[gmx-users] How to install gromacs on cpu cluster

[Benson Muite]

Hi Yeping,

May want to use GCC 7 or GCC 8

https://gcc.gnu.org/

Follow instructions for how to get GCC working, see

https://gcc.gnu.org/install/

Once have a new version of GCC in your own directory, you will probably 
want to then compile an MPI library (eg. OpenMPI - 
https://www.open-mpi.org/or MPICH - https://www.mpich.org) in your home 
directory as well, the MPI library should be compiled with the GCC 
version that you use. I have not used PBS in a while, but the MPI 
library should pick this up. For programs on a single node, PBS should 
be able to just run the compiled executable.

What version of cmake do you have on your system?

Will try to write a short script later today. You may also want to look 
at Spack which  offers an automated GROMACS installation (but it can be 
helpful to set it up yourself for good performance):

https://github.com/spack/spack

Regards,

Benson

On 6/30/19 3:36 AM, sunyeping wrote:
> Hi,  Benson,
>
> I can install gcc-4.9 for compiling the latest version of gromacs 
> (gromacs_2019.3) in my own account directory 
> (/data/home/sunyp/software/GCC. For proper submission of task with PBS 
> system, which options of cmake should I use?
> According to the "Quick and dirty cluster installation" section of the 
> gromacs installation guide, it seems that a quick and dirty 
> installation should be done, and then another installation with MPI 
> should be done to the same location with the non-MPI installation. I 
> am not very clear how these should be done exactly. Could you give the 
> exact commands?
> Best regards
> Yeping
>
>
>       Q
>
>
>       <sunyeping at aliyun.com>; gromacs <gmx-users at gromacs.org>
>
>     Subject:Re: [gmx-users] How to install gromacs on cpu cluster
>
>     Hi Yeping,
>
>     Minimum required compiler version for the latest release is GCC
>     4.8.1 :
>
>     http://manual.gromacs.org/documentation/current/install-guide/index.html
>
>     GROMACS 4.5 seems to indicate support for GCC 4.5
>     (http://www.gromacs.org/Documentation/Installation_Instructions_4.5)
>
>     Is CMAKE on your cluster? If so what version?
>
>     Regards,
>
>     Benson
>
>     On 6/29/19 12:08 PM, sunyeping wrote:
>     Hello Benson,
>
>     Thank you for respond to my question. There is no GPU on my cluster.
>
>     Best regards,
>
>     Yeping
>     ------------------------------------------------------------------
>     From:Benson Muite <benson_muite at emailplus.org>
>     Sent At:2019 Jun. 29 (Sat.) 16:56
>     To:gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
>     Subject:Re: [gmx-users] How to install gromacs on cpu cluster
>
>     Hi Yeping,
>
>     It may be easier to install a newer version of GCC. Are there any GPUs
>
>     on your cluster?
>
>     Benson
>
>     On 6/29/19 11:27 AM, sunyeping wrote:
>     >
>     > Dear everyone,
>     >
>     > I would like to install gromacs on a cpu cluster of 12 nodes, with each node containing 32 cores. The gcc version on the cluster is 4.4.7. Which version of gromacs can be properly compiled with this gcc version?
>     >
>     > The cluster support PBS job submission system, then what is the correct options for cmake (or maybe configure) when compiling gromacs?
>     >
>     > Thank you in advance.
>     >
>     > Best regards.
>     > Yeping
>
>