sorry for lot of questioning!
While running make test the first failure is of "cd myoglobin" but there is
no such directory in /test.
any comments?
On Wed, 14 Mar 2018 at 20:53 malkeet singh Bahia <msbahia17.gmail.com>
wrote:
> 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 <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 - 12:30:02 PDT
