Hello,
here I will describe the steps I followed in order to install the latest version of gromacs in ubuntu Trusty:
1) install the cmake package by going here: https://launchpad.net/~george-edison...untu/cmake-3.x
and which will add a repository which will install the latest version of cmake
In order to test that it was installed successfully type:
Then, open synaptic and install:
2) libxml2-dev
3) libfftw3-single3 along with bin and dev files
4) download the latest gromacs package
5) untar it and follow these guidelines to test a possible installation:
which will allow you to remove the old file so as to recheck for a new possible installation.
In other words step 5 will show you if you are missing any (more) libraries that need to be installed.
6) Then follow gromacs installation sequence of commands:
i) enter, if not already, the gromacs folder:
ii) create empty folder build:
iii) change to build directory:
iv) use cmake by denoting that you will use the proposed gromacs library (if you do not want, you can omit the corresponding argument):
v) compile gromacs
vi) check the process
vii) install gromacs
Done!
From step 6iv and on you will have to wait a little while until the process is finished. You can check if everything is ok by typing:
on the same terminal that you typed all the previous commands (especially the very last one, which you should type very time you wish to use the new version of gromacs unless you make a link).
If you are not happy with the installation, then go back to the folder you did the installation and type:
Hope it helps,
Regards!
I am using ubuntu 14.04 version, please tell me which version of GROMACS I have to use for this ubuntu 14.04 version. And give me the Installation steps.
here I will describe the steps I followed in order to install the latest version of gromacs in ubuntu Trusty:
1) install the cmake package by going here: https://launchpad.net/~george-edison...untu/cmake-3.x
and which will add a repository which will install the latest version of cmake
In order to test that it was installed successfully type:
Then, open synaptic and install:
2) libxml2-dev
3) libfftw3-single3 along with bin and dev files
4) download the latest gromacs package
5) untar it and follow these guidelines to test a possible installation:
$ tar xfz gromacs-5.x.x.tgz
$ cd gromacs-5.x.x
$ mkdir build-gromacs
$ cd build-gromacs
$ cmake ..
every time you would like to test if you have installed a dependency for gromacs do not forget to type:$ cd gromacs-5.x.x
$ mkdir build-gromacs
$ cd build-gromacs
$ cmake ..
which will allow you to remove the old file so as to recheck for a new possible installation.
In other words step 5 will show you if you are missing any (more) libraries that need to be installed.
6) Then follow gromacs installation sequence of commands:
i) enter, if not already, the gromacs folder:
ii) create empty folder build:
iii) change to build directory:
iv) use cmake by denoting that you will use the proposed gromacs library (if you do not want, you can omit the corresponding argument):
v) compile gromacs
vi) check the process
vii) install gromacs
viii) make the current terminal to understand that you will use the new version of gromacs (if you have already installed the previous version of gromacs via synaptic):
Done!
From step 6iv and on you will have to wait a little while until the process is finished. You can check if everything is ok by typing:
on the same terminal that you typed all the previous commands (especially the very last one, which you should type very time you wish to use the new version of gromacs unless you make a link).
If you are not happy with the installation, then go back to the folder you did the installation and type:
Hope it helps,
Regards!
Active1 year, 1 month ago
I am new to Ubuntu. I have just installed gromacs (version 5.1.2) on my Ubuntu (16.04) by using the command:
But I can not run the program. The gmx file is in
/usr/bin
when I use the command: My computer Processor type is x86-64. I have also tried by installing gromacs manually from http://www.gromacs.org/Downloads and then I used command:
I don't know what is the problem and how to solve it! I appreciate any advice.
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Mi.SolMi.Sol
2 Answers
I had this problem too. At the first I installed gromacs from an instruction that I found in one of the YouTube clips. Apparently I had a successful installation but when I wanted to run the program l had an error like you had:
After a lot search l understood that source of gromacs should be:
NOT
Finally l could solve my problem by using instruction of installation from gromacs site but before I removed my Ubuntu and installed a new one.
This is an instruction that I used from this link.
Quick and dirty installation
- Get the latest version of your C and C++ compilers.
- Check that you have CMake version 2.8.8 or later.
- Get and unpack the latest version of the GROMACS tarball.
- Make a separate build directory and change to it.
- Run cmake with the path to the source as an argument
- Run make, make check, and make install
Or, as a sequence of commands to execute:
This will download and build first the prerequisite FFT library followed by GROMACS. If you already have FFTW installed, you can remove that argument to cmake. Overall, this build of GROMACS will be correct and reasonably fast on the machine upon which cmake ran. If you want to get the maximum value for your hardware with GROMACS, you will have to read further. Sadly, the interactions of hardware, libraries, and compilers are only going to continue to get more complex.
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Ali YasamianAli Yasamian
I have also tried by installing gromacs manually from http://www.gromacs.org/Downloads and then I used command:
tar xfz gromacs-version.tar.gz
but again it doesnt workSupposed that
gromacs-version.tar.gz
is a valid filename (older versions had names asgromacs-5.1.4.tar.gz
, while versions of the GROMACS 2016 series follow the schemegromacs-2016.4.tar.gz
)- the gzipped tar file is not corrupt
- you're in the right directory
- the directory where the archive resides is writable
tar xfz gromacs-version.tar.gz
should unpack the file to a directory structure with the README, a bunch of scripts and the source code.Note that unpacking the
tar.gz
is just the first step in building GROMACS. At this stage, you are far from having a usable GROMACS system!It can be advantageous to have a GROMACS installation tailored to your own system, particularly when the logs of runs using a GROMACS build installed via
apt
contain hints like Binary not matching hardware - you might be losing performance.
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE2
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE2
However, I'm with
steeldriver
and karel
on this: Don't!Install GROMACS from the package manager and learn to use it before you start any optimizations!
As
steeldriver
and karel
have already mentioned, source gmx
will not get you anywhere, neither will gmx
alone ;-)Starting with version 5.0, all tools in GROMACS that were separate binaries in earlier versions, e.g.
pdb2gmx
, are now only accessible as gmx
subcommands!My suggestion is:
- Use the GROMACS version from the repo.
- Work through some recent tutorials based on GROMACS 5.0 (or later) to get familiar with the workflows. A really god point to start are the tutorials by Justin A. Lemkul.
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