Hi Ross,
Yes, I forgot to mention that I applied all the bug fixes you mention below -- any thoughts on what's happening?
On Feb 23, 2012, at 10:37 PM, Ross Walker wrote:
> Hi Ram,
>
>> As for the bug fixes, I decided to start from scratch and install a
>> fresh copy of AmberTools and Amber. I was able again to correctly
>> install the serial and parallel versions without errors (except for a
>> few discrepancies in the test scripts). Unfortunately I get a new set
>> of errors when trying to compile the CUDA binaries, that look like
>> this:
>
> But did you take that fresh copy and apply all the bugfixes for AMBER and
> AMBERTools from the website? - The bugfixes are required for compatibility
> beyond cuda 3.2. The procedure is:
>
> 1) tar xvjf Amber11.tar.bz2
> 2) tar xvjf AmberTools-1.5.tar.bz2
> 3) export AMBERHOME=/path_to/amber11
> 4) cd $AMBERHOME
> 5) wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
> 6) patch -p0 < bugfix.all
> 7) rm -f bugfix.all
> 8) wget http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2
> 9) wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x
> 10) chmod 700 apply_bugfix.x
> 11) ./apply_bugfix.x $AMBERHOME/bugfix.all
> 12) cd $AMBERHOME/AmberTools/src/
> 13) ./configure gnu
> 14) make
> 15) cd ../../
> 16) cd src
> 17) make serial
>
> At this point you have the serial (non-GPU) versions of AMBERTools and AMBER
>
> built. Best to test them at this point.
>
> 18) cd $AMBERHOME/AmberTools/test/
> 19) make test
>
> Check the test logs to see if everything worked.
>
> 20) cd $AMBERHOME/test
> 21) make test
>
> Again check the test logs to see if everything worked.
>
> Now we can build the serial GPU code.
>
> 22) cd $AMBERHOME/src/
> 23) make clean
> 24) cd $AMBERHOME/AmberTools/src/
> 25) make clean
> 26) ./configure -cuda gnu
> 27) cd ../../
> 28) cd src
> 29) make cuda
>
> Hopefully this time it should build correctly.
>
> 30) cd ../test
> 31) make test.cuda
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
> _______________________________________________
> 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
Received on Thu Feb 23 2012 - 21:00:02 PST
