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 (India, watts app only)
> +972-584553434 (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 (India, watts app only)
> +972-584553434 (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
Received on Tue Mar 20 2018 - 00:30:02 PDT
