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
>
--
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)
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Received on Tue Mar 20 2018 - 03:30:03 PDT
