Hi Michael,
This error means that the files required for AMBER 14 are not in your
AMBERHOME directory. I suspect that only the AmberTools14.tar.bz2 file was
extracted prior to commencing the installation. For simplicity I would
start again from the beginning with:
cd $AMBERHOME
cd ../
rm -rf amber14
tar xvjf AmberTools14.tar.bz2
tar xvjf Amber14.tar.bz2 (be sure to do both of these untar commands)
cd amber14
./configure gnu (say yes to the updates)
make install
make test (optional)
make clean
./configure -mpi gnu
make install
export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
make test (optional)
make clean
unset $DO_PARALLEL
./configure -cuda gnu
make install
make test (optional)
make clean
./configure -cuda -mpi gnu (only needed if you want to run across 2 GPUs
in a single job at the same time).
make install
export DO_PARALLEL='mpirun -np 2' (or whatever syntax your mpi uses)
make test (optional)
make clean
unset $DO_PARALLEL
Good luck,
All the best
Ross
On 12/30/14, 1:49 PM, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:
>Dear Adrian,
>
>Yes our university group has academic license for amber14,
>so I have both amber14 and amber tools.
>The details about my workstation:
>
>cpu:Intel(R) Core(TM) i7-3820 CPU . 3.60GHz
>gpu: GeForce GTX TITAN
>cuda: version 6.0
>
>linux:
>
> Ubuntu 14.04.1 LTS
>Release: 14.04
>Codename: trusty
>
>The problem is that I used the commands for amber14 GPU installation
>the same as you have suggested but
>I have received an error message
>after running the commands:
>
>./config -cuda gnu
>make install
>
>
>
>shokhen.quant-lnx:~/amber14$ make install
>cd AmberTools/src && make install
>make[1]: Entering directory `/home/shokhen/amber14/
>AmberTools/src'
>AmberTools14 has no CUDA-enabled components
>(cd ../../src && make cuda )
>make[2]: Entering directory `/home/shokhen/amber14/src'
>make[2]: *** No rule to make target `cuda'. Stop.
>make[2]: Leaving directory `/home/shokhen/amber14/src'
>make[1]: [cuda] Error 2 (ignored)
>make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>==============================================================
>/home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>This is expected if you do not have Amber14.
>==============================================================
>
>All the best,
>Michael
>
>
>
>
>*****************************
>Michael Shokhen, PhD
>Associate Professor
>Department of Chemistry
>Bar Ilan University,
>Ramat Gan, 52900
>Israel
>email: michael.shokhen.gmail.com
>email: shokhen.mail.biu.ac.il
>
>
>On Tue, Dec 30, 2014 at 10:56 PM, Adrian Roitberg <roitberg.ufl.edu>
>wrote:
>
>> Michael
>>
>> Try looking at
>> http://jswails.wikidot.com/installing-amber14-and-ambertools14
>>
>> It has really good instructions for installation.
>>
>> Now, one question that Ross asked is important. Do you have a license
>> for amber14? Basically, did you buy it?
>>
>> Ambertools is free now, and you can download it from the amber web site.
>> Amber14 itself requires license. Ross asked his question because the
>> error you got when installing it what one should expect if amber14 is
>> not present anywhere.
>>
>> Adrian
>>
>> On 12/30/14 3:51 PM, Michael Shokhen wrote:
>> > Dear Ross,
>> >
>> > You are expert in AMBER.
>> > In contrast, as I wrote in my previous email I am a new AMBER user.
>> > I read in AMBER14 website that it includes full GPU support in PMEMD.
>> > I need to install PMEMD on my linux ubuntu workstation (see details
>>in my
>> > previous
>> > email). Unfortunately, I didn't find any relevant protocol in AMBER14
>> User
>> > Gide,
>> > neither in the AMBER website for the PMEMD installation at a
>>workstation.
>> > I would appreciate your help in such protocol.
>> >
>> > Many thanks,
>> > Michael
>> >
>> >
>> > *****************************
>> > Michael Shokhen, PhD
>> > Associate Professor
>> > Department of Chemistry
>> > Bar Ilan University,
>> > Ramat Gan, 52900
>> > Israel
>> > email: michael.shokhen.gmail.com
>> > email: shokhen.mail.biu.ac.il
>> >
>> >
>> > On Tue, Dec 30, 2014 at 10:11 PM, Ross Walker <ross.rosswalker.co.uk>
>> wrote:
>> >> Hi Michael,
>> >>
>> >> AmberTools does not have any programs that utilize GPUs. Do you have
>>a
>> >> full copy of AMBER 14 or just AmberTools since the error message
>>implies
>> >> the later?
>> >>
>> >> All the best
>> >> Ross
>> >>
>> >>
>> >> On 12/30/14, 11:31 AM, "Michael Shokhen" <michael.shokhen.biu.ac.il>
>> >> wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> I am a new Amber user.
>> >>> I have succeeded with installation of amber14 regular variant,
>> >>> but unfortunately failed to install amber14 with GPU CUDA.
>> >>> I would appreciate if somebody can send me a set of commands
>> >>> relevant for amber14 with GPU CUDA installation on my Linux
>> workstation.
>> >>>
>> >>> Thank you,
>> >>> Michael
>> >>>
>> >>> See below the details about my workstation,
>> >>> and system report about failed installation
>> >>>
>> >>> I have received an error message
>> >>> after running the commands:
>> >>>
>> >>> ./config -cuda gnu
>> >>> make install
>> >>>
>> >>>
>> >>>
>> >>> shokhen.quant-lnx:~/amber14$ make install
>> >>> cd AmberTools/src && make install
>> >>> make[1]: Entering directory `/home/shokhen/amber14/AmberTools/src'
>> >>> AmberTools14 has no CUDA-enabled components
>> >>> (cd ../../src && make cuda )
>> >>> make[2]: Entering directory `/home/shokhen/amber14/src'
>> >>> make[2]: *** No rule to make target `cuda'. Stop.
>> >>> make[2]: Leaving directory `/home/shokhen/amber14/src'
>> >>> make[1]: [cuda] Error 2 (ignored)
>> >>> make[1]: Leaving directory `/home/shokhen/amber14/AmberTools/src'
>> >>> ==============================================================
>> >>> /home/shokhen/amber14/src/Makefile not found, or -noamber was set.
>> >>> This is expected if you do not have Amber14.
>> >>> ==============================================================
>> >>>
>> >>> *****************************
>> >>> Michael Shokhen, PhD
>> >>> Associate Professor
>> >>> Department of Chemistry
>> >>> Bar Ilan University,
>> >>> Ramat Gan, 52900
>> >>> Israel
>> >>> email: michael.shokhen.gmail.com
>> >>> email: shokhen.mail.biu.ac.il
>> >>> _______________________________________________
>> >>> 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
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Dec 30 2014 - 14:30:02 PST
