>> test and the date.
>>>>
>>>> Note that just saying you typed "make test" is not very helpful, since
>>>> we would need to know what the most recent flags to configure were. The
>>>> expected Amber workflow is this:
>>>>
>>>> ./configure gnu (say)
>>>> make install #installs serial programs
>>>> make test # tests serial programs
>>>>
>>>> ./configure -cuda gnu
>>>> make install #installs cuda programs
>>>> make test # tests cuda programs
>>>>
>>>> Be *sure* that serial cuda programs are working for you before
>>>> proceeding to parallel cuda programs. And try to ensure that you really
>>>> need parallel cuda capability before trying to install it. Unless you
>>>> have good hardware, and a need to run a single simulation at the fastest
>>>> possible speed, you will probably find that installing parallel cuda
>>>> programs are not very helpful.
>>>>
>>>> ....dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>> --
>>> Thanks & Warm Regards
>>>
>>>
>>> Malkeet S. Bahia, PhD
>>> Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
>>> PBC Indo-Israel Post-doc fellowship
>>> Dept. of Chemistry, Building 211, Room no. 211
>>> Bar Ilan University, Ramat Gan, 5290002, ISRAEL
>>>
>>> Mobile: +91-9815988501 <098159%2088501> (India, watts app only)
>>> +972-584553434 <+972%2058-455-3434> (Israel number)
>>> --
>>> Thanks & Warm Regards
>>>
>>>
>>> Malkeet S. Bahia, PhD
>>> Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
>>> PBC Indo-Israel Post-doc fellowship
>>> Dept. of Chemistry, Building 211, Room no. 211
>>> Bar Ilan University, Ramat Gan, 5290002, ISRAEL
>>>
>>> Mobile: +91-9815988501 <098159%2088501> (India, watts app only)
>>> +972-584553434 <+972%2058-455-3434> (Israel number)
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
--
*******************************************
Maciej S. Maciejczyk, PhD
Division of Physics and Biophysics
Faculty of Food Sciences
University of Warmia and Mazury in Olsztyn
ul. Oczapowskiego 4
10-719 Olsztyn
Poland
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Received on Tue Mar 20 2018 - 05:30:04 PDT
