Hi Paul,
> Attached are the test logs running the test suite on a CentOS 5.6
> machine
> with a Tesla C2070.
The gb_ala3 case is, I believe, just an issue with the random number stream being different. This can happen a lot with ntt=3 since the use of random numbers changes depending on the hardware configuration. Working around this, for test purposes, hurts performance a lot. This failure (and dhfr_ntb2_ntt3). The rest look to just be rounding differences so I think you are good. I am not sure why there are so many differences though since the test case saved outputs should be based on C2070's. Thus given the modifications you made below I would be a little wary.
> There was a bit of massaging to compile the cuda config. In fact, I had
> to
> modify PMEMD_CU_FLAGS to include the arlibs of libnetcdf.a and
> libnetcdff.a
> along with the full path to the installation path of the shared
> libraries.
I am little confused why you needed to make these changes. Unless something in AMBER Tools 1.5 has messed up the GPU compilation. AMBER should compile it's own netcdf so you should not need to make any changes here. Did you also apply all the bugfixes? - I guess I should find (invent) time to try building AMBER 11 + patches + AmberTools 1.5 myself. - What NVIDIA cuda compiler version are you using?
The development tree off of what AMBERTools 1.5 was based works fine for me and there will be a big GPU update shortly so I never bothered to test with AMBERTools 1.5 so it is possible someone messed something up with the netcdf libraries etc but I am still surprised you had to modify things to get it to build.
Does the rest of AMBER (AmberTools and AMBER CPU etc build fine in serial or parallel?) - You should really make sure all the CPU compilation and tests run fine before trying to build the GPU version.
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 Wed May 25 2011 - 10:00:04 PDT
