Getting ACEMD Basic

Installing ACEMD

With conda installed, you can now easily install ACEMD Basic. ACEMD Basic comes together with HTMD, so you can easily install it by running the following commands::

conda install -c acellera -c psi4 htmd

Register

Basic mode first requires registration and acceptance of our EULA. to do this, please run the command htmd_register and enter your details.

Start to run

ACEMD may then be run from the command line with the command acemd, or via HTMD

In case you do not have conda

First, check if you already have conda:

conda -V

If this command reports the conda version, follow to the Installing ACEMD section. If not, download the appropriate following package:

Linux

64-bit (bash installer)

Now, to install the conda package manager, go to directory where to you downloaded the previous package and run:

bash Miniconda3-latest-*-x86_64.sh

And follow the instructions.

Prerequisites

Hardware: ACEMD requires a modern NVIDIA GPU: we recommend the Geforce 980, 1080 or Tesla K and P-series GPUs. The latest NVIDIA Driver should be installed, available from here

Software: ACEMD requires a 64bit Linux OS. ACEMD is formally qualified with Red Hat EL6, but will work with any Linux distribution supported by NVIDIA CUDA, provided the GLIBC version is 2.12 or higher. Note that RHEL 5 and SLES 10 are not supported. For replica exchange support, please ensure that the OS’s openmpi packages are installed.

More information

Nvidia driver update procedure

It is generally not recommended updating the driver unless there is a necessary bug fix in a later version. That said, here is what you should do assuming the OS is CentOS:

  • As root, “yum update”. Reboot if the kernel is updated.
  • Download the new driver from here
  • chmod +x NVIDIA-Linux-x86_64-XXX.XX.run
  • As root, telinit 3 to drop the text mode
  • Run NVIDIA installer, answering yes to all questions
  • reboot

Replica exchange and MPI

ACEMD supports ensemble simulations for replica exchange molecular dynamics. This is implemented using MPI for parallel communication. Because there are many different MPI implementations, all with different binary interfaces, ACEMD includes a wrapper library to allow it be used with whichever MPI your system is configured with.

If you do not intend to use ensemble methods, and receive no warnings or errors when running ACEMD, you do not need to take any further action.

The wrapper library, libmpiwrapper.so, provided with ACEMD is built against OpenMPI and compatible with Red Hat / Centos 6+ OS packages. If you wish to use a different MPI, you must recompile the wrapper as follows:

    $ cd [HTMD installation home]/mpiwrapper
				    $ make
			    

If you receive any errors, check that the MPI development packages and C compiler are installed. If successful, the libmpiwrapper.so in the lib directory will be reconfigured for your system.

If you encounter any problems installing ACEMD Basic or Pro, please contact us directly at support@acellera.com