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> (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
>>>> 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> (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)
> _______________________________________________
> 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=
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Received on Wed Mar 14 2018 - 11:30:03 PDT
