thanks!
I didn't find any *.dif file. Below are make test results
62 file comparisons passed
35 file comparisons failed
0 tests experienced errors
Do they indicate anything about the installation error? Is my Amber
installation ok to proceed further for running simulation?
Thanks!
On Wed, 14 Mar 2018 at 20:15 Roitberg,Adrian E <roitberg.ufl.edu> wrote:
> you need to check mdout.dhfr.ntr1.dif like the message says and see how
> large the difference between the template and your run is
>
> Sent from my iPad
>
> > On Mar 14, 2018, at 14:11, malkeet singh Bahia <msbahia17.gmail.com>
> wrote:
> >
> > 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
> >>>>>>>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=te8pCMcMaXPMR8_Rovae-8FQOgEBQChyAK0w_vwnVq4&s=xHCqNYNp6O3Pruw3GCzin54t_-PTvMJANlzzLJ6MQ8k&e=
> >>>>>>>>
> >>>>>>> --
> >>>>>>> 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>
> <098159%2088501> (India,
> >>> watts app only)
> >>>>>>> +972-584553434 <+972%2058-455-3434> <+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>
> <098159%2088501> (India,
> >>> watts app only)
> >>>>>> +972-584553434 <+972%2058-455-3434> <+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>
> <098159%2088501> (India,
> >>> watts app only)
> >>>>> +972-584553434 <+972%2058-455-3434> <+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)
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=te8pCMcMaXPMR8_Rovae-8FQOgEBQChyAK0w_vwnVq4&s=xHCqNYNp6O3Pruw3GCzin54t_-PTvMJANlzzLJ6MQ8k&e=
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=te8pCMcMaXPMR8_Rovae-8FQOgEBQChyAK0w_vwnVq4&s=xHCqNYNp6O3Pruw3GCzin54t_-PTvMJANlzzLJ6MQ8k&e=
> >>>
> >> --
> >> 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
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=te8pCMcMaXPMR8_Rovae-8FQOgEBQChyAK0w_vwnVq4&s=xHCqNYNp6O3Pruw3GCzin54t_-PTvMJANlzzLJ6MQ8k&e=
> _______________________________________________
> 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 Wed Mar 14 2018 - 12:00:04 PDT
