Upgrade to Gromacs 4.5.3 or Gromacs 4.5.4 in rocks-5.4

bio-roll of rocks-5.4 come with gromacs-4.0.5, there are newer version of gromacs-4.5.3 and gromacs-4.5.4

how does one upgrade?

The git site has newer bio roll that include gromacs 4.5.3, one can just download a snapshot


by clicking the snapshot

or just the gromacs tree


then clicking the snapshot

first get a copy of rocks-5.4 source tree: hg clone http://fyp.rocksclusters.org/hg/rocks-5.4  to have a good build environment

I just run the cmd under /opt/rocks so the rocks-5.4 source will be under /opt/rocks/rocks-5.4

under /opt/rocks/rocks-5.4/src/roll/bio/src/gromacs

there should only have three files

  • Makefile
  • gromacs-4.0.5.tar.gz
  • version.mk

Now move this version of gromacs to gromacs-4.0.5 and put the new version of gromacs in the snapshot in his place

  • Makefile
  • gromacs-4.5.3.tar.gz
  • version.mk

Inspection of the Makefile, it require gcc44, one can install gcc44 from the centos5.5 or SL5.5 DVD

  • gcc44-4.4.0-6.el5
  • libstdc++44-devel-4.4.0-6.e15
  • libgfortran44-4.4.0-6.el5
  • gcc44-c++-4.4.0-6.el5
  • gcc44-gfortron-4.4.0-6.e15

After the installation of all these  gcc44, (may be just gcc44 is enough)

under rocks-5.4/src/roll/bio/src/gromacs

one just do

make build

if there is no error then

make rpm

it will create


to install on the frontend

rpm -qa |grep gromacs


to install the new 4.5.3 rpm

rpm -vU  /opt/rocks/rocks-5.4/src/roll/bio/RPMS/x86_64/gromacs-4.5.3-1.x86_64.rpm

to add the new version to the compute node one would need to put the new rpm to the directory /export/rocks/install/contrib/5.4/x86_64/RPMS

one more things to make sure the gcc44 packages are install on each compute nodes

one copy all three gcc44  rpms to  /export/rocks/install/contrib/5.4/x86_64/RPMS

in /export/rocks/install/site-profiles/5.4/nodes/extend-compute.xml


  • <package> gcc44</package>
  • <package>libstdc++-devel</package>
  • <package>libgfortran44</package>
  • <package> gcc44-c++</package>
  • <package> gcc44-gfortron</package>
  • <package>gromacs-4.5.3-1</package>

run xmllint –noout extend-compute.xml

cd /export/rocks/install

rocks create distro

re-install all compute nodes

For newer version of Gromacs 4.5.4, one will need to download the source

replace the gromacs-4.5.3.tar.gz with gromacs.4.5.4.tar.gz

modify the version.mk to match 4.5.4

make build will give you error “a local symbol’ can not be used when making a shared object; recompile with –fPIC “

it turn out that configure file change from 4.5.3 to 4.5.4

line 3682 enable_shared=no in 4.5.3

line 3682 enable_shared=yes in 4.5.4

After make this modification, then re-create gromacs-4.5.4.tar.gz

make build went through without error

Other steps are same as for 4.5.3


About laotsao 老曹

HopBit GridComputing LLC Rockscluster Gridengine Solaris Zone, Solaris Cluster, OVM SPARC/Ldom Exadata, SPARC SuperCluster
This entry was posted in ROCKS. Bookmark the permalink.

8 Responses to Upgrade to Gromacs 4.5.3 or Gromacs 4.5.4 in rocks-5.4

  1. Joao says:

    I made exactly this procedure in my cluster. The frontend is running 4.5.4, but the nodes are still running 4.0.5. What can be wrong?

  2. laotsao says:

    i donot have access to any rockscluster now, sorry
    nextweek when i finish my vac, i will check again

  3. laotsao says:

    if the gromacs is installed under /share/apps/bio
    then the compute nodes should see the new version

  4. laotsao says:

    Dear joao
    thank your for your interest, I come back from vacation and make some adjustment to the procedure, I make a mistake thinking that bio roll was installed under /share/apps

  5. Joao says:

    Thank you for your effort. Now everything works perfectly!

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