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

[Benson Muite]

Hi Yeping,

The basic steps are the same as in the documentation. The steps below 
should get GROMACS running on a linux computer where Cmake can be 
installed. You may need to change $HOME to an absolute path and give the 
exact location of the C and C++ compilers you will use to compile 
GROMACS. You need not use the same C and C++ compilers to compile CMake, 
though recent versions of Cmake also need a recent compiler. It may be 
the case that you will need to update your path variable to make your 
installation of GCC get picked up as the first compiler that is tried. 
Typical linux systems (but not all) should have most prerequisites for 
CMake:

wget 
https://github.com/Kitware/CMake/releases/download/v3.15.0-rc3/cmake-3.15.0-rc3.tar.gz
tar -xvf cmake-3.15.0-rc3.tar.gz
mkdir cmake-3.15.0-rc3-build
cd cmake-3.15.0-rc3-build/
  ../cmake-3.15.0-rc3/bootstrap 
--prefix=$HOME/InstallGromacs/cmake-3.15.0-rc3-install
gmake
make install
cd ..
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.3.tar.gz
tar -xvf gromacs-2019.3.tar.gz
cd gromacs-2019.3/
mkdir build
cd build/
$HOME/InstallGromacs/cmake-3.15.0-rc3-install/bin/cmake .. 
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
-DCMAKE_INSTALL_PREFIX=$HOME/InstallGromacs/gromacs-2019.3-install/ 
-DCMAKE_CXX_COMPILER=/usr/bin/c++ -DCMAKE_C_COMPILER=/usr/bin/gcc
make
make check
make install

On 6/30/19 7:41 AM, Benson Muite wrote:
> 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
>>
>>