[gmx-users] Regarding Gromacs 5.0 parallel installation

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Sat Dec 6 09:48:17 CET 2014

Dear All,
     I am facing some problem in runiing mdrun using -nt flag. In my
cluster I have installed gromacs 4.5.5 and 5.0. For checking I made 5.0
with DOUBLE=ON. Now I can run  mdrun using -nt= 30 in Gromacs 4.5.5 by
allowing mdrun in 30 CPUs. But the same command is not working in Gromacs
5.0. The mdrun_d  -s em.tpr -nt 30 is showing error. After careful
inspection, I came to know that Gromacs 5.0 is unable to access the threads
by default. I tried many ways using many different flags in each trial
installation(e.g,. -DGMX_THREAD_MPI=ON   or  -DGMX_SHARED_THREAD=ON or
-DGMX_FLOAT=ON -DGMX_SSE=ON). But the error is telling Non-default thread
affinity set. Even during cmake run, i got few warnings.

The command

-DCMAKE_INSTALL_PREFIX=/user1/tanpaku/bussei/bics at 1986/Bikash/cmake/gro/gro5.0

CMake Warning:
  Manually-specified variables were not used by the project:

This means the thread sharing is not successful. How can I modify the cmake
command. In my cluster there are 288 CPUs (SGI Al0x UV 100;  CPU - Intel
Xeon X7542). In the same cluster gromacs 4.5.5 is working fine, but gromacs
5.0 is not running for mdrun. Other commands like pdb2gmx, grompp,
editconf, solvate, genion etc are running well. But mdrun is not running as
it is unable to share the threads/nodes.

can somebody suggest how to set the environment as per the last line of
error message is concern (Highlighted in red)

GROMACS:      gmx mdrun, VERSION 5.0.2
Executable:   /user1/Bikash/gro5.0/bin/gmx
Library dir:  /user1Bikash/gro5.0/share/gromacs/top
Command line:
  mdrun_d -v -s em.tpr -nt 30

Back Off! I just backed up md.log to ./#md.log.2#

Number of hardware threads detected (288) does not match the number
reported by OpenMP (276).
Consider setting the launch configuration manually!
Reading file em.tpr, VERSION 5.0.2 (single precision)
The number of OpenMP threads was set by environment variable

Non-default thread affinity set, disabling internal thread affinity
Using 5 MPI threads
Segmentation fault

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