Re: [AMBER] error while installing AMBER for GPU

From: malkeet singh Bahia <msbahia17.gmail.com>
Date: Mon, 19 Mar 2018 18:11:23 +0000

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
‚Äč
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 Mon Mar 19 2018 - 11:30:02 PDT
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