[AMBER] Issues compiling Amber with CUDA support

From: Sivy, Shawn <ssivy.tcnj.edu>
Date: Wed, 24 Aug 2016 14:47:10 -0400


I’m hoping someone could help me with compiling the Amber software on our
systems. I have an older model Intel Xeon 5500 server with an NVIDIA
Quadro NVS 510 (GK107) GPU card in it. I’ve successfully compiled the
serial and parallel versions of Amber using gcc 4.8.5. I’m trying to
compile the serial CUDA version now. The “make install” builds without
errors, but the “make test” gets “possible failures” on 9 comparisons.
I’ve tried building with CUDA 7.5 and CUDA 8.0 resulting in the same
failures. Does anyone have a suggestion on what to try next? I’m assuming
“make test” needs to run without any errors. I suspect maybe the GPU I’m
using doesn’t have the precision that a Tesla or recent GTX card has.

Below is some sample output from the “make install” and the resulting log
and diff files. The complete contents of the log and diff files can be
found at https://www.tcnj.edu/~ssivy/amberlogs/

Thanks in advance for any assistance.


make[2]: Leaving directory `/opt/tcnjhpc/amberdev/amber16/test'
130 file comparisons passed
9 file comparisons failed
0 tests experienced errors
Test log file saved as /opt/tcnjhpc/amberdev/amber16/
Test diffs file saved as /opt/tcnjhpc/amberdev/amber16/
make[1]: Leaving directory `/opt/tcnjhpc/amberdev/amber16/test'

Example from log file:

cd cellulose/ && ./Run.cellulose_nvt DPFP /opt/tcnjhpc/amberdev/amber16/
diffing mdout.cellulose_nvt.GPU_DPFP with mdout.cellulose_nvt
possible FAILURE: check mdout.cellulose_nvt.dif

Example from diff file:

possible FAILURE: check mdout.cellulose_nvt.dif



< Etot = 5.8651 EKtot = 273.2191 EPtot =

> Etot = 5.8650 EKtot = 273.2191 EPtot =

### Maximum absolute error in matching lines = 1.00e-04 at line 212 field 3

### Maximum relative error in matching lines = 1.71e-05 at line 212 field 3


[image: The College of New Jersey] <http://tcnj.pages.tcnj.edu/> Shawn Sivy
HPC System Administrator
School of Science
PO Box 7718 Ewing, NJ 08628-0718
ssivy.tcnj.edu <email.tcnj.edu>
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Received on Wed Aug 24 2016 - 12:00:03 PDT
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