one more thing when i ran 'make test' some test are failed and one example
is below
cd dhfr/ && ./Run.dhfr.ntr1 SPFP
/private/gnss/AMBER_instal_files_malkeet/amber14/include/netcdf.mod
diffing mdout.dhfr.ntr1.GPU_SPFP with mdout.dhfr.ntr1
possible FAILURE: check mdout.dhfr.ntr1.dif
Is it fine with the installation?
best,
msb
On Wed, 14 Mar 2018 at 20:14 malkeet singh Bahia <msbahia17.gmail.com>
wrote:
> Hi!
>
> Is P100 GPU supported for Amber14?
>
> I installed AMBER in my machine (as below). Thanks for your help.
> ./configure gnu
> make install
> ./configure -mpi gnu
> make install
> ./configure -cuda gnu
> make install
> ./configure -mpi -cuda gnu
> make install (is it OK?)
>
> Thanks!
> Malkeet
>
> On Wed, 14 Mar 2018 at 17:49 Dr. M. Shahid <mohammad.shahid.gmail.com>
> wrote:
>
>> Hi,
>>
>> As far as I remember, you need to first compile the serial binaries, then
>> the mpi, then the cuda and at the end cuda-mpi (if you have multiple
>> GPUs).
>> good luck...
>>
>> --
>> Shahid.
>>
>>
>> On Wed, Mar 14, 2018 at 3:53 PM, malkeet singh Bahia <msbahia17.gmail.com
>> >
>> wrote:
>>
>> > Hello!
>> >
>> > I installed AMBER using ./configure -cuda -mpi gnu
>> > when i ran make test, some of the test are failed, does it has
>> something to
>> > deal with installation?
>> > Moreover I am able to see only few files in the bin folder. Do i need to
>> > compile AMber without -cuda and -mpi flag as well to get the CPU related
>> > programs?
>> >
>> > Thanks!
>> >
>> >
>> > On Tue, 13 Mar 2018 at 20:37 malkeet singh Bahia <msbahia17.gmail.com>
>> > wrote:
>> >
>> > > in case of solely CUDA install, i tried adding following
>> > (CUDA_HOME/lib64
>> > > as per your suggestion) to my source file but still shared library
>> error
>> > > exists.
>> > > setenv CUDA_HOME /usr/local/cuda-6.5/
>> > > setenv LD_LIBRARY_PATH /usr/local/cuda-6.5/lib64
>> > >
>> > >
>> > > On Tue, 13 Mar 2018 at 20:34 malkeet singh Bahia <msbahia17.gmail.com
>> >
>> > > wrote:
>> > >
>> > >> one more thing, Do I need to modify some paths in my source file now?
>> > >>
>> > >>
>> > >> On Tue, 13 Mar 2018 at 20:14 malkeet singh Bahia <
>> msbahia17.gmail.com>
>> > >> wrote:
>> > >>
>> > >>> Thanks!
>> > >>> I tried using ./configure_mpich from AMBERHOME/AMBERTOOL/////src and
>> > and
>> > >>> as per suggestions installed mpich in this directory. then running
>> > >>> configure script created a bin folder in AMBERHOME. bin directory
>> > contain
>> > >>> ~20 files like mpi** . Now what to do?
>> > >>> should i go back to amberhome and use./configure -mpi gnu ?
>> > >>>
>> > >>> Many thanks in advance!
>> > >>>
>> > >>> On Tue, 13 Mar 2018 at 18:34 Daniel Roe <daniel.r.roe.gmail.com>
>> > wrote:
>> > >>>
>> > >>>> On Tue, Mar 13, 2018 at 12:14 PM, malkeet singh Bahia
>> > >>>> <msbahia17.gmail.com> wrote:
>> > >>>> > Than I tried with mpi flag and getting same error as earlier (i'm
>> > >>>> working
>> > >>>> > on it)
>> > >>>>
>> > >>>> The issue with your MPI build is with your compilers, as Dave
>> > >>>> previously indicated. Your MPI compiler is configure for Intel, and
>> > >>>> your Intel license appears expired. One workaround is to download
>> and
>> > >>>> unpack Mpich or Openmpi in $AMBERHOME/AmberTools/src and then use
>> > >>>> 'configure_mpich' or 'configure_openmpi' to build your own MPI
>> (which
>> > >>>> will live in $AMBERHOME).
>> > >>>>
>> > >>>> > when i used -cuda flag the installation is complete but in make
>> > test,
>> > >>>> it
>> > >>>> > showed 'error while loading shared libraries:libcurand.so.6.5:
>> > cannot
>> > >>>> open
>> > >>>> > the shared object file.
>> > >>>> >
>> > >>>> > I have added few paths in the .cshrc file, please have a look on
>> > this
>> > >>>> and
>> > >>>> > tell me if anything needed to be changed
>> > >>>> >
>> > >>>> > setenv CUDA_HOME /usr/local/cuda-6.5/
>> > >>>> > setenv LD_LIBRARY_PATH
>> > >>>> >
>> "/usr/local/cuda-6.5/targets/x86_64-linux/lib/:${LD_LIBRARY_PATH}"
>> > >>>> > setenv PATH "${path}:${CUDA_HOME}/bin"
>> > >>>>
>> > >>>> Try $CUDA_HOME/lib64 instead.
>> > >>>>
>> > >>>> -Dan
>> > >>>>
>> > >>>> _______________________________________________
>> > >>>> 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> <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> <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 <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 (India, watts app only)
+972-584553434 (Israel number)
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Received on Wed Mar 14 2018 - 11:30:03 PDT
