From: Kenneth Huang (kennethneltharion_at_gmail.com)
Date: Tue Jul 26 2016 - 08:09:12 CDT
I haven't used cuda 5.0 before, but I remember that the newer versions of
NAMD (2.10 and up?) need at least cuda 6.0 to properly run, which I'm
assuming you're running.
Best,
Kenneth
On Tue, Jul 26, 2016 at 1:56 AM, krishna <krishnendu39_at_gmail.com> wrote:
> Dear All
> We have gpu k20 and I want to use 1gpu and 16 cpu for md run. I'm using
> script below. I set cuda path correctly.
>
> #!/bin/bash
> #SBATCH --job-name=krishna
> #SBATCH --nodes=1
> #SBATCH --ntasks-per-node=1
> #SBATCH --gres=gpu:1
> #SBATCH --begin=now
> #SBATCH -e slurm.err
> #SBATCH -v
>
> cd $SLURM_SUBMIT_DIR
> echo "CWD:" $SLURM_SUBMIT_DIR
> echo "NODELIST:" $SLURM_JOB_NODELIST
>
> source /etc/profile
> export PATH=/opt/cuda-5.0/bin:$PATH
> export
> LD_LIBRARY_PATH=/opt/cuda-5.0/lib64:/opt/cuda-5.0/lib:$LD_LIBRARY_PATH
> # SET FOR NUMBER OF CORES(THREADS) TO USE
> export OMP_NUM_THREADS=16
>
> charmrun +p16 ++local namd2 +setcpuaffinity +idlepoll npt30.inp > npt30.out
>
>
> But the error message:
> namd2: error while loading shared libraries: libcudart.so.4: cannot open
> shared object file: No such file or directory
>
> Please help
>
>
> *********************************************
> Regards
> Krishnendu Bera
> PG Student
> Department of Bioinformatics
> Central University of South Bihar, India
> https://sites.google.com/site/krishnendu2345/
> http://krishna-biodiesel.webs.com/
>
> **********************************************
>
-- Ask yourselves, all of you, what power would hell have if those imprisoned here could not dream of heaven?
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