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

[sunyeping]

Thank you Benson. These are very helpful.

Yeping
------------------------------------------------------------------
From:Benson Muite <benson_muite at emailplus.org>
Sent At:2019 Jul. 1 (Mon.) 20:41
To:孙业平 <sunyeping at aliyun.com>; gromacs.org_gmx-users <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject:Re: [gmx-users] How to install gromacs on cpu cluster

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