[gmx-users] Installing GROMACS 4.6.7 on Intel Cluster

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Nov 9 01:43:01 CET 2014

Dear Users

I figured out from the trailing mails as to how to use the "new installed
version of CMAKE" for installing GROMACS

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>
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

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
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 :


 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 -
 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.


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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