Hello!
thanks for reply!
I didn't check the 'min.out' file so have no idea about the error message
inside. Anyhow, I re-downloaded min.in parameters file from Amber
tutorials, modified it and tried. It worked !
I think, I need more time to go over manuals (believe me manual is so
lengthy) :) and have better understanding of Amber Code.
Thanks!
Malkeet
On Tue, 20 Mar 2018 at 16:46 Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Malkeet,
>
> Did you take a look at the mdout file? It should have contained a very
> clear error message generated by the following code:
>
> Line 2277 of src/pmemd/src/mdin_ctrl_dat.F90 of a fully patched Amber 16 +
> AmberTools17
>
> #ifdef MPI
> if ( imin .ne. 0 ) then
> write(mdout, '(a)') 'CUDA (GPU): Minimization is NOT supported in &
> ¶llel on GPUs. Please use'
> write(mdout, '(a)') ' the single GPU code for
> minimizations.'
> inerr = 1
> end if
> #endif
>
> If it did not then we need to take a closer look at why that error trap is
> not triggering or is missing from your version of the source code.
>
> All the best
> Ross
>
> > On Mar 19, 2018, at 14:14, malkeet singh Bahia <msbahia17.gmail.com>
> wrote:
> >
> > one more thing, when I replaced 'min.in' file with 'heat.in' file
> > (parameters for NVT) then pmemd.cuda.MPI is working on both of my GPUs!!!
> >
> >
> > On Mon, 19 Mar 2018 at 20:17 malkeet singh Bahia <msbahia17.gmail.com>
> > wrote:
> >
> >> 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> <098159%2088501> (India, watts
> app only)
> >> +972-584553434 <+972%2058-455-3434> <+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 - 08:00:03 PDT
