[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

[Mark Abraham]

Hi,

This means that "make" is somehow running out of memory. That should never
happen, but what's going wrong for you is impossible for us to tell.
Switching compiler won't help - the compiler is not used in the
installation phase.

Mark

On Sun, Nov 9, 2014 at 1:42 AM, Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:

> Dear Users
>
> I figured out from the trailing mails as to how to use the "new installed
> version of CMAKE" for installing GROMACS
>
> I used  -DGMX_BUILD_OWN_FFTW=ON  -DCMAKE_INSTALL_PREFIX=......... .
> By default I think "icc" and "icpc" compilers were chosen.
>
> This step progressed smoothly. So , next I issued the command : "make".
> This step also completed without any error messages.
>
> However "make install" did not finish as expected. The installation process
> looked like a never ending process. Ultimately the following error message
> came up :
>
> terminate called after throwing an instance of 'std::bad_alloc'
>   what():  std::bad_alloc
> make: *** [install] Aborted
>
> I do not understand what to do next. I am thinking of using "gcc" and "g++"
> now. Kindly provide further suggestions.
>
>
>
> ------------------------------------------------------------------------------------------------------------------------------------
>
> ---------- Forwarded message ----------
> From: Mohd Farid Ismail <mohd.farid.ismail at yandex.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>, "
> gromacs.org_gmx-users at maillist.sys.kth.se" <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> Cc:
> Date: Sat, 08 Nov 2014 09:19:14 +0800
> Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
> What he meant was to specify full path of your cmake, i.e.
> /work/user/GROMACS/cmake-2.8/bin/cmake .. -DGMX_FFT_LIBRARY..... (and so
> on); instead of just typing cmake .. -DGMX_FFT_LIBRARY....
>
> This is really a linux issue instead of gromacs.
>
>
> 08.11.2014, 06:00, "Agnivo Gosai" <agnivogromacs14 at gmail.com>:
>
> Dear Users
>
> 1 . I am not sure as to how to set the full path in the cmake command line.
> Do I need to use the export command to set the path ?
>
> An example will be of great help. I am also searching the web but can not
> find a satisfactory answer.
>
> As highlighted in my step 5 ( trailing mail ) , I think install_prefix will
> install the gromacs version in the specified directory or am I wrong ?
>
> 2. Yes , I understand it after reading the instructions. I think mdrun will
> pick up MPI threading automatically.
>
> I have also installed FFTW 3.0 in a local folder , how do I set its path in
> the cmake command line and I also have gcc in the root folder , along with
> icc.
>
> Pardon my ignorance as I think these are very basic questions related to
> the linux architecture.
>
> ---------- Forwarded message ----------
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Cc:
> Date: Fri, 07 Nov 2014 16:26:56 -0500
> Subject: Re: [gmx-users] Installing GROMACS 4.6.7 on Intel Cluster
>
>
> On 11/7/14 4:20 PM, Agnivo Gosai wrote:
>  Dear Users
>
>  I checked and found that the CMAKE version installed in my university
>  cluster is 2.6-patch 4 however GROMACS 4.6.7 requires CMAKE 2.8 or higher.
>  So I installed CMAKE 2.8.11 in my local work directory :
> /work/user/GROMACS/cmake-2.8/
>
> bin/cmake
>
>  Now I want to use Intel MKL , so after reading the GROMACS installation
>  instruction I have decided to use the following workflow :-
>
>  1.  tar xfz gromacs-4.6.7.tar.gz
>  2. cd gromacs-4.6.7
>  3. mkdir build
>  4. cd build
>  5. cmake .. -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -
>  DCMAKE_INSTALL_PREFIX=/work/user/GROMACS
>  6. make
>  7. make install
>  Now when I check install location of CMAKE it points to the old version
>  located in the Cluster root directory.
>
>  Now , I want to use the new version which I believe to have installed
>  correctly. So please help in solving this problem.
>
> Specify the full PATH of your cmake, otherwise the environment will just
> pick up the default cmake on the cluster.
>
>  Also I would request the users to check my workflow of the installation
>
>  process and provide suggestions.
>
> There is no point in compiling the whole suite of tools with MPI; nothing
> makes use of MPI except mdrun.  So if you want to compile all the tools
> (preprocessing and analysis), don't set GMX_MPI.  If you are using GMX_MPI,
> then set -DGMX_BUILD_MDRUN_ONLY=ON to get MPI-enabled mdrun.  Strictly
> speaking, MPI is not required, but it depends on what you want to do
> whether or not you need it.
>
> -Justin
>
> -------------------------------------
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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