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

[Benson Muite]

Hi Yeping,

A full build may be helpful to run the initial correctness tests, once 
you have done this can then use -DGMX_BUILD_MDRUN_ONLY=on for production 
runs. Having a full version of GROMACS on a node with access to the same 
file system where you do runs is also helpful since there may be 
features required for pre and post processing. If you have built your 
own MPI, you probably also want to use the flags:

-DMPI_C_COMPILER=/path/to/your/mpicc

-DMPI_CXX_COMPILER=/path/to/your/mpiccxx

It may be helpful to name the MPI and Shared memory executables 
differently or install them in different places. The size of the system 
you are simulating will likely determine whether the MPI build will be 
useful for you. In most cases, the default

-DGMX_DOUBLE=off

is fine, The flag

-DGMX_SIMD=xxx

is also helpful, you will need to replace xxx with appropriate choice 
for your platform as indicated at:

http://manual.gromacs.org/documentation/current/install-guide/index.html#simd-support

Finally if you use ccmake rather than cmake, some of the other possible 
compilation options should appear.

Regards,

Benson

On 7/1/19 2:21 PM, sunyeping wrote:_
> Hi Benson,
>
> I feel I may need to add the following options to cmake?
> -DGMX_MPI=on
> -DGMX_SIMD=xxx
> -DGMX_BUILD_MDRUN_ONLY=on
>
> Should I?
>
>     ------------------------------------------------------------------
>     From:孙业平 <sunyeping at aliyun.com>
>     Sent At:2019 Jun. 30 (Sun.) 08:36
>     To:gromacs <gmx-users at gromacs.org>; Benson Muite
>     <benson_muite at emailplus.org>
>     Subject:Re: [gmx-users] How to install gromacs on cpu cluster
>
>     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
>
>
>