On Thu, 2014-09-18 at 11:39 +0300, Fabian Glaser wrote:
> Hi all,
>
> We have updated all the following drivers on ReadHat 6.4 (see below),
> and still running pmemd.cuda I get a different error this time, sander
> works normally:
>
> -bash-4.1$ pmemd.cuda -O -i md.in -p RIT_6mol_h_wat.prmtop -c
> RIT_6mol_h_wat_eq5.rst -ref RIT_6mol_h_wat_eq5.rst -o
> RIT_6mol_h_wat_md1.out -x RIT_6mol_h_wat_md1.mdcrd -r
> RIT_6mol_h_wat_md1.rst
>
> pmemd.cuda: error while loading shared libraries: libcurand.so.5.5:
> cannot open shared object file: No such file or directory
>
> Is this something known to you?
> Looking into different forums, our technical people don't find the
> specific library....
The libcurand.so.5.5 library is part of the CUDA toolkit distribution.
If you run "./configure -cuda gnu", the end of the configure step you
should see a message like this:
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools.
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/home/swails/build_amber/amber/amber.sh file in your shell. Consider adding the line
test -f /home/swails/build_amber/amber/amber.sh && source /home/swails/build_amber/amber/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the
/home/swails/build_amber/amber/amber.csh file in your shell. Consider adding the line
test -f /home/swails/build_amber/amber/amber.csh && source /home/swails/build_amber/amber/amber.csh
to your startup file (e.g., ~/.cshrc)
If you have not already done so, you may need to add /opt/cuda/5.5/lib
and/or /opt/cuda/5.5/lib64 to LD_LIBRARY_PATH using the command
export LD_LIBRARY_PATH="/opt/cuda/5.5/lib:${LD_LIBRARY_PATH}" (bash, sh)
setenv LD_LIBRARY_PATH "/opt/cuda/5.5/lib:${LD_LIBRARY_PATH}" (tcsh, csh)
--------------------------------------------------------------------------------
The last piece of advice -- namely adding $CUDA_HOME/lib and/or
$CUDA_HOME/lib64 to your LD_LIBRARY_PATH -- is the root cause of your
error. On my computer, CUDA_HOME happens to be set to /opt/cuda/5.5.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 18 2014 - 05:00:03 PDT
