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==Using AmberTools 21== <!--T:23-->
===Using AmberTools 21=== <!--T:23-->
Currently, AmberTools 21 is available on all clusters. AmberTools Provide the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI. After loading ambertools module set AMBER environment variables:
Currently, AmberTools 21 is available on all clusters. AmberTools Provide the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI. After loading ambertools module set AMBER environment variables:
  source $EBROOTAMBERTOOLS/amber.sh
  source $EBROOTAMBERTOOLS/amber.sh


=== CPU-only version === <!--T:24-->  
===Using Amber 20=== <!--T:30-->
Currently, Amber20 is available on all clusters. There are two versions of amber/20 modules: 20.9-20.15 and 20.12-20.15. The first one uses MKL and cuda/11.0, while the second uses FlexiBLAS and cuda/11.4. MKL libraries do not perform well on AMD CPU, and FlexiBLAS solves this problem. It detects CPU type and uses libraries optimized for the hardware. Cuda/11.4 is required for running simulations on A100 GPUs installed on Narval.


<!--T:25-->
CPU-only modules provide all MD programs available in AmberTools/20 plus pmemd (serial) and pmemd.MPI (parallel). GPU modules add pmemd.cuda (single GPU), and pmemd.cuda.MPI (multi - GPU).
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 ambertools/21
source $EBROOTAMBERTOOLS/amber.sh
 
<!--T:26-->
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, and sander.OMP
 
=== GPU version === <!--T:27-->
 
<!--T:28-->
module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 ambertools/21
source $EBROOTAMBERTOOLS/amber.sh
 
<!--T:29-->
Provides the following MD engines: sander, sander.LES, sander.LES.MPI, sander.MPI, sander.OMP, sander.quick.cuda, and sander.quick.cuda.MPI
 
==Loading Amber 20== <!--T:30-->
Currently, Amber20 is available on all clusters. There are two versions of amber/20 modules: 20.9-20.15 and 20.12-20.15. The first one uses MKL and cuda/11.0, while the second uses FlexiBLAS and cuda/11.4. MKL libraries do not perform well on AMD CPU, and FlexiBLAS solves this problem. It detects CPU type and uses libraries optimized for the hardware. Cuda/11.4 is required for running simulations on A100 GPUs installed on Narval.
 
=== Loading CPU-only versions === <!--T:31-->
 
<!--T:32-->
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.9-20.15 
or
module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.12-20.15
 
<!--T:33-->
These modules provide all MD programs available in AmberTools/20 plus pmemd (serial) and pmemd.MPI (parallel).
 
=== Loading GPU versions === <!--T:11-->
 
<!--T:34-->
module load StdEnv/2020 gcc/9.3.0  cuda/11.0  openmpi/4.0.3 amber/20.9-20.15
or
module load StdEnv/2020 gcc/9.3.0  cuda/11.4  openmpi/4.0.3 amber/20.12-20.15
 
<!--T:35-->
These module provide all MD programs available in ambertools/20 plus pmemd (serial), pmemd.MPI (parallel), pmemd.cuda (single GPU), and pmemd.cuda.MPI (multi - GPU)


=== Submission of GPU-accelerated AMBER on Narval === <!--T:37-->
=== Submission of GPU-accelerated AMBER on Narval === <!--T:37-->
AMBER modules compiled with cuda version < 11.4 do not work on A100 GPUs. Use amber/20.12-20.15 module on Narval.
AMBER modules compiled with cuda version < 11.4 do not work on A100 GPUs. Use amber/20.12-20.15 module.


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