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 |
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Received on Thu Feb 23 2012 - 21:00:02 PST
